GLOBAL PROJECT FOR THE MAINTENANCE OF DOMESTIC
ANIMAL GENETIC DIVERSITY
(MoDAD)
DRAFT PROJECT FORMULATION REPORT
August 1995
FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS
i
GLOSSARY
Animal Genetic
Resources
In the narrow sense, as used in this document: the genetically
unique breed populations formed throughout all domestication
processes within each species used for production of food and
agriculture, together with their immediate wild relatives.
Allele
One gene may have several different variants and these variants are
called alleles.
Analysis
In this document refers to evaluation of data resulting from
assaying using statistical procedures.
Assaying
In this document refers to evaluations of DNA samples of using
molecular genetic screening tools.
Breed
Either a homogenous, subspecific group of domestic livestock with
definable and identifiable external characteristics that enable it to
be separated by visual appraisal other similarly defined groups
within the same species, or, it is a homogenous group for which
geographical separation from phenotypically similar groups has led
to general acceptance of its separate identity. Breed is more a
cultural than a strict scientific term.
Conservation
(of Diversity)
Sum total of all operations involved in the management of animal
genetic resources, such that these resources are documented, best
used and developed to meet immediate and short term
requirements for food and agriculture, and to ensure the diversity
they harbour remains available also to meet possible longer term
needs.
Crossbreeding
Mating of different breeds/lines/strains to combine desired traits
and/or exploit heterosis.
Diversity
In the narrow sense, as used in this document: the genetic variation
existing among the species, breeds and individuals. Also termed
Domestic Animal Diversity or DAD.
Field Sampling
In this document refers to: Choosing animals within a breed to be
sampled, taking the blood sample and isolating the DNA.
Gene
The functional unit of heredity.
Genetic Variation
Levels of variation in the genetic composition of individuals within
breeds, among breeds within species, and among species; the
heritable genetic variation within and among populations.
ii
Genome
The total genetic constituency or "blueprint" of an animal.
Heterosis
The increased performance of offspring, compared to average of
parental performance, for one or more traits. Also referred to as
hybrid vigour.
Heterozygosity
Different alleles present at a locus.
Indigenous
Populations whose ancestors inhabited a geographical area and
which now occur native to that area through adaptation to the
prevailing agroecosystem.
Loci
Gene locations on a chromosome.
Management
(of AnGR)
Sum total of all operations by humankind involved in the
characterization, development, use and preservation of AnGR such
that unique resources are sustainably used to best meet short term
needs and maintained to ensure their ready availability to meet
possible longer term requirements.
Microsatellite
Marker
Short variable segments of DNA randomly dispersed throughout
the genome.
Phylogenetic
Pertains to the evolutionary history of a particular breed or
population.
Population
Generic term but used in a genetic sense it defines a group of
individuals with common ancestry that are more likely to mate
with one another than with individuals from another such group.
Species
A group of animals capable of interbreeding freely with each other
but not with members of other species.
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ACRONYMS
AnGR
Animal Genetic Resources
CDAD
Centre for Domestic Animal Diversity
CBA
Cost Benefit Analysis
CGIAR
Consultative Group in Agriculture Research
DAD
Domestic Animal Diversity
EAG
Expert Advisory Group (for Project MoDAD)
FAO
Food and Agriculture Organization of the United Nations
FAO AnGR
FAO Global Programme for the Management of Animal Genetic
Programme Resources
GEF
Global Environment Facility
ISAG
International Society for Animal Genetics
MCA
Multiple Criteria Analysis
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
PCR
Polymerase Chain Reaction
SMS
Safe Minimum Standards
UNEP
United Nations Environment Program
UNCED
United Nations Conference on Environment and Development "Earth
Summit"
iv
TABLE OF CONTENTS
GLOSSARY ................................................................................................................................. i
ACRONYMS .............................................................................................................................. iii
EXECUTIVE SUMMARY ........................................................................................................ 1
1. INTRODUCTION ................................................................................................................... 3
2. BACKGROUND ..................................................................................................................... 4
A. THE IMPORTANCE OF GLOBAL ANIMAL GENETIC
RESOURCES ........................................................................................... 4
B. FAO’S GLOBAL PROGRAMME FOR THE MANAGEMENT
OF ANIMAL GENETIC RESOURCES (FAO AnGR
Programme) ............................................................................................... 5
3. PROJECT RATIONALE AND DESIGN CONSIDERATIONS .......................................... 7
A. PROJECT RATIONALE ................................................................................... 7
B. DESIGN CONSIDERATIONS........................................................................... 8
Quality and Uniformity of Base-line Data ................................................. 8
Cost-effectiveness and Timeliness ............................................................. 9
Project Design Options............................................................................... 9
Sample Ownership and Property Rights .................................................. 10
Country Participation................................................................................ 10
Project Coordination................................................................................. 10
4. THE PROJECT ......................................................................................................................
A. GENERAL DESCRIPTION ............................................................................
Project Objectives .....................................................................................
Project Components .................................................................................
Breed Selection and Field Sampling .................................................
DNA Extraction .................................................................................
Microsatellite Marker Development .................................................
Laboratory Assaying ..........................................................................
Data Storage and Analysis.................................................................
Technical Assistance and Training ...................................................
Project Co-ordination and Management ...........................................
Long-term DNA Repositories ...........................................................
B. PROJECT OUTPUTS ......................................................................................
C. TECHNICAL ACTIVITIES.............................................................................
Use of Existing Data and Research Results .............................................
Breed Selection and Field Sampling ........................................................
Collection of Biological Material......................................................
DNA Extraction, Purification and Shipment ...........................................
DNA Storage ............................................................................................
Material Transfer Agreements ..........................................................
DNA Assaying..........................................................................................
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v
Choice of laboratories for assaying ..................................................... 21
Choice of genetic markers for base-line assays ............................... 22
Criteria for choice of microsatellite genetic markers ........................ 22
Laboratory assay of microsatellite variation ..................................... 23
Data Analysis, Management and Dissemination .................................... 23
Data Analysis ..................................................................................... 23
Data Management.............................................................................. 24
Publication and Reporting ................................................................. 25
D. TECHNICAL ASSISTANCE AND TRAINING ............................................ 25
Technical Assistance ................................................................................ 25
Training .................................................................................................... 25
E. PROJECT ORGANIZATION AND MANAGEMENT .................................. 26
Project Co-ordination ............................................................................... 26
Expert Advisory Group ............................................................................ 26
Data Interpretation and Dissemination..................................................... 27
Long-term DNA Repositories .................................................................. 27
F. PROJECT COSTS ............................................................................................ 27
G. PROJECT SUSTAINABILITY AND PARTICIPATION ............................. 28
5. INSTITUTIONAL FRAMEWORK AND PROJECT IMPLEMENTATION .................... 31
A. PROJECT ORGANIZATION AND MANAGEMENT .................................. 31
B. PROJECT IMPLEMENTATION ..................................................................... 32
6. PROJECT JUSTIFICATION, BENEFITS AND RISKS ....................................................
A.SPECIAL CONSIDERATIONS IN ASSESSING THE
ECONOMICS OF ANIMAL GENETIC RESOURCES ......................
B. MoDAD AND THE GLOBAL CONSERVATION OF ANIMAL
GENETIC RESOURCES .......................................................................
C. ECONOMIC EVALUATION..........................................................................
Methodological Considerations ...............................................................
Business as Usual Scenario ......................................................................
Conservation of Threatened Breeds Scenario ..........................................
Economic Evaluation of MoDAD and GEF Criteria ..............................
Distributional and Incentives Issues.........................................................
D. PROJECT RISKS .............................................................................................
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7. ISSUES AND FOLLOW-UP ............................................................................................... 43
Issues ......................................................................................................... 43
Follow-up.................................................................................................. 44
8. REFERENCES ..................................................................................................................... 44
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LIST OF TABLES
1. NUMBER OF BREEDS TO BE SAMPLED BY SPECIES
2. ASSUMPTIONS AS TO NUMBER OF COUNTRIES WITHIN REGION
IN WHICH SAMPLING WOULD BE CONDUCTED
3. PROJECT COMPONENTS BY YEAR
4. EXPENDITURE ACCOUNTS BY YEAR
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28
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LIST OF FIGURES
1. MoDAD ORGANIZATIONAL CHART
2. MoDAD IMPLEMENTATION SCHEDULE
LIST OF APPENDICES
1. WORKING GROUP PARTICIPANTS
2. REFERENCE GROUP PARTICIPANTS
LIST OF ANNEXES
1.
2.
3.
4.
5.
6.
7.
BREED SELECTION AND SAMPLING
DNA EXTRACTION, PURIFICATION, SHIPMENT AND STORAGE
BASE-LINE ASSAYING
STATISTICAL ANALYSIS AND DATA STORAGE
ECONOMIC ANALYSIS
PROJECT COSTS
MoDAD PRIMARY STRATEGY AND ACTIVITIES
15
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1
EXECUTIVE SUMMARY
This report describes a project designed to quantify the genetic diversity
amongst breeds of the 14 major species of domestic animals throughout the world. The
project has been named MoDAD which stands for the Global Project for the
Maintenance of Domestic Animal Genetic Diversity. With a global total of an
estimated 4,500 breeds, of which more than 30% are at risk of loss; resources at the
national and global levels are simply not adequate to launch an all encompassing and
effective program of conservation management. MoDAD represents the only option for
providing base-line data required for the development of cost-effective management
programs by determining where significant breed diversity exists. From the perspective
of maintaining adequate genetic variation, perhaps this might be achieved with as low
as 800 to 1,000 breeds being sustainably managed to provide for the range of short and
longer term needs of humankind. As such, MoDAD is an imperative to the realization
of the effectiveness of FAO’s Global Programme for the Management of Farm Animal
Resources which seeks to provide for the necessary infrastructure to conserve domestic
animal diversity required to meet the current and future needs of humankind.
MoDAD has been designed by a Working Group of international experts to
provide a country and global basis for the conservation of domestic animal diversity as
cost-effectively and expediently as possible. In the design of the project, all options for
its conduct were rigorously examined with final recommendations made largely on the
basis of cost-effectiveness. MoDAD would be carried out over a 4 year period.
MoDAD would collect blood from representative animals of a sample of breeds
representing the full geographic and taxonomic range of the domestic species
addressed in the project. As such, upwards of 55 countries might be involved in field
sampling. At the most, 50 breeds per species would be sampled. Four regional
laboratories in Asia, Africa, Central or Eastern Europe and Latin America, would be
selected to coordinate field sampling activities for a specific species, and would also be
responsible for the analysis of base-line data. DNA material would be extracted and
samples would be stored, one each, at the national and at the global repositories, which
could be the regional laboratories involved. DNA would be analyzed using
microsatellite marker techniques. The location(s) for assay of DNA samples has yet to
be decided, but would either involve 1 commercial lab or a minimum of 4 regional
research labs. This decision has yet to be taken as both options offer substantial
benefits. Regardless of which option is selected, the regional research labs would
assume responsibility for quality control monitoring for each component of MoDAD.
MoDAD is to provide for the essential base-line field sampling, DNA
storage, laboratory assaying, data collection, collation, analysis, database maintenance,
and formal reporting of results at the species level. MoDAD is also responsible for the
associated coordination and technical advisory activities. MoDAD does not provide for
ongoing advanced assaying and analyses. However, the research and development of
new assaying and analytical techniques, and future training activities, all will benefit
greatly from MoDAD having been conducted; particularly from the establishment
globally of the unique data and DNA repositories.
Effective co-ordination of the project was a major design consideration.
Because of the global nature of the project, and in order to realize MoDAD’s primary
objective of producing high quality results in a cost-effective and timely manner, it
2
would be imperative that the project be effectively co-ordinated. FAO would be
responsible for the co-ordination of the project, aided by an internationally recognized
group of animal genetics research and development experts. An added advantage of
FAO co-ordination is that it would link MoDAD closely to FAO which has been
mandated to put in place a country-based global management programme for farm
animal genetic resources (AnGR). FAO involvement ensures that the data would be put
to maximum use in the global management of AnGR; and that the DNA repositories
would be of immense benefit to training and research of advanced procedures in the
future. All withdrawals or use of DNA from the repositories would require
authorization from the country of origin.
Total project costs over four years, are estimated at US$ 10.53 million
inclusive of physical and price contingencies, with a foreign exchange component of
about US$ 4.22 million. Sustainability is provided for in the long-term maintenance of
the Global DNA And data repositories. The substantial commitment to technical
assistance and training empowers nations to better manage their AnGR. Many of the
costs are significantly dependent on the number of countries to be included in the field
sampling operations and the number of breeds that would be sampled; but the
fundamental experimental design for the project has been developed by an international
group of experts as being minimal to be effective. The Working Group did not have the
time nor the expertise to select the breeds and determine the sampling locations. This
and the actual mobilization of the project are major outstanding issues which should be
quickly resolved by FAO.
Economic analysis of MoDAD showed it to be a very sound investment.
MoDAD was evaluated according to several indicators of cost-efficiency: as an
insurance premium against loss of diversity and the potential benefits accruing from
identification of breeds having maximal opportunities for hybrid vigour upon crossing.
AnGR conservation costs are estimated to range between US$ 20 to US$ 50 million
annually. Assuming a combined cost with MoDAD of US$ 50 million, these costs
represent only .01% of a very conservative estimate of the annual global value of
livestock production of US$ 500 billion per year. Moreover, if MoDAD averted a
single catastrophic event, this event would only need to entail losses of US$ 1.2 million
per year for 20 years for the project to pay for itself. Further, potential benefits from
crossbreeding in dairy cattle are conservatively estimated to be as high as US$ 500
million annually. Thus, the MoDAD would need make only a small contribution to
current breeding programs to generate benefits to more than offset its costs.
Participation of countries in the conduct of MoDAD was an important
consideration in project design. Project activities have been designed to increase
country participation in the implementation of the project within what have been
considered acceptable limits of data quality and timeliness of results, and to facilitate
global co-ordination. MoDAD would make a large commitment to capacity building.
Technical assistance and training of personnel would be required for field sampling,
storage, database management, laboratory assaying and analysis. In addition, research
personnel from developing countries would receive training in research and
management of domestic animal genetic diversity conservation. Furthermore, the
regional network training activities have been designed to increase the impact of
MoDAD in terms of encouraging countries, particularly less developed ones, to
measure and manage their domestic AnGR, and to seek global co-operation in their
own endeavours.
3
1. INTRODUCTION
This report describes a project designed to quantify the genetic diversity
amongst breeds of the major species of domestic animals throughout the world1/ . The
project has been named MoDAD which stands for "Global Project for the Maintenance
of Domestic Animal Genetic Diversity". MoDAD would collect blood from
representative animals of a selected sample of breeds from the 14 most important
domestic species. Genetic material (DNA) would be extracted and assayed using up-todate rigorous molecular genetic techniques. MoDAD would provide in the most costeffective manner possible a comprehensive database of the genetic variation amongst
the breeds sampled globally. The results of the project would provide an objective basis
for realizing major ongoing cost savings and substantially enhanced effectiveness in
management of domestic animal diversity (DAD) at both country and global levels.
Management of DAD is important for the current and future benefit of humankind due
to unique and irreplaceable genetics which i) are currently at high risk of loss; ii) remain
substantially unknown but could be important if exploited; and iii) may be vital at some
future time due to changing circumstances of climate, disease, production system or
consumer preferences.
This report was developed in consultation with a Working Group of
international experts which convened in Rome for four days in April 19952/ , and a
Reference Group of experts throughout the world who were consulted via Internet
before, during and after the workshop3/ . The report of a previous Working Group,
convened to establish the feasibility of MoDAD, served as a key reference document
(Barker et al. 1993).
MoDAD has been designed as a two phase project. This is because the
scale of the second phase would depend on the results of genetic variation measured
during the first phase. In the first phase, to be implemented over four years, a sample of
breeds within a species would be involved. At the most 50 breeds would be sampled
per species across its geographic range. This sampling approach is based on
experimental design calculations and the experiences of past genetic variation research,
and is designed to cost-effectively maximize the opportunity of identifying within
species genetic variation. Where significant within species genetic variation is
uncovered, a second phase would be indicated in order to provide improved resolution
as to which breeds need to be conserved. The second phase of MoDAD could also
include additional domestic animal species other than the 14 that would be included in
the first phase.
The report consists of two volumes. Volume I outlines the background to
MoDAD, followed by the project rationale and an explanation of the design options
which were considered in the formulation of the project. MoDAD is then briefly
described, and the outputs and components of the project are elaborated. Following this,
the institutional and implementational aspects of MoDAD are detailed. The justification
1
/ While the focus of the project would be on measuring between breed genetic variation,
within breed genetic variation would also be measured.
2/
A list of members is provided in Appendix 1.
3/
A list of participants is given in Appendix 2.
4
for MoDAD, and the associated benefits and risks of the project, are given. Finally the
outstanding issues and follow-up actions are set out. Volume II contains details relating
to the technical, methodological and protocol features of MoDAD, as well as the
economic analysis and project costs.
2. BACKGROUND
A. THE IMPORTANCE OF GLOBAL ANIMAL GENETIC RESOURCES
The 40+ species of animals that have been domesticated during the past
12,000 years contribute directly and indirectly some 30-40% of the total value of food
and agriculture. Conservative calculations based on conventional livestock products
yield annual production values close to US$ 500 billion (see Annex 5). Should other
values of livestock production be included, such as draught power, manure, transport
and store of wealth functions, the real value of domestic animal production is much
higher.
Animal production environments throughout the world range from wet to
dry tropics through to tundra. Across the diverse spectrum of production systems used,
digestibility and nutritive quality of animal feeds, temperature, disease stresses and the
type of management, vary widely. A challenge of enormous magnitude confronts
humankind to achieve sustainable increases in production, and productivity, throughout
the world’s broad range of environments available for food and agriculture.
In order to meet future demands for animal products on a sustainable basis,
genetic resources must be utilized which are adapted to serve specific production
systems. It is now apparent that utilization of a diverse array of genetic material will be
imperative to meet future food and agriculture production requirements. Undoubtedly,
over time changing human requirements, prevalence of animal disease, and long term
climatological change will put more pressure on the range of genetic material that will
be required to achieve sustainable farming systems and universal food security.
In addition to producing food, animal genetic resources (AnGR) serve as a
storehouse for the wide range of desirable production traits. Clearly, breeding
improvements and responses to changing demand requirements and environmental
conditions cannot proceed without the wealth of genetic variation embodied in the
existing breeds of domestic animals. Within a species, genetic variation is found within
and between breeds. Within-breed variation is crucial for continued survival and
improvement of a breed. Also many examples exist of the use of between-breed
variation through cross-breeding programmes which were able to tap useful alleles
present in certain breeds. For example, much of the world commercial meat industry
relies on hybrid vigour in cross-breeds. More dramatic are situations which have relied
on ready access to alternative breed resources to avert complete devastation of an
industry due to sudden disease epidemics or changing livestock management
conditions.
Biology dictates that species, breeds, and individual animals within breeds,
all provide unique genetic material to a production system. Only through their
combined management can sustainable production and productivity gains be realized.
5
It is imperative therefore that national, regional and global management strategies take
account of biological diversity. Conservation of domestic animal diversity must
encompass identifying, monitoring and characterizing genetic resources for their
best short term use, whilst ensuring their long-term ready availability.
A cursory review of the literature indicates that about half the complex
genetic differences for production and adaptation within each of the main domestic
animal species are unique to the breed level. These differences have been established
over thousands of years as humans migrated to new environments, taking with them
samples of livestock, and subsequently selecting successive generations of parents to
meet their demands.
It is now thought that about 4,500 breeds of domestic animals still exist
world-wide, many-fold fewer than the total number of varieties of plant species used for
food and agriculture1/ . The unique resources among these 4,500 breeds of livestock are
irreplaceable within foreseeable time-frames. The breed level domestic animal
diversity then becomes a critical primary focus for the maintenance and cost-effective
management of AnGR for individual countries and globally.
B. FAO’S GLOBAL PROGRAMME FOR THE MANAGEMENT OF ANIMAL
GENETIC RESOURCES (FAO AnGR Programme)
MoDAD is a central element of the FAO Global Programme for the
Management of Animal Genetic Resources, hereafter referred to as the FAO AnGR
Programme. The FAO AnGR Programme provides a framework for the management
of genetic resources at the global level (Hammond and Leitch, 1995). Urgency to
implement this programme has been mounting due to documented reports that well over
30% of the world’s domestic AnGR are at a high risk of extinction. The catalyst for the
FAO AnGR Programme was the endorsement at UNCED of Agenda 21, and the
signing of the Convention on Biological Diversity2/ . In fact, the database on domestic
animal genetic diversity - which would be the major output of MoDAD - is an
imperative to the realization of effective within-country and global management and
conservation systems capable of meeting the future animal output needs of humankind3/
.
The purpose of the FAO AnGR Programme is to overcome the erosion of
AnGR and to ensure wider development and better utilization of these resources
globally. The FAO AnGR Programme specifically aims to:
•
1/
assist all countries to design and implement comprehensive national
FAO has commenced surveying the 28 species of domestic animals and is continuing
to upgrade its Global Databank on Animal Genetic Resources. Together with UNEP,
FAO have published the first edition of the World Watch List for Domestic Animal
Diversity (FAO/UNEP, 1993) and the second edition will be released in October, 1995.
2/
Now ratified by 117 countries.
3/
The term conservation is used to encompass: (i) identification and characterization
including monitoring; (ii) best short term use and development; and (iii) maintenance to
ensure long term availability; and (iv) access.
6
strategies for the management of their AnGR; and to
•
co-ordinate policy and management at the regional and global levels.
The FAO AnGR Programme consists of the following integrally related
activities, viz.
• a global information system of domestic animal diversity (DAD-IS); as
the
information axis for all management operations, to properly
involve countries, NGOs, training and research groups and other
international agencies, and to provide the early warning system for
domestic animal sector of biodiversity;
•
the MoDAD project to measure this diversity and establish the genetic
uniqueness of AnGR; in order to minimize the size and increase the
cost-effectiveness of the total ongoing management activity required;
•
in-situ and ex-situ conservation strategies designed to make best use of
indigenous and adapted animal genetic resources, and to maintain
those unique resources, of little current interest for use by farmers, to
meet the range of future needs;
•
the establishment of a country-based global animal genetic resource
management structure to be co-ordinated by FAO. This structure
incorporates regional and country focal points assisted by an advisory
board of experts.
•
a specialized intergovernmental mechanism as a dedicated forum for
discussion of detailed technical aspects concerning the
characterization, development, sustainable use and maintenance of
this sector of agrobiodiversity.
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3. PROJECT RATIONALE AND DESIGN CONSIDERATIONS
A. PROJECT RATIONALE
At the current rate of human population growth the demand for food is
increasing dramatically. Food requirements will almost double over the next two
generations, with the requirement for animal products increasing more rapidly than that
for plants. To meet these ever increasing requirements for food, humankind will
become increasingly reliant on tapping the existing biological diversity within domestic
animal species. Paradoxically however, as noted in Section 2, very little is known about
the extent of domestic animal biodiversity. The recent realization that about one third of
all AnGR are at risk of loss augments the urgency to identify the rapidly eroding base of
diversity. Fortunately, molecular genetic techniques have advanced dramatically in
recent years; such that, it is now not only technically feasible, but also cost-effective, to
quantify animal biodiversity on a global scale. These combined facts provide a strong
rationale for MoDAD.
AnGR support the contribution made by domestic animals to world food
production by serving as a storehouse for the wide range of desirable production traits.
Clearly breeding improvements and responses to changing demand requirements and
environmental conditions cannot proceed without the wealth of genetic variation
embodied in the existing breeds of domestic animals. Within a species, genetic
variation is found within and between breeds. Within breed variation is crucial for
continued survival and improvement of a breed. Between breed variation enables
adapted genetic resources to be properly fitted to and further developed in particular
agroecosystems. Also many examples exist of the exploitation of between-breed
variation through cross-breeding which were able to tap useful genetic trait
combinations present in certain breeds. More dramatic are situations which have relied
on ready access to alternative breed resources to avert complete devastation of an
industry due to sudden disease epidemics or changing livestock management
conditions.
Very little existing AnGR diversity has been exploited. Animal breeders
and livestock producers have increasingly promoted and facilitated the universal use of
a few "superior" breeds. It is now clear that this approach, which involves the
introduction of high-input/high-output exotic breeds developed in relatively benign
environments into low- to medium-input, high stress environments will not achieve
high levels of production, productivity and sustainability for each of the broad range of
production environments. This suggests that a new strategy is urgently required for
animal genetic research and development. This approach would involve developing the
production traits in one or more indigenous breeds which are already adapted to their
environments and which local farmers are prepared to use. MoDAD would provide
vital base data for this approach by identifying the preferred combinations of these
unique genetic resources.
Compared to initiatives for plant genetic resources which began in the
1960’s, conservation issues relating to domestic animal genetic diversity have only
recently come to the forefront. There are many similarities between animal and plant
genetic resources in terms of genetic principles and gene action. Also for both, some
8
90% of breeds/varieties are found in developing countries. However, because plant
genetic resources are easier to collect, conserve and manage, and because they exist in
much larger numbers, different strategies for the conservation of AnGR are called for,
although both face some measure of threat due to reliance on one or few
breeds/varieties. Also, in contrast to plant resources, the flow of domestic animal
genetic material is predominantly from the North to the South and this serves to weaken
and threaten the indigenous genetic base which is primarily located in developing
countries. Ensuring the crucial breeds of domestic animals are properly characterized
and conserved for current and future use is imperative and a key rationale for MoDAD.
Countries have agreed to take action to conserve biodiversity including that
used for the production of food and agriculture. While such an international mandate
exists, it is important that a cost-effective and objective action programme is
formulated and implemented. Rather than concentrating scarce international funds on
rescuing a small number of breeds from extinction, emphasis must be on implementing
sound country and global management infrastructures and technical programmes which
would help countries design, implement and maintain national action plans. MoDAD
would establish the amount of genetic variation between indigenous breeds. MoDAD
would also provide objective criteria and increased animal genetic research and
management skills to guide global AnGR conservation and research efforts. These
would not only have the direct benefit of reducing the number of breeds that need to be
conserved, but also the likelihood that AnGR important for current and future
production are conserved.
The molecular and reproductive technology required to engineer in vitro,
uniquely adapted AnGR does not currently exist and is unlikely to within the next 100
years. This fact provides further rationale for characterizing the existing and rapidly
eroding base of animal genetic diversity as soon as possible. Furthermore, the costs
required to manage existing unique genetic resources are negligible compared to the
massive costs which would be required to produce a breed artificially from scratch,
even if it were technically feasible.
B. DESIGN CONSIDERATIONS
MoDAD has been designed to provide a global information base of
domestic animal diversity as cost-effectively and as expediently as possible. In
designing the project the following factors were considered to be of paramount
importance.
Quality and Uniformity of Base-line Data
Quality and uniformity of the database required to be produced were
considered to be of utmost importance in designing the project. This affected various
aspects of project design ranging from the methods of field sampling, DNA extraction
and storage, assaying, data analysis and archive on the database, as well as the
dissemination and application of the results. Accordingly, training, technical assistance,
project co-ordination and quality control mechanisms have been designed to ensure that
the results of the project would be of the highest possible quality within acceptable costeffective limits.
9
Cost-effectiveness and Timeliness
Cost-effectiveness and timeliness of obtaining the results were considered
to be important project design criteria. Consequently options for all project activities
were considered from a cost-effectiveness standing in designing the project (see below Project Design Options).
Timeliness in producing the base-line genetic diversity data was considered
to be important. An adequate provision of funds to cover all incremental costs
associated with the MoDAD, the global co-ordination by FAO, and an
organizational/implementational configuration of using national and international
genetics research institutions, linked to the FAO AnGR Programme, strategically
combined (depending on assaying option chosen) with rapid assaying capabilities of a
commercial lab. Such a project configuration would ensure that project results would
be produced in a timely manner.
Project Design Options
Various project activity options were defined and assessed in relation to
cost-effectiveness. The options considered, and their associated advantages and
disadvantages, are outlined briefly in Section 4D and detailed in Annexes 1 to 4. In
general, the least-cost options were incorporated in the final project design, although in
a number of instances other criteria such as quality of results, technical considerations
and the degree of participation of national institutions, were also important
considerations in the final choice of options.
The preferred option for field sampling was considered to be that which
would use staff of the national genetics research institutions in each of the countries
where sampling would be required. This option, while being the most cost-effective
sampling option considered, had the added advantage of increasing the involvement of
countries in the conduct of the project.1/
Two options have been selected for the base-line assaying the DNA
samples. A further option of conducting assaying in every country sampling was also
considered. This latter option was discarded on the basis of high costs, mainly
attributable to the fact that economies of scale due to high throughput could not be
captured, and too high a risk that the data generated would be of an unacceptable quality
because of non-uniformity of laboratory assaying procedures. Option 1 would involve
a minimum of 4 regional research laboratories which may be located at recognized
international or national genetics research institutions. Option 2 involves a strategic
combination of a single private commercial laboratory, with the public sector regional
research laboratories. In the case of Option 1, the regional research labs would be
located in developing countries but linked to labs in Western Europe and North
America, to provide for additional technical and species related knowledge. There are
1
Due to savings in travel and daily allowances which outweighed higher quality
control costs compared to the other sampling options considered of using regional
sampling teams and international consultants.
10
various advantages and disadvantages associated with each of these options related to
cost, ease of management, speed, capacity building, quality control and political
assessment. A Multiple Criteria Analysis of these two options revealed little difference
between them (Annex 3). However, such an analysis depends on the importance
attached to each criterion and the way in which each option is scored.
The choice of which option to use for carrying out assaying of samples is an
outstanding issue which must yet be addressed (see Section 7). The project funder, as
well as the MoDAD participating countries, should be consulted before a final choice is
taken as it may be a particularly sensitive issue. Advantages of incorporating the single
commercial laboratory include: (i) speed and quality control of assaying procedures;
(ii)ease of management and co-ordination of all assaying activities; (iii) costeffectiveness, and; (iv) joint involvement of both public and private sectors.
Disadvantages of the commercial laboratory option include: (i) it would partly remove
the most resource demanding part of the project from the public sector regional
laboratories where the network training, data analysis and DNA long-term storage
would be centred; (ii) if not carefully operated, it could engender political sensitivity
and mistrust over property rights and unauthorized use of genetic material. The latter
disadvantage could be dissipated, but not eliminated, by including in the contractual
agreement with the commercial identity that all DNA samples would be destroyed after
assaying.
Sample Ownership and Property Rights
Ownership and property rights over stored genetic material are very
important considerations which have been taken into account in designing MoDAD.
Protocols have need be designed (see Annex 2) to protect ownership and property
rights.
Country Participation
Participation of countries in the conduct of MoDAD has also been an
important consideration in project design. The field sampling, assaying, analysis and
reporting activities have been designed to increase country participation in the
implementation of the project within what have been considered acceptable limits of
data quality and timeliness of results, and to facilitate co-ordination of the global
activities and consideration and full utilization of the results. Furthermore, the regional
network training activities have been designed to increase the impact of MoDAD in
terms of encouraging countries, particularly less developed ones, to measure and
manage their domestic AnGR, and to seek global co-operation in their own endeavours.
Project Coordination
Effective co-ordination of the project was a major design consideration.
Because of the global nature of the project, and in order to realize MoDAD’s primary
objective of producing high quality results in a cost-effective and timely manner, it
would be imperative that the project be effectively co-ordinated globally. FAO would
11
be responsible for the co-ordination of the project, aided by an internationally
recognized group of animal genetics research and development experts. An added
advantage of FAO co-ordination is that it would link MoDAD closely to FAO which
has been mandated to put in place a global management programme for farm AnGR.
This would ensure that the data and DNA samples generated by MoDAD would be
maintained and held in trust. Furthermore it would greatly assist countries to ensure
that the output data would be put to maximum use in the management of their AnGR.
Also the global co-ordination would facilitate the incorporation, as far as possible, of
the results of the many isolated genetics research projects underway in several
laboratories world-wide. This research has focused on few species (cattle, sheep and
pigs) and few breeds in a limited number of countries.
12
4. THE PROJECT
A. GENERAL DESCRIPTION
Project Objectives
The overall objective of the FAO AnGR Programme (see Section 2B) is
realize for FAO members the documentation, better development and use, and the
maintenance of many more of Earth’s unique animal genetic resources important to
humankind for the production of food and agriculture. In order to achieve this
objective, it will be necessary to identify, describe, monitor, better utilize and maintain,
the AnGR required for the sustainable production of food and agriculture.
The primary objective of MoDAD is to simplify, rationalize and reduce the
total cost to humankind of managing country and global AnGR. Specifically MoDAD
would seek to:
($) measure the genetic diversity existing in each of 14 species of
domestic animals most important to humankind in the
production of food and agriculture (the 14 species concerned
are listed in Table 1);
($) evaluate the genetic uniqueness of each AnGR within each
species;
($) ensure this information is made available for the development
of country-based and global strategies for managing the
remaining AnGR of each of these species.
Table 1. Number of breeds to be sampled by species
Species
Cattle
Sheep
Goat
Pig
Buffalo
Horse
Ass/Donkey
Chicken
Camel
Llamoids
Turkey
Duck
Domestic Goose
Rabbit
Number of breeds
50
50
50
50
20
50
20
50
20
6
20
20
20
50
Total 476
13
Table 2. Assumptions as to number of countries within region in which sampling
would be conducted.
Region
Number of countries involved in
sampling
Africa
12
Asia and Pacific
15
North America and Latin America
8
Europe and Former USSR
15
Near East
6
Total 56
Project Components
The first phase of MoDAD would consist of eight components which
would be implemented over a four year period (see Figure 1). Briefly the components
would consist of the following activities. The project activities are discussed in more
detail in Sections 4C to 4E and in Annexes 1 to 4.
Breed Selection and Field Sampling (US$ 1.65 million)1/
Breeds to be sampled would be co-ordinated by the MoDAD Expert
Advisory Group (EAG). Field sampling would be carried out by Government animal
research staff of the respective countries the animals are sampled in, and co-ordinated
by the government appointed National Focal Points of the FAO AnGR Programme (see
Section 2B). MoDAD would cover all incremental costs associated with the field
sampling activities.
DNA Extraction (US$ 1.70 million)
DNA would be extracted in the country in which sampling of animals
occurs. The DNA extraction activities would be co-ordinated by the National Focal
Points for the FAO AnGR Programme, supported by the MoDAD regional laboratories.
MoDAD would cover all of the incremental costs associated with DNA extraction and
would support this work at one nominated laboratory in each country.
1/
Costs are inclusive of physical and price contingencies.
14
Microsatellite Marker Development and Optimization (US$ 0.74 million)
For six of the fourteen species of domestic animals included in MoDAD
(viz. camel, llamoids, turkey, duck, domestic goose and rabbit) microsatellite markers
have not yet been developed. MoDAD would instigate and financially support this
development effort at selected internationally recognized animal science laboratories
with the appropriate technical and scientific resources. The molecular genetic
procedures required to isolate and characterise new microsatellites is well established
and the time required to develop a panel of 30 suitable microsatellites in a single species
can be estimated to be approximately 18 person-months. The amount of work required
can be reduced by using a co-ordinated strategy of marker development for related
species. For example, many of the markers characterized for the two camel species
would be suitable for use in the llamoid species and vice versa. This is because the two
groups are closely related.
Adequate numbers of microsatellite markers have already been produced
for the other species of domestic animals included in the project, and MoDAD would
utilize the results of this work. For some species hundreds of markers are available. An
optimal panel of markers need be selected for use in genetic distancing work. Criteria
for their inclusion in the reference panel are given in Annex 3. The International
Society of Animal Genetics has resolved to assemble panels of specific microsatellites
for genetic diversity studies in certain domestic animal species. MoDAD would adhere
to these recommendations.
15
Figure 1: Project MoDAD Primary Strategy & Activities
KEY
Indicates data flow
Indicates DNA sample flow
GLOBAL COORDINATION BY FAO
CDAD
MoDAD
Expert
Advisory
Group on
protocols,
procedures,
results
Indicates DNA repository
Intergovermental
CGRFA
Accessing
Country
DNA + DATA
Coordinate/
Assist
Countries
Funding
Coordinate/
Assist
Regions
Project Management
Species
Reporting
Domestic Animal Diversity
Information System (DAD-IS)
Funding
Project Management
Equipment
Species / Breed Sampling
Quality Control
Quality Control
Storage
Storage
Baseline Assaying & Analysis
Training
Training
MoDAD Global
Databank
for
all Species
MoDAD
Global DNA
Repositories
Field
Sampling
(all Sps)
Country Coordination
MoDAD Studies
refereed
electronic
journal
Baseline
Assaying
Split Samples
National
MoDAD
Repositories
(all Sps)
Not provided for in MoDAD
Phase I
Indicates a possible option
for Baseline Assaying
Review
MoDAD
MoDAD
Regional
Laboratories
Baseline
Global
Analyses for
each Sps
Baseline
Analysis
Advanced
Global
Analyses for
each Sps
Advanced
Assaying
Baseline
Assaying by
Commercial
Lab
16
Laboratory Assaying1/ (US$ 4.03 million)
Laboratory assaying of the DNA samples would be carried out at four
regional laboratories located in Asia, Africa, Latin America, and Central or Eastern
Europe, or alternatively at one commercial laboratory, with the regional laboratories
responsible for quality control. For both alternatives the costs of assaying are expected
to be about the same. The criteria which would be applied in selecting the regional
laboratories to be engaged in MoDAD are set out in Annex 3. All samples of any one
species would be assayed at the same laboratory to ensure analytical uniformity and to
facilitate quality control. MoDAD would finance all of the operational costs associated
with the required assaying at the regional laboratories.
Data Storage and Analysis (US$ 0.07 million)
MoDAD would finance all of the incremental costs associated with the
storage and analysis of the genetic diversity data generated at the regional laboratories.
A management information system will be provided to assist the management of the
project at the national, regional and global levels. For regional laboratories MoDAD
will provide a uniform database management system for entry, validation and reporting.
Technical Assistance and Training (US$ 1.13 million)
MoDAD would make a large commitment to capacity building. Technical
assistance and training of personnel would be required for field sampling, storage,
database management, laboratory assaying (required for the regional laboratories
option) and analysis. In addition research personnel from developing countries would
receive training in research and management of domestic animal genetic diversity
conservation. The project provides for the incremental costs associated with these
activities.
The cost of technical assistance required for quality control under the
regional laboratory option for assaying would be about US$ 42,000. This cost would be
a saving under the commercial laboratory assaying option. The cost of quality control is
however very small compared to the cost of assaying (less than 1.5%).
Project Co-ordination and Management (US$ 0.92 million)
MoDAD would cover the costs of co-ordination and management of the
project. This would include the full costs of a project co-ordinator located at FAO
Headquarters in Rome, and the costs associated with the Expert Advisory Group
(EAG). The EAG are required to advise on all technical aspects of the project including
field sampling, assaying, data analysis, dissemination and application of the results in
national and global AnGR management.
1
/ Laboratory assaying refers here to a determination of the microsatellite genotypes
for an individual animal using molecular genetic technology.
17
Long-term DNA Repositories (US$ 0.29 million)
During the implementation period of MoDAD the project would finance the
storage of DNA samples at national repositories. MoDAD would also finance longterm storage of DNA samples at the four regional laboratories and would
form the global repositories. These regional laboratories, ideally part of the system of
International Agricultural Research Centres, would serve as primary storage for the set
of species for which they are responsible for sample assay or quality control (in the
situation where a commercial laboratory is contracted to carry-out the assays); and
would served as back-up storage for a set second set of species. In all cases, trust
agreements would be developed with FAO and countries of origin.
B. PROJECT OUTPUTS
The following outputs would be generated by MoDAD.
•
For each species, a base-line range of genetic variation parameters
describing the diversity among and within breeds. Details on the
outputs from specific analyses are outlined on page 21.
•
A unique global repository of data on the breeds sampled - integrating
the assay and analytical data with the field sampling data, details on the
production environment and photographs for use in further training,
research and awareness programmes.
•
A unique store of DNA samples for the breeds of each species
surveyed which would be owned by the countries providing the
material. Through signed agreement, these samples could be used for
further research and development, with the proviso that derived
benefits would be shared according to the agreement.
•
An increase in the number of trained personnel in field sampling
techniques, database maintenance, animal molecular genetic research
and enhanced knowledge in domestic animal diversity.
•
Rationalization of longer-term management of AnGR by objectively
reducing the number of breeds that will need to be maintained to
conserve current animal genetic diversity.
•
Improved identification of specific breed combinations with potential
for increasing in environmental fitness and animal production;
enabling rapid and substantial increases in sustainable animal
production from future research and development on the world’s 14
most important domestic animal species.
•
An increased awareness within participating countries, and globally, of
the importance of better managing AnGR, and the need to formulate
sound AnGR management policies.
18
C. TECHNICAL ACTIVITIES
Use of Existing Data and Research Results
Genetic mapping projects are already underway for some sub-sets of cattle,
sheep and pigs in a few countries. A large number of microsatellite markers1/ have been
developed as a result of these activities. The vast majority of these markers are in the
public domain and will be available for the analysis of genetic variation in the MoDAD
project. The knowledge base resulting from the genome2/ analysis projects would also
be exploited to develop new microsatellites for species where there are no pre-existing
markers.
At the outset of MoDAD it would be necessary to conduct a thorough
review of the literature in order to retrieve as much information as possible about the
genetic relationships among breeds, in relation to the types of field sampling, assaying
and analytical approaches used. This would be an invaluable aid in determining which
populations and breeds should be included in the MoDAD global surveys. With the
exception of cattle, little co-ordinated research to comprehensively assess genetic
variation in domestic livestock has been carried out. An ongoing project at Trinity
College, Dublin provides a model for the genetic surveys encompassed by MoDAD.
This project has established the fundamental genetic relationships among 20 globally
disparate breeds of cattle populations in Africa, Asia and Europe.
Databanks resulting from the genetic mapping projects could reveal a great
deal about the extent of allele3/ variation at each microsatellite marker used. This is
because in most cases, widely divergent crosses were used in order to maximize
heterozygosity4/ and hence the information content of each pedigree. For example, the
cattle projects made use of zebu/taurine crosses and the pig projects used
European/Asian crosses. The information from this work is useful for the MoDAD
project because it should reveal the maximum range of existing variation within the
species.
A large number of laboratories maintain DNA samples of cattle, sheep,
horse and pig breeds. Every effort should be made to involve these laboratories in the
MoDAD project and possibly reduce the number of breeds which would need to be
sampled and hence the total cost. In order to maximize opportunities to utilize existing
information and to encourage further studies, the protocols for the MoDAD project and
the central databank would be widely publicized from project start-up.
1
/ Microsatellite markers are short variable segments of DNA randomly dispersed
throughout animal genomes (which are the genetic "blueprints" of organisms). Genetic
variation at these markers can be established very rapidly using standard molecular
genetic techniques.
2
/ Genome is the term used to describe the total genetic constituency or "blueprint" of
an organism.
3
/ Alleles - One gene may have several different variants and these variants are called
alleles. In the case of microsatellites, the alleles are sequence length variants.
4
/ Heterozygosity is where different alleles are present at a locus. A locus refers to
location of gene on a chromosome.
19
Breed Selection and Field Sampling
Breed selection for each of the 14 species would be conducted under the
direction of the MoDAD EAG and the selection criteria (see Annex 1) would be based
on the known evolutionary history of the species in question, previous genetic
characterisation, current distributions, economic considerations and environmental
factors. For species with more than 200 breeds, 50 breeds would be sampled. For
species consisting of less than 200 breeds, 25% of the current populations would be
surveyed. At least 20 breeds would be sampled from species with less than 80 breeds.
Where there are less than 20 breeds in a species, all breeds would be sampled.
Blood samples would be taken from 50 animals per breed and every
attempt would be made to obtain equal ratios of females to males. The field personnel
would always try to ensure that only pure-bred animals from each breed are collected
and that these individuals are as unrelated as possible. Phenotypic data would also be
collected according to FAO breed survey questionnaires. Photographic documentation
would also be obtained of typical representative animals and where feasible of all the
animals actually sampled. Information on the production environment would also be
collected.
Two possible options for sampling were considered: (i) sampling by species
and organising field missions separately for each species; or (ii) sampling by country or
region and where possible, sampling the breeds for all species within a particular
country or region. Due to logistical constraints and cost savings, it was decided that the
second option would be the most suitable and would not necessitate any extra
equipment or expertise. This strategy would also enhance the participation of local
personnel in the management of their national AnGR.
The organizational structure for field sampling involved a country focal
point with a central co-ordinator, and training carried out on a regional basis for the
country focal points. Four strategies were considered for the sampling activity and
these are covered in more detail in Annex 1:
(a) Country Focal Point with Central Co-ordination. Co-ordinators would
be identified for each country. These co-ordinators would be brought to
regional training courses and introduced to the project and all the field
activities. They would then return to their respective countries and organise
small training workshops for the actual personnel carrying out the sampling
missions. The field sampling would be co-ordinated from the FAO in
Rome.
(b) Country Focal Point with Regional Co-ordination. This option is
basically the same as the strategy outlined above, however the co-ordination
of the sampling missions would be on a regional basis. This option was
more expensive than the first option.
(c) Regional Focal Point (Co-ordination and Sampling). This would
involve assembling a team of perhaps 10 people who would be assigned to
20
sample all breeds in each region. This option was discounted for
various reasons which are detailed in Annex 1.
(d) Contract Work. This option would involve the identification of a
number of consultants with extensive experience of field sampling in
adverse conditions. They would be responsible for organising the missions
with minimal co-ordination from FAO Headquarters. This option was
discounted mainly on the grounds of high cost and minimal country
participation in project implementation.
Collection of Biological Material
Blood samples are considered the medium of choice for extraction of
DNA. However, provision would also be made for collection of alternative tissues
such as ear biopsies, hair samples, feathers and buccal smears where blood sampling is
not feasible.
Various methods for sample collection are detailed in Annex 1 including a
description of how blood samples would be preserved for transportation.
A detailed list of sampling data would be collected for each animal
sampled and this is also outlined in Annex 1.
DNA Extraction, Purification and Shipment
DNA would be extracted in field laboratories using a simple protocol
outlined in Annex 2. Animal health and the avoidance of transmission of pathogens
were the primary considerations in the choice of protocol. The method chosen uses a
number of steps involving highly degradative chemicals which would eliminate the
possibility of pathogen transmission via the samples.
After DNA samples have been extracted, purified and labelled, the samples
would be split into three sub-samples. One sub-sample would be stored in the country
of origin under the care of country co-ordinators for inclusion in the National DNA
Repository. One each of the other 2 sub-samples would be sent to the regional
research lab and the second sub-sample would go to 1 of the other 3 regional labs for
backup storage. Further sub-samples would be created. The number of sub-samples
created would be dependant on the option adopted for assaying. OPTION 1 - The
sample received by the regional lab would be further split into 2, one sub-sample
would be used for base-line assaying and the other retained for storage. OPTION 2 Two sub-samples would be created on a routine basis; one sub-sample retained for
storage, and the other sent to the commercial laboratory for assaying. going to the
Global Repository and the other sent to the commercial lab for assaying. To facilitate
quality control measures, on a random basis a thrid sub-sample would be created for
assaying by the regional laboratory.
All necessary permits required to satisfy international veterinary
requirements would be included with the shipment. Shipment of DNA would use
secure courier mail services.
21
DNA Storage
One of the main supplementary benefits of the project is the opportunity to
preserve representative DNA samples from a large number of diverse breeds within
each of the 14 main domestic animal species. This material would be of immense
benefit in the future, providing a vital resource for animal genetic research and
training, and it would increase in importance as the repertoire of evaluation of
advanced assaying techniques, for molecular biology techniques expands, providing
more information which could be applied in future conservation and breeding
programmes.
Although primary ownership of the samples would always remain with the
country of origin, the DNA collected over the course of the MoDAD project would be
stored in triplicate. One set of 50 samples for each breed would be maintained by the
relevant authority in the country of origin, a second set of samples would be
maintained by the regional laboratory responsible for assaying or quality control for
that specific set of species. A third set of samples would be stored by 1 of the other 3
regional research laboratories. Samples would be coded and distributed according to
the procedures outlined in Annex 2. A simple and unambiguous alphanumeric coding
system would be used for sample labelling and distribution.
Material Transfer Agreements
The legal and technical issues surrounding ownership and international
movement of the biological material encompassed by MoDAD are also detailed in
Annex 2. Precise legal definitions would have to be developed concerning: (i) the
country of origin and ownership; (ii) forbidding of sample duplication without
authorisation; and (iii) performing supplementary assays only with permission from
FAO and the country of origin.
The necessary health permit specifying that the DNA extraction protocol
satisfies veterinary requirements for international shipment need also be obtained prior
to shipment of samples. For some countries, such certification measures are already in
place for the international shipment of DNA samples.
The longterm DNA repositories will be ideally be part of the system of
International Agricultural Research Centres of the CGIAR, with all material being held
in trust under an agreement involving the country of origin, FAO and the CGIAR.
DNA Assaying
Choice of laboratories for assaying
The criteria developed for determining which laboratories should be
nominated to perform the assaying phase of MoDAD are outlined in detail in the
Annex 3.
Various options were considered regarding the number and type of
laboratories to be used for the assaying phase. These included: (i) performing the
assaying where possible in the country of origin at government animal research
22
laboratories; and (ii) a smaller number of international or national animal research
laboratories allocated on a regional basis by species but emphasing developing country
regions to best assist with the associated capacity building activities; (iii) contracting
the assaying activity to a single or a small number of commercial laboratories, in
association with the regional laboratory option where these regional laboratories would
retain all other roles and add a quality control responsibility for the large-scale assaying
done by the commercial laboratory. Since a number of important factors impinge on
the choice of which of these options should be used (see Section 4B and Annex 3) this
decision has been left as a follow-up issue (Section 7). Under the regional and
regional laboratory plus commercial options, four public sector laboratories would be
appointed in Africa, Asia, Latin America and Central or Eastern Europe. Further, it is
proposed that these be part of the International Research Centres of the CGIAR system
to enable this regional laboratory system to also serve as the Global Respository.
Linkages and collaboration with laboratories in Western Europe and North America
would be encouraged to enrich the project with prior data, species-specific knowledge
and analytical techniques.
Choice of genetic markers for base-line assays
A number of criteria are set out in Annex 3 outlining requirements for
suitable genetic markers for the MoDAD project. These markers should be DNAbased and accessible using the Polymerase Chain Reaction (PCR), a technique which
allows rapid and accurate genetic typing from a small amount of starting material. A
range of different genetic approaches have been considered (see Annex 3), each based
on a different type of genetic marker. However, when all factors are taken into
consideration, including cost, ease of use, amenability to rapid assay and analysis, and
availability for most species, the most sensible choice are genetic markers called
microsatellites which are short variable segments of DNA. The variation observed at
these DNA regions is based on incremental differences in the length of simple repeated
sequences (see Annex 3). Based on theoretical and practical considerations, 30
different microsatellite markers would be used to assay genetic variation in each of the
14 domestic animal species.
The DNA Repositories (country, and global) will foster advanced assaying
by providing a cost-effective source of samples. As such, MoDAD provides a
powerful facility for cost-effective research, based on current and future technologies.
Advanced analysis which might be carried out parallel to MoDAD, by the regional
laboratories or non-contracted laboratories, involves the assay of DNA sequence
variation in mitochondrial DNA. Results from such molecular screening would permit
resolution of large-scale divergence between groups of breeds within a species and
sex-mediated gene flow between members of divergent breed groups. Assay of Ychromosomal variation would also provide an insight into male-specific variation and
gene flow.
Criteria for choice of microsatellite genetic markers
There are a number of technical criteria for the choice of microsatellite
markers to be used for each species surveyed during the MoDAD project. These are
outlined in Annex 3 and are mainly concerned with accuracy of the resulting
23
information and the ease of assaying. In the case of the main domestic animal species,
there are an abundance of candidate markers and for some species there are already
international bodies in place for assembling panels of markers suitable for genetic
surveys.
Very few or no microsatellite genetic markers have been developed for six
of the domestic species encompassed by MoDAD. In these cases a panel of
microsatellite markers need be developed. This would involve about 18 person-months
of work per species. In some cases markers developed in one species can also be used
to test for genetic variation in another species. For example, it may be possible to use
markers developed in llamoid species for surveys of genetic variation in camelid
species and vice versa.
The International Society of Animal Genetics (ISAG) has committed to
assist in the selection of the panel of markers to be used for each species.
Laboratory assay of microsatellite variation
A rapid-throughput protocol for assaying variation at microsatellite loci is
described in Annex 3. The salient features of this protocol are: a) straightforward and
unambiguous; b) standardisable and consistent between laboratories; and c) potentially
automatable, . All genotypic assays for a single species can be performed by one or
two technicians and the system outlined would allow a throughput of hundreds of
samples per day.
The laboratory protocol is a simple three-step procedure. The first step is
PCR amplification of the microsatellite marker from the original DNA sample. This
can be carried out on a large number of samples simultaneously and is essentially an
automatic process. The second step is electrophoretic separation of the microsatellite
alleles on a suitable gel medium. The third step is data collection and conversion to an
electronic form.
Data Analysis, Management and Dissemination
Data Analysis
There are a number of analyses which would be performed on the data
resulting from the MoDAD genetic surveys in each species. These can be broadly
divided into analyses which provide information about the genetic structure of
individual breeds and analyses that quantify levels of genetic variation within and
among breeds. These analyses are detailed in Annex 4 and include the pattern and
partitioning of genetic variation within a breed, the flow of genetic information
between breeds, the genetic distances among discrete breeds within a species and
phylogenetic representations of these distances among breeds and among individual
animals.
However, to obtain the critical information required for markedly improving
the management of global animal genetic resources, MoDAD concentrates on the
between breed questions. Some of the outputs from these various analyses are outlined
24
below:
(a) A framework for rationalisation and maximisation of genetic diversity
within a domestic animal species to provide effective genetic buffers against
future environmental challenges.
(b) A concise understanding of the genetic relationships and diversity
among breeds to aid in the cost-effective conservation of breeds with unique
adaptive traits.
The base-line data analysis would be conducted at the regional laboratory
level, for the species they are responsible for, and co-ordinated for all species by FAO.
The computing resources necessary for these analyses are in most cases minimal and
are detailed in Annex 4.
A suitable suite of population genetic software would be required which is available
gratis via the Internet, and also through FAO’s DAD-IS.
The access to analytical software makes straightforward the conduct of
additional analysis which provide for an extra project dimension in terms of data
usage. The output of such analyses would provide,
(c) A method to determine any hidden or cryptic genetic variation within a
species which may be used for future production gains through exploitation
via crossbreeding programmes.
(d) Characterisation of valuable endangered breeds in terms of their
"genetic health." This can be achieved with outputs from the MoDAD
analyses such as inbreeding levels, gene flow from other populations,
effective population sizes and molecular population structure.
Data Management
The requirements for an integrated system of data management at the
global, regional and national levels are detailed in Annex 4. In brief, there are two
stages to the management of the data and information that would be generated by the
MoDAD project. In the first stage the raw genotypic data derived from the assaying
activitiy would be stored and maintained in a uniform database system developed to
operate through FAO’s distributed DAD-IS information system. All laboratories will
have access to this with a serires of user protocols appropriately securing data. The
species specific MoDAD databases will be maintained on this data managment system
by the regional laboratories responsible for the particular species under FAO trust. The
database system will also be used for generation of data for base-line and (future)
advanced statistical analyses.
The MoDAD database will be a component of the Domestic Animal
Diversity Information System (DAD-IS) based in FAO. The DAD-IS will operate
using the World Wide Web system on the Internet, with the necessary validation and
security protocols. To support users with limited Internet access electronic mail will
be used for non-interactive connectivity. For users with no connection to the Internet a
25
standalone version of DAD-IS will be provided on CD-ROM.
Using the above functionality of DAD-IS, regular updates of the data can be
generated by all laboratories involved. DAD-IS would also contain relational links to
other sites with microsattellite data. Following validation and approval the
information would be accessible to participating countries and the scientists involved
and at a second level to interested parties electronically via the Internet or by
conventional means where necessary.
As part of DAD-IS, a Management Information System (MIS) would be
developed for MoDAD to facilitate project coordination and operation at the national,
regional, and global levels. The MIS is discussed further in Section 5A.
Publication and Reporting
The initial reporting effort will focus on presentation by FAO of results to
governements to assist them in rationization of the AnGR management programs,
which is
the prime objective of MoDAD. The rapid communication of results will
commence in year 3 of the project. Data and analytical results would be made
generally available to the global scientific community.
The nature of the data generated from MoDAD necessitates two approaches
to the dissemination of the information. The raw genotypic data would be of interest to
many scientists, but due to its scale and volume, would not be published in normal
scientific journals. Instead a refereed electronic journal would be established,
provisionally entitled MoDAD Studies. This would be the ideal method for
disseminating the large genotypic datasets in a scientifically validated manner. The
condensed data resulting from the analytical phase would be published in conventional
form under the conditions outlined in Annex 4.
D. TECHNICAL ASSISTANCE AND TRAINING
Technical Assistance
Technical assistance would be required during the first year of the project to
conduct four regional field sampling workshops. If the regional laboratory option is
adopted for assaying, technical assistance would be provided in setting up this
component. In addition technical assistance would be required during the first three
years of the project to install and supervise quality control of field sampling, DNA
storage, laboratory assaying, database management and analysis. Quality control
activities have been designed to ensure that acceptably high levels of sample and data
integrity are attained.
Training
The project would support regional training workshops on field sampling
and storage for the national and regional coordinators. In-country field sampling
training courses in each of the countries where breed sampling would be required
would also be financed by MoDAD.
26
The complexity of management decisions, in terms of project management
and volume of data generated necessitate use of management information and database
management software. Training would also be provided at the national and regional
levels in management information systems, including database management.
MoDAD would support on-the-job training for researchers from developing
countries in analytical techniques for genetic genotyping research. One of the aims of
this training would be to promote further evaluation and analysis methods to enhance
the utility of the results which would be generated through MoDAD.
Training on the management of AnGR would be conducted as part of
MoDAD. A regional research and training network would be established at the
regional laboratories.
E. PROJECT ORGANIZATION AND MANAGEMENT
Project Co-ordination
MoDAD would be co-ordinated by a project co-ordinator located in the
Animal Health and Production Division of FAO in Rome. The co-ordinator would be
responsible for the implementation, co-ordination, monitoring and reporting of the
project. MoDAD would cover all of the costs of the project co-ordinator, including
travel and incremental office costs.
MoDAD would tap into the global co-ordination network that is being
established for the FAO AnGR Programme. This network is based on a Global Focus
at FAO in Rome, Regional Focal Points and formal National (technical) Focal Points
with a country contact as the national technical co-ordinator. National Focal Points
and contact personnel are being identified specifically for the FAO AnGR Programme
by participating governments, with 50 already in place throughout Europe and Asia
and those for the Americas about to be implemented. The country contact is
responsible for developing and maintaining the national technical network for the
management of AnGR.
The FAO global information system (DAD-IS) would provide a low-cost
communications link and shell for MoDAD communications and databases.
Expert Advisory Group
The Expert Advisory Group (EAG) would advise the FAO on matters
pertaining to field sampling, protocols, and technical procedures, data storage, analysis
and dissemination, and prepare the necessary global species reports. Additionally the
EAG would consider opportunities for enhancing the base-line assaying and analyses
as future technologies are developed. Provision has been made for the EAG to meet for
four days each year over four years. The EAG would be in constant contact with the
project co-ordinator via the Internet.
27
Data Interpretation and Dissemination
An additional responsibility of the EAG would be to advise on the
interpretation of the data generated by MoDAD and funds have been included, under
the Project Co-ordinator activity in FAO, to finance dissemination of the results via a
refereed electronic journal.
Long-term DNA Repositories
The project would fund the storage of DNA samples at the DNA extraction
laboratories in the countries where DNA sampling takes place. Funds would be
provided to purchase the equipment needed and to fund associated storage operational
costs during the implementation period of MoDAD.
The project would also fund the set-up costs of DNA repositories at four
regional laboratories/global repositories. In addition funds would be provided to cover
the repository operational costs for 10 years.
F. PROJECT COSTS
Total project costs over four years, are estimated at US$ 10.53 million
inclusive of physical and price contingencies, with a foreign exchange component of
about US$ 4.22 million (about 40% of total costs inclusive of contingencies). Project
costs have been estimated in US dollars at a constant exchange parity rate. An
inflation factor of 2.5% per year has been added to all foreign costs components and
10% per year to all local costs. Physical contingencies of 10% have been added to all
costs.
Full details of the project costs are given in Annex 6 and are summarized by
component and by expenditure category in Tables 3 and 4 respectively. The field
sampling and DNA extraction components account for almost equal proportions of
total base costs at 16% and 17% respectively while microsatellite development costs
account for 7% (Table 3). The most costly component is laboratory assaying which
makes up 35% of total base costs, while technical assistance and training account for
11%, and project co-ordination and management a further 9%. The data storage and
analysis, and DNA repositories, make up the remaining 1% and 3% respectively. In
relation to expenditure categories (Table 4) investment costs account for 37% of total
base costs and recurrent costs 63% of total base costs. The most significant
expenditure categories are travel and field allowances (20% of total base costs),
followed by laboratory consumables/operating costs (18% of total base costs),
technical assistance and training (17% of total base costs) and equipment (16% of total
base costs).
Many of the costs are significantly dependent on the number of countries to
be included in the field sampling operations and the number of breeds that would be
sampled. The Working Group which has prepared this report, did not have the data
nor the time to accurately determine the breed sampling by country (refer Annex 1).
The breeds to be sampled, and the countries in which the field sampling would be
28
undertaken is a follow-up issue which would need to be addressed by various world
renowned species experts (to be identified by FAO) as soon as possible. However, for
the purpose of estimating the project costs, it has been assumed that field sampling
would involve 56 countries sampling a total of 476 breeds (see Table 6.3 Annex 6 for
details).
G. PROJECT SUSTAINABILITY AND PARTICIPATION
MoDAD has been designed to obtain global information on domestic
animal genetic diversity as quickly and as cost-effectively as possible. Most of the
costs of the project would comprise incremental operational costs of existing genetics
research facilities, that would be incurred in obtaining the information. Investment
costs in laboratory equipment are not large and the recurrent expenditure associated
with this equipment after project completion would be easily absorbed within the
recurrent budgets of the recipient national and regional laboratories.
One issue related to project sustainability is that of maintaining the DNA
repositories after the completion of MoDAD. It would be imperative that the DNA
samples collected by the project are stored long-term so that as molecular screening
technology becomes available advanced assaying could be carried out so that the
results and utility of MoDAD would be considerably enhanced.
MoDAD has been intentionally designed to facilitate participation of
countries by linking the project to national and international animal genetics research
institutions. In the countries where field sampling would be carried out, national
personnel would be involved in the field sampling activity, and DNA extraction. The
advantages of this design configuration are: firstly it would reduce the costs of field
sampling (see Section 3B); secondly it would increase the exposure of the project at
the country level; thirdly it would increase the sense of ownership of the project at the
international level; fourthly it would reduce potential political problems which may
arise over ownership and property rights of the collected genetic material and data. The
network training activity would further enhance the exposure the project in developing
countries throughout the world, by including participants from countries other than
those directly involved in the field sampling activities. This participation would
increase project impact in national and global management of AnGR.
MoDAD would empower nations to further investigate between breed
diversity. From this standpoint, MoDAD would provide a powerful data and
capability base which would facilitate further investigations of additional breed
diversity by nations or regions themselves.
29
Table 3. Global Project for the Maintenance of Domestic Animal Diversity
Project Components by Year - Totals Including Contingencies (US$’000)
Totals Including Contingencies
% Foreign
Exchange
(Base Costs)
% Total
Base
Costs
1996
1997
1998
1999
Total
1 151.0
1 097.5
739.7
70.0
503.8
603.9
1 514.7
-
1 634.6
-
882.9
-
1 654.8
1 701.5
739.7
4 032.2
70.0
35
45
29
32
80
16
17
7
35
1
33.3
51.0
192.2
-
117.2
314.3
95.9
323.5
-
33.3 51.0
405.3
637.8
95
95
37
95
1
4
7
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
276.5
431.5
419.4
-
1 127.3
75
11
188.4
26.0
197.3
26.7
206.9
27.3
217.2
28.0
809.9
108.1
72
100
8
1
Subtotal Project Coordination
H. Long-term DNA Repositories
214.4
34.9
224.0
173.9
234.3
25.0
245.3
57.3
918.0
291.1
76
68
9
3
3 584.1
3 451.8
2 313.3
1 185.5
10 534.7
45
100
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Total PROJECT COSTS
30
Table 4. Global Project for the Maintenance of Domestic Animal Diversity
Expenditure Accounts by Years - Totals Including Contingencies (US$ ’000)
Totals Including Contingencies
% Foreign
Exchange
(Base Costs)
% Total
Base
Costs
1996
1997
1998
1999
Total
596.9
500.5
172.5
606.1
474.6
107.0
253.3
488.6
85.4
132.1
159.1
-
1 588.4
1 622.9
364.9
80
90
30
16
17
3
1 269.8
1 187.7
827.3
291.3
3 576.1
82
37
548.6
17.8
63.8
585.1
145.8
581.6
832.5
18.3
36.2
169.8
78.0
598.1
616.9
18.7
415.8
364.7
19.2
265.8
2 362.6
74.0
100.1
754.9
223.8
1 861.3
0
100
0
0
85
50
20
1
1
7
2
18
12.5
359.0
13.6
517.6
14.9
419.8
16.2
228.3
57.2
1 524.6
15
20
14
Total Recurrent Costs
2 314.2
2 264.1
1 486.0
894.2
6 958.5
23
63
Total PROJECT COSTS
3 584.1
3 451.8
2 313.3
1 185.5
10 534.7
45
100
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
31
5. INSTITUTIONAL FRAMEWORK AND PROJECT IMPLEMENTATION
A. PROJECT ORGANIZATION AND MANAGEMENT
Many countries and institutions would be involved in the implementation of
MoDAD. Sampling of the some 476 breeds may involve up to 56 countries scattered
around the globe (see Table 1 and 2). Many more countries would be involved through:
•
sharing of data generated by MoDAD; and
•
via the MoDAD animal genetic resource research and management
regional network training programmes.
The project would be co-ordinated by FAO and implemented through the
FAO AnGR Programme regional and national network of focal animal genetic research
institutions throughout the world. The organizational structure and activities of
MoDAD are illustrated diagrammatically in Figure 1.
The central aim of MoDAD is to provide a database for improving the
management of animal biodiversity both in-country and globally. Hence, all countries
must be given the opportunity to be involved in MoDAD, to review progress of the
results of the 14 species included, and to negotiate guiding protocols for access to their
own samples in the databases and DNA repositories. This would be achieved through
FAO’s Intergovernmental Commission on Genetic Resources for Food and Agriculture
(CGRFA).
An efficient and effective co-ordination of the project would be essential in
order to realize the objectives of MoDAD, i.e. the generation of a minimum-set genetic
resource database of the world’s 14 most important domestic animal species in a
minimum time and at low cost. FAO’s Centre for Domestic Animal Diversity (CDAD)
would provide the necessary global technical co-ordination for MoDAD. The project
co-ordinator would be the specialist animal production officer for genetic resources
characterization. The specific functions of the Project Co-ordinator are detailed in
Annex 7. In brief, the Project Co-ordinator would co-ordinate all protocol, procedural,
funding and global procedural aspects associated with the implementation of all of the
MoDAD activities. The Project Co-ordinator would be assisted in an advisory capacity
by the EAG on all technical matters associated with the generation of AnGR data from
breed selection to field sampling, DNA extraction, assaying, as well as data analysis,
storage and dissemination. National laboratories, national contact personnel, and the
regional laboratory personnel, would operationalize the field sampling, DNA extraction,
storage of DNA samples and data, and data analysis activities. National and regional
MoDAD co-ordinators would be appointed to co-ordinate these activities and provide
focal linkages to the Project Co-ordinator. Where already in place, these co-ordinators
would be the national and regional focal points under the FAO AnGR Programme.
The Project Co-ordinator would be responsible for the continuous
monitoring of the physical and financial progress of MoDAD and would be aided by
management information systems (MIS) software. This software would be specifically
designed within the DAD-IS system to assist in project management at the national,
32
regional and global levels. MIS software would facilitate monitoring of ongoing
activities and continuous evaluation of verifiable indicators of project performance.
Project performance indicators would include:
•
the number of breeds sampled;
•
the number of animals sampled;
•
the number of DNA samples assayed;
•
the number of base-line analyses;
•
the number of people trained in AnGR research and management;
•
the financial progress of each project component and activity.
Monitoring of all technical aspects of the project would be the responsibility
of the EAG. While this would be a continuous process during the whole
implementation period, it would be a key agenda item during the annual meetings of the
EAG.
B. PROJECT IMPLEMENTATION
The project has been designed as a first phase to be implemented over four
years. This would enable sampling of some 476 breeds across 14 species of domestic
animals (Table 1). Some 50 animals would be sampled per breed. A possible second
phase of the project could involve the sampling of additional breeds of any of the 14
species included in Phase I where the results of Phase I show large genetic variation
between breeds.
An implementation schedule of the project components and major activities
is presented in Figure 2. The project would commence with the appointment of the
Project Co-ordinator in FAO. The initial priority activities of the Project Co-ordinator
would be to finalize the field sampling logistics for the breeds to be sampled, arrange
the technical assistance for field sampling, organize the regional field sampling
workshops, coordinate implementation of the DNA repositories, and finalize
arrangements for microsatellite marker development, optimization and laboratory
assaying. Following this, in-country field sampling training could begin and field
sampling quality control mechanisms would be installed during this time. Field
sampling operations would then commence. Training and field operations would begin
in one region and subsequently operations in the other three regions would be taken up.
Likewise training on quality control (in the case of decentralized assaying), data
management and the laboratory assaying operations, would be initiated one region at a
time, most probably following the same order as the initiation of the regional field
sampling activities.
Field sampling would not terminate until during the third year and
laboratory assaying would continue until about half way through the fourth and final
year of the project.
33
Data storage and analysis would start early in the second year following the
technical assistance input in the latter part of the first year that would be required to
initiate the storage and analysis activities at the four regional laboratories. Database
management software would be developed for use at the national, regional and global
levels.
Technical assistance for the field sampling and assaying regional training
workshops would be conducted during the first year, and a technical assistance input
would be required to initiate and maintain field sampling and assaying quality control
activities during the first two years spilling over into the initial part of the third year.
Training activities would be implemented during the first three years. Field
sampling and laboratory assaying training would be completed during the first year.
The training in animal genetic resources management and research, which would be
conducted at four regional laboratories, would be initiated in the first year and
completed during the third year.
The project co-ordination activity would be required over the four year
project period. The activities of the EAG would also extend over the four years. Data
interpretation and dissemination activities would be implemented during the third and
fourth years. The national DNA repositories, the four regional laboratory repositories,
and the global repository, would all be installed in the first year.
Care would be taken to ensure DNA sample ownership rights are respected
during and after the implementation of MoDAD. This would be achieved through the
strict adherence to the procedures and protocols associated with the sampling, transport
and storage of DNA, which are elaborated in Annexes 1 to 4.
34
Figure 2: Implementation schedule for MoDAD
PROJECT COMPONENTS/ACTIVITIES
TECHNICAL ACTIVITIES
Microsatelite Marker Development
Field Sampling
DNA Extraction
Laboratory Assaying
Data Storage and Analysis
TECHNICAL ASSISTANCE AND TRAINING
Field Sampling
Regional Network Training
Quality Control
Laboratory Assaying and Analysis
PROJECT ORGANISATION AND MANAGEMENT
Project Coordination (FAO)
Expert Advisory Group
Long-term DNA Repositories
Data Interpretation and Dissemination
YEAR 1
YEAR 2
YEAR 3
YEAR 4
35
6. PROJECT JUSTIFICATION, BENEFITS AND RISKS
The economics and risks of the MoDAD project are addressed in this
section. A detailed elaboration of the benefits and methodological issues associated
with analyzing the economics of MoDAD are provided in Annex 5. Preliminary
economic analysis indicates that investment in the MoDAD project is fully justifiable
from an economic standpoint, with expected economic benefits far exceeding the costs.
A. SPECIAL CONSIDERATIONS IN ASSESSING THE ECONOMICS OF
ANIMAL GENETIC RESOURCES
There are a number of considerations specific to AnGR highlighted in
Annex 5 which complicate the economic analysis of MoDAD but which further add
justification for the project. In brief these considerations are:
•
The rate of loss of AnGR has been rising in recent times, probably
exponentially. Rates of losses are in many cases not known so that
predicting future losses is difficult.
•
AnGR can be characterized as international resources with many public
good qualities. Co-ordinated global action is called for to reduce the
increasing rates of genetic erosion and market failures associated with
their use.
•
It is difficult to quantify the potential benefits associated with improved
information about genetic variability with any certainty. Although the
potential gains are expected to be enormous based on past breeding
research and development, predicting these gains is fraught with
massive uncertainty because the potential benefits from exploiting
breed distinctiveness are of unknown magnitude.
•
Although the commercial value of domestic animals is normally very
important, other values must be recognized which may be of even
greater importance than the commercial dimension, such as cultural,
draft power and manure.
B. MoDAD AND THE GLOBAL CONSERVATION OF ANIMAL
GENETIC RESOURCES
The MoDAD project must be considered within the overall context of the
global conservation of AnGR. A three-tiered structure is suggested:
•
MoDAD: This is the project level and represents the focus for the
evaluation (see the description of objectives, activities and outputs in
Section 4).
36
•
FAO Global AnGR Programme: This is the programme level within
which MoDAD constitutes a key activity of one element,
characterization. The FAO constituted programme has a broad
objective for promoting the better management and conservation of
AnGR but would not itself undertake physical conservation (see
Section 2B).
•
Overall Global Conservation Effort: This is the level enveloping all
national and international conservation programmes and includes the
physical conservation, documentation, characterization and in situ and
ex situ activities. The major costs of conservation are most likely to be
concentrated at this level and are to be guided by efforts at the previous
two levels.
An economic evaluation of MoDAD must specifically analyze only the
benefits and costs of the MoDAD project and not confuse these with the benefits and
costs at the other two levels described above. For instance, MoDAD itself would not
undertake conservation of germplasm, but provide information on genetic diversity to
help in targeting conservation efforts, thus increasing their efficiency, by rationalizing
the total management effort. The overall benefits liable to accrue as a result of global
conservation efforts should not be attributed to MoDAD alone. Indeed, a wide range of
analyses can be undertaken relating to the economics of conserving AnGR, as cited in a
recent FAO publication concerned with the implications of the Convention on
Biological Diversity for the conservation of animal genetic resources (Strauss, 1994),
but few if any of these are relevant for an analysis of MoDAD on its own.
How would the outputs of the project contribute to global conservation
efforts? Firstly, project outputs would provide for a better understanding of the genetic
relationships among breeds and levels of inbreeding would similarly allow for better
breeding programme management but also assist with reducing the numbers of breeds
to be conserved and rationalizing breed definitions. Such knowledge would also aid in
identifying and targeting those rare and endangered breeds which are most in need of
conservation assistance. Secondly, by enabling national conservation programmes to
recognize those breeds harbouring the greatest genetic diversity, a buffer is provided
against future environmental challenges. Thirdly, the pairwise distance estimates for
individual breeds, could assist with conservation programme planning and improving
active breeding programmes by allowing estimation of "diversity functions".
Fourthly, project outputs would result in better prediction of the potential "heterosis" or
hybrid vigour arising from crosses between breed groups, increasing the probability of
immediately realizable production benefits and permitting improved management of
active breeding programmes. These would be an important component in the
development of optimal conservation programmes, where maintenance of the greatest
diversity is one of the objectives.
Limits to the usefulness of the information forthcoming from the project
should not be ignored in the desire to see MoDAD as a panacea for addressing genetic
erosion. For example, an understanding of specific gene effects within breeds would
not be obtained as an output of the project. Similarly, genetic diversity information
cannot be the sole criterion for evaluating breed value, as this must be supplemented
37
with efforts to identify specific genes and markers and their chromosomal location.
Finally, some of the proposed benefits stemming from the project are liable to be
indirect. Economically important traits cannot be analyzed as a component of genetic
diversity studies directly. Instead, genetic diversity information allows the targeting of
crosses more likely to result in heterosis, since heterosis is correlated with greater
diversity in the parents. Moreover, heterosis itself does not guarantee non-additive
improvements in productive traits (it has no impact on purely additive traits), but is a
necessary condition for these to occur.
C. ECONOMIC EVALUATION
Methodological Considerations
Several methods exist for evaluating the economics of MoDAD.
Economists have developed alternatives to the standard cost-benefit analysis (CBA)
approach, used in the evaluation of most investment projects, for situations where there
is uncertainty involved in making decisions about the preservation or loss of animal or
other genetic resources. Such techniques recognize that full knowledge about the
potential benefits from adopting the project is not possible, nor are their probabilities of
occurrence. Although such information might be forthcoming as time passes, it is not
available now, and yet important decisions about the preservation or extinction of wild
and domesticated AnGR must be made in the interim. Alternative methods that could
be used to evaluate the economics of MoDAD include: The Precautionary Principle;
Safe Minimum Standards (SMS); Cost-Benefit Analysis (CBA); and Multiple Criteria
Analysis (MCA). In Annex 5 a mixture of SMS and CBA techniques are used to
evaluate MoDAD.
The economic analysis compares the situation with the proposed project
(the "with project" situation) to two possible "without project" scenarios:
•
Business as Usual Scenario - Conservation activities continue more-orless as at present, with a steadily increasing rate of breed loss, despite
the existence of national and international (FAO AnGR Programme)
conservation programmes. Research on adaptive traits and genetic
diversity continues in an unco-ordinated way, with gains being made
but some opportunities lost. Some – albeit
small -- risk of catastrophic losses at a national, regional or global level
continue because valuable genes or alleles are lost inadvertently.
•
Conservation of Threatened Breeds Scenario - This alternative assumes
that a massive conservation effort is undertaken to conserve most
threatened livestock breeds to ensure that virtually all significant
genetic diversity is preserved. This extreme case is intended to present
an alternative to MoDAD where the global conservation objectives are
similar, however the costs are liable to differ.
38
Business as Usual Scenario
Three important benefits can be analyzed in comparing the situation with
the project, to one where current and planned conservation programmes proceed
without the genetic diversity information expected to emerge from the project. Firstly,
the project would constitute a form of insurance against unforeseeable, and perhaps
catastrophic, production losses which might arise in the future as a result of disease or
genetic vulnerability. Similarly, by providing useful information about the
relationships among breeds MoDAD could result in production benefits, as breeders
are better able to respond to changing livestock management conditions or shifts in
consumer demand and tap previously unknown sources of desirable traits. Secondly,
the project should lead to more conventional production benefits relating to known
traits of economic importance by increasing the efficiency of active breeding
programmes. Experience from prior breeding programme successes allow
quantification of the typical gains to be realized but the increased probability of these
gains being achieved, as a result of the project, cannot be estimated. Thirdly, a
reduction in costs for active breeding programmes and genetic research activities is
liable to occur with the project, once breed information becomes more centrally coordinated and duplication and other inefficiencies can be avoided. Little quantification
of such a benefit is possible, although some representative savings can be cited.
MoDAD as an Insurance Premium
Since the likelihood or magnitude of losses associated with either a
potential catastrophic event involving national or global livestock production or a
missed opportunity to exploit some hitherto unknown economic trait is not known,
alternatives to the standard CBA approach must be sought. The Safe Minimum
Standard (SMS) of conservation is one approach that has been used. Examples of the
SMS method are cited in Annex 5 and an application of the method is applied to
MoDAD at the global level. The present value costs of MoDAD are about US$ 10
million. Global costs for AnGR conservation are presently unknown but are estimated
to range between US$ 20 to US$ 50 million in present value terms. Assuming the
combined costs of global animal conservation programmes and MoDAD total US$ 50
million, these costs represent only 0.01% of the very conservative estimate of the
annual global value of livestock products of US$ 500 billion per year (Annex 5).
Moreover, if MoDAD alone resulted in the avoidance of a single catastrophic event,
this event would only need to entail losses of US$ 1.2 million per year for 20 years for
the project to pay for itself, assuming an opportunity cost of capital of 12%. This
averted loss is equivalent to 0.0002 % of the estimated annual value of domestic animal
production. It is concluded in Annex 5 from the application of the SMS method to
MoDAD and other national examples, that the costs of preserving a safe minimum level
of genetic diversity are not high relative to the production values being safeguarded.
Conventional Production Benefits
MoDAD would produce information about breed diversity which would
assist breeding programmes with identifying suitable matches for cross-breeding,
thereby increasing the prospects for heterosis. While the magnitude of potential
benefits, across the full range of globally important species and production traits, would
be impossible to quantify precisely, based on crossbreeding work of Bos taurus and Bos
39
indicus species of cattle for milk production, it is concluded in Annex 5 that production
benefits from crossbreeding programmes are high.
Potential benefits from
crossbreeding programmes in the dairy industry have been crudely estimated to be as
high as US$ 500 million annually. Comparing such benefits to the meagre project costs
for MoDAD (approximately $US 10 million), suggest that the project need make only a
small contribution to current active breeding programmes to generate benefits which
would offset its costs.
Efficiency Benefits and Reduced Costs in Animal Breeding Research
Benefits may not just accrue from newly realized production gains, as
described in the previous section, but from reduced costs for achieving the production
benefits of on-going breeding programmes. By improving the dissemination of breed
characterization information and by reducing duplication and the other inefficiencies
associated with highly decentralized, uncoordinated crossbreeding research
programmes, the project would reduce the costs of achieving a given improvement in a
production trait. Thus, production improvements liable to be achieved regardless of the
project would be obtained at lower cost. This benefit is therefore distinct from and
additive with the benefits described above.
Conservation of Threatened Breeds Scenario
There is a consensus among researchers concerned about global AnGR that
good management of these resources is not possible under present conditions for cost
and logistic reasons. With a global total of some 4,000 breeds or so, global and national
conservation efforts simply cannot cope. As a result, there is a need to reduce the total,
from the perspective of maintaining adequate genetic variation, to perhaps as low as
800 to 1,000 breeds. The project would simplify and reduce the costs of global and
national domestic animal genetic resource conservation by providing information
which would help identify the most genetically diverse breeds. Recognizing this
situation, this "without project" scenario assumes that the necessary efforts to conserve
all important livestock genetic resources proceeds without the information about genetic
variation stemming from the project.1/
The primary benefit of MoDAD would be a reduced cost for breed
conservation, since important genetic diversity could be maintained with a much
smaller number of breeds. However, at this stage how much smaller this number of
breeds would be is not known and therefore a sensitivity analysis of a range of
possibilities would be appropriate. A notional benefit could be approximated by
comparing the costs of global conservation for a number of combinations of breeds
conserved under the two alternatives. The cost savings accruing to the project would
depend upon how many fewer breeds need be conserved.
In Annex 5 the average present value of conservation costs per breed,
weighted for developed and developing countries, is calculated at US$ 100,000. From
solely the point of view of conserving a minimum amount of AnGR at least cost, it is
1/
While this scenario is considered here as an alternative "without project" scenario, it could have been
considered as an alternative to the project, both options being measured against the first "without project"
scenario.
40
shown that MoDAD is likely to generate substantial benefits net of project costs ranging
from US$ 6 million to US$ 71 million in present value terms, depending on the
reduction in the number of breeds that would need to be conserved.1/ At minimum, if
MoDAD can bring about a reduction of at least 90 breeds in the number targeted for
conservation efforts the project would pay for itself - this assumes that no other benefits
would be generated by MoDAD.
MoDAD would provide objective criteria to guide global conservation
efforts. In the absence of an objective database on AnGR diversity, there is no
guarantee that conservation programmes worldwide would actually target the right
breeds, and once lost there is no opportunity to recapture the unique genetic variation.
Although difficult to quantify, enormously large potential benefits would be generated
from MoDAD besides reduced costs of conservation, which would be captured in
increased future domestic animal productivity, as a result of better targeting the AnGR
to be conserved.
Economic Evaluation of MoDAD and GEF Criteria
The economic evaluation methodology adopted in this report is consistent
with standard investment project assessment techniques, but would require some
modification for GEF funding consideration. These matters are addressed in Annex 5.
Clearly, few countries would be inclined to undertake the genetic diversity studies
comprising MoDAD on their own, both for cost, public good and scale reasons. Even if
they do, these are liable to be inefficient and unco-ordinated from a global perspective,
and to result in pressure on international agencies to provide conservation assistance in
an ad hoc manner. Moreover, possible extra-national or global benefits from a coordinated effort would be lost if each nation were to go it alone. Instead, such an effort
is best situated at the global level, which internalizes all livestock breeds and achieves
substantial "economies of scale" (for example, there is no need to duplicate breed
analyses simply because they occur simultaneously in different countries).
Distributional and Incentives Issues
There are several issues surrounding the intellectual property rights
associated with the information compiled by MoDAD and important political
considerations respecting ownership and access to this information. These issues are
critically important and have been considered in the formulation of MoDAD (refer to
Annexes 1-4 for details relating to protocols and procedures concerning ownership of
DNA samples and data).
Several issues concerning the distribution of benefits and costs of the
project have been addressed in Annex 5. Of these the main issues are:
•
1/
An uneven distribution of benefits. Countries with more distinct livestock
breeds stand to benefit more than countries with fewer since the former
could target a much smaller number of breeds to be conserved than would
In the sensitivity analysis the reduction in the number of breeds conserved globally ranged from
150 to 800.
41
otherwise be the case. Also countries having greater genetic
diversity in their livestock breeds would benefit proportionately more from
the project from their domestic breeding applications and would be able to
market their breeds internationally with more certainty of their desirable
genetic properties.
•
Those countries having a greater number of breeds would incur higher
collection and storage costs, and would benefit more if these costs are
financed by the project.
•
Participants in the project would not just benefit in terms of their immediate
domestic breed improvement programmes but would have access to the
global database (DAD-IS) to supplement those benefits (the so-called
"global public good" benefits). Many countries, particularly in the
developing world, could also benefit from the transfer of technology and
from MoDAD training activities.
.
Countries would have different incentives for participating in the project and
these are likely to be critical determinants in the success of the project.
•
•
The inclusion or exclusion of geographically specialized species, such as the
llamoids and yaks, may be an important determinant of the distribution of
the project’s benefits on a regional or even national basis and have a bearing
on the incentive to participate in the project for some countries.
D. PROJECT RISKS
In a balanced economic evaluation it is also necessary to consider the risks
associated with the project itself. There are a number of risks associated with the
complex technological and global characteristics of MoDAD. While these are likely to
be substantially less than the uncertainty relating to not managing and preserving animal
genetic resources appropriately, they should not be ignored. There is a range of
technical activities with significant risk attached which have been taken account in
designing the project (see Annexes 1 to 3 and 7).
The risks associated with the project are outlined below. It has been
recognised during the design of MoDAD that many of these risks would be mitigated
through safeguards incorporated in the protocol, procedural and communication
guidelines and in effective co-ordination.
•
The use of national repositories alone for storage of DNA for use in further
training, research and development, is considered too high a risk. For this
reason storage at global repositories has been included in the project.
•
The use of a number of laboratories in the execution of MoDAD generates a
high risk level through more complex logistics and varying procedures and
techniques. For this reason project design recognizes one key research
laboratory in each country for the execution of field sampling, DNA
42
extraction/storage, data analysis. The base-line assaying would
be streamlined through the inclusion of leading internationally recognized
regional laboratories, and possibly a single commercial laboratory.
•
The use of microsatellite markers as a means of characterizing breeds is still
a reasonably new technology and variation with the technique (for instance,
detection and classifying marker alleles), may complicate the project.
•
The effort required to organize, consolidate, store and disseminate the
results of the project’s analyzes is immense. There is some risk that such a
global organizational effort might founder, for reasons of scale or if
participating countries are not able to agree on protocols governing key
procedures.
•
Because individual countries face mixed incentives for participating in the
project it may be difficult to overcome some of the negative incentives,
regardless of the organizational prowess of the project staff.
43
7. ISSUES AND FOLLOW-UP
Issues
The breeds to be sampled, and the countries in which the field sampling
would be undertaken is a follow-up issue which would need to be addressed by various
world renowned species experts (to be nominated by FAO). The issue should be
addressed as expediently as possible because: (i) the decisions taken on the number of
breeds to be sampled, and where they are to be sampled, will influence the project costs;
and (ii) so the making of these decisions do not delay project start-up.
In this report two options are put forward for the most expensive project
component - assaying the DNA samples. The two options are: (i) using at least 4
species specific regional research laboratories, and (ii) using a single private sector
commercial laboratory, and the regional laboratories serve as quality control. The costs
of both options are expected to be about the same. However, a number of other
important aspects must be considered including ease of co-ordinating the assaying
operations, speed and quality of the service, capacity building and political acceptability
(see Section 4C and Annex 3). The choice of the most appropriate option to use will
require further investigation of the technical, cost-effectiveness, management and
political implications. Furthermore, it is quite likely that the project financing
institution may wish to have an influence on the choice of option.
There are legal and technical issues surrounding ownership and
international movement of the biological material encompassed by MoDAD. Precise
legal definitions would have to be developed concerning: (i) the country of origin and
ownership; (ii) forbidding of sample duplication without authorization; and (iii)
performing supplementary assays only with permission from FAO and the country of
origin. These issues should be addressed as soon as possible so that they do not delay
project implementation. Although animal health and the potential for transmission of
pathogens were the primary considerations in the choice of protocol for DNA
extraction, eliminating the possibility of pathogen transmission via the DNA samples,
quarantine regulations which could possibly restrict movement of DNA internationally
remain to be thoroughly investigated and a standard protocol for transfer of DNA
prepared.
A further outstanding issue relates to the economic analysis. In this report
only a preliminary economic evaluation could be carried out under the time and
resource constraints operative during project formulation. Issues pertaining to a more
detailed economic analysis of MoDAD are elaborated in Annex 5. Certainly
consideration for GEF financing would necessitate modification of the economic
analysis contained in this report and this issue is also addressed in Annex 5.
44
Follow-up
To advance the further development of MoDAD the Animal Genetic
Resources Group of the Animal Production and Health Division of FAO should:
(i)
actively seek funds for the project from GEF, FAO trust funds and bilateral
aid donors. Priority should be given to approaching GEF for funding;
(ii)
organize a group of international animal species experts who will via the
Internet specify the breeds of each of the 14 species to be sampled, and the spatial (by
countries) distribution of the sample.
8. REFERENCES
Barker, J.S.F., Bradley, D.E., Fries, R., Hill, W.G., Nei,M. and Wayne, R.K. 1993 An
integrated global programme to establish the genetic relationships among the breeds of
each domestic animal species. FAO Animal Production and Health Paper. Rome
FAO. 1992. The management of global animal genetic resources. FAO Animal
Production and Health Paper No 104
FAO/UNEP. 1995. World Watch List for Domestic Animal Diversity, Second Edition.
(Eds.: Scherf, B.), FAO, Rome
FAO, 1995. Global Project for Research on Animal Genetic Resources, Identification
Report, March.
Hammond, K. and Leitch, H. W. 1995. The FAO Global Program for Management of
Farm Animal Genetic Resources. J. Animal Science. in press
Strauss, M. S. 1994. Implications of Conservation on Biological Diversity.
Management of Animal Genetic Resources and the Conservation of Domestic Animal
Diversity. FAO, Rome
1
APPENDIX 1
WORKING GROUP PARTICIPANTS
Prof. Alessandro Nardone, CHAIRMAN OF WORKING GROUP
President European Association of Animal Production
Istituto di Zootecnia, Universita Tuscia
Via de Lellis, 01100 Viterbo
Tel.: 0761 357442
Fax.: 357 434
e-mail: [email protected]
Dr Alessio Valentini
Istituto di Zootecnia, Universita Tuscia
Via de Lellis, 01100 Viterbo
Tel.: 0761 357442
Fax.: 357 434
e-mail: [email protected]
Dr Dan Bradley
Genetics Department
Trinity College
Dublin 2 - Ireland
Tel.: 353 1 6081088
Fax.: 353 1 6798558
e-mail: [email protected]
Dr Kenneth K. Kidd
Department of Genetics SHM 1-351
Yale University School of Medicine
333 Cedar Street
New Haven, CT 06520 8005
USA
Dr Edward Rege
International Livestock Research Institute (ILRI)
Animal Production and Management Section
P.O. Box 5689
Addis Ababa - Ethiopia
Tel.:
Fax.:
e-mail: [email protected]
Mr Duncan J. Knowler
Department of Environmental Economics and Environmental Management
University of York
Heslington, York
United Kingdom - Y01 5DD
e-mail: [email protected]
2
Dr David Mac Hugh
Genetics Department
Trinity College
Dublin 2 - Ireland
Tel.: 353 1 6081088
Fax.: 353 1 6798558
e-mail: [email protected]
FAO Staff:
Dr Keith Hammond
Mr David Steane
Ms Martha Kassa
Mr Bill Sorrenson
Dr Helen Leitch
1
APPENDIX 2
REFERENCE GROUP PARTICIPANTS
Professor J.S.F. Barker
Department of Animal Science
University of New England
Armidale NSW 2351
Australia
Tel.: 61 67 73 3924
fax.: 61 67 73 3275
e-mail: [email protected]
Dr. John Gibson
Department of Animal and Poultry Science
University of Guelph
Guelph, Ontario
Canada N1G 2W1
Tel: 519 824 4120
e-mail: [email protected]
Prof. Illia A. Zakharov
Professor, D. Sci. Deputy Director
Head of the Animal Genetics Laboratory
Vavilov Institute of General Genetics
Russian Academy of Sciences
Gubkin St. 3, 117809 Moscow B-333 Russia
Tel.: 7 095 1351289
Fax.: 7 095 1351289
e-mail: [email protected]
Dr Alan Teale
International Livestock Research Institute
P.O. Box 30709, Nairobi, Kenya
Tel.: 254 2 630 743
Fax.: 254 2 631499
e-mail: [email protected]
Dr Louis Ollivier
SGQA 78352 Jouy en Josas - France
Tel.: 33 1 34652190
Fax.: 33 1 34652210
e-mail: [email protected]
2
Dr Allan M. Crawford
Agricultural Research Molecular Biology Unit
Department of Biochemistry
University of Otago
P.O. Box 56 - Dunedin
New Zealand
Tel.: 643 479 7663
Fax.: 643 477 5413
[email protected]
Dr Barbara Harlizius
Department of Animal Breeding and Genetics
Hannover School of Veterinary Medicine, Germany
e-mail: [email protected]
Dr Joel Ira Weller
Institute of Animal Sciences
A.R.O. The Volcani Center
P.O. Box 6
Bet Dagan 50250
Israel
Tel.: 972 8 475075
Fax.: 972 8 475075
e-mail: [email protected]
Dr Frank Nicholas
Department of Animal Science
University of Sydney
NSW 2006 - Australia
Tel.: 61 2 351 2184
Fax.: 61 2 351 2114
e-mail: [email protected]
Dr James Derr
Assistant Professor of Veterinary Pathobiology and Genetics
The Texas Veterinary Medical School
Department of Veterinary Pathobiology
College Station, Texas 77843 4467
Tel.: 409 862 4775
Fax.: 409 845 9972
e-mail: [email protected]
3
Prof. L.L. Cavalli-Sforza
Genetics Department, MS5120
Stanford University
94306 Stanford CA - USA
Tel.: 1 - 415 723 5804
Fax.: 1 415 498 5315
e-mail: [email protected]
Dr John Williams
Roslin Institute
Fax.: 0131 440 0434
Tel.: 0131 440 2726
e-mail: [email protected]
Dr Mike Bruford
Institute of Zoology
Regents Park,
London, NW1 4RY, UK.
e-mail: [email protected]
Prof. Asko Maki-Tanila
Dept. of Animal Breeding
Agricultural Research Centre
SF-31600 Jokioinen, Finland
e-mail: [email protected]
Dr Arthur Mariante da Silva
EMBRAPA/CENARGEN
Caixa Postal 02372
70849-970 Brasilia-DF Brazil
e-mail: [email protected]
Dr Mark Shriver
Dept. of Human Genetics
130 DeSoto St.
A300 Crabtree Hall
Pittsburgh, Pennsylvania 15261 USA
e-mail: [email protected]
Dr Bruce Walsh
e-mail: [email protected]
Prof. Robert Wayne
e-mail: [email protected]
1
ANNEX 1
BREED SELECTION AND SAMPLING
A. BREED SELECTION WITHIN EACH SPECIES
1.
The sampling of breeds within a species should be designed to select those
breeds which are likely to be most distinct genetically. Information from the
archaeological record, historical sources and local experts on the origins and
migratory history of domesticated populations can be particularly useful in this
regard. Previous genetic characterisation using classical genetic polymorphisms such
as blood group or allozyme polymorphisms can also assist in determining which
breeds or populations to sample. Another important consideration is spatial
geographic distance between populations. This is commonly a reasonable indicator of
genetic distinctness.
2.
As a component of FAO’s Global AnGR Programme, Project Identification
Missions are being undertaken. These missions are collecting breed information
which, together with the information in the FAO Global Databank, could contribute
to the preparation of up-to-date breed lists. The purpose of Phase 1 of this project is
to evaluate the complete range of diversity within each species. This working group
considers the selection of breeds for the initial estimation of levels of genetic
variation to be a critical activity for the success of this project. Failure to do this
carefully may lead to uninformed decisions in the future and a consequent loss of
genetic diversity. It is therefore recommended that breed selection should be carried
out by a small group of experts with extensive knowledge of the evolutionary and
recent history of the species. Historical events which will have had an influence on
the genetic structure of particular populations should also be considered. These events
could include phenomenon such as population bottlenecks due to famine or
epizootics and gene flow and consequent admixture between populations. This expert
consultation would be carried out via the Internet at minimal cost as a formal meeting
would not be required.
3.
For Phase 1, the report by Barker et al. (1993) proposed that 50 breeds be
sampled for species with 200 or more breeds and at least 25% of all breeds should be
sampled for each of the remaining species for Phase 1. The present Working Group
gave more consideration to this matter and recommended the following protocol:
>200 breeds then sample 50 breeds
80 to 200 breeds then sample 25%
20 to 80 breeds then sample 20 breeds
<20 breeds then sample all
4.
For species which consist of more than 20 breeds, an attempt should be
made to cover the entire range of extant diversity. In order to achieve this goal,
the following criteria should be considered in breed selection (see below):
2
1. The current knowledge of the evolutionary history of the species.
2. Historical and recent patterns of migration, including known hybridisation events.
3. Whether particular breeds are endangered or under threat of extinction.
4. The uniqueness of the environment where the breed originates. All regions and
countries within the natural range of a breed should be considered
5. Current economic importance.
6. Uniqueness of phenotypic characteristics /qualities.
5.
In the absence of up-to-date lists of breeds by country, it was not
possible for the Working Group to make recommendations on breeds to be
sampled. However, on the basis of the total number of breeds within each
species, breed distribution across regions, number of breeds for which
information is available within each region and the need to include breeds from
all regions, the WG estimated the number of breeds to be sampled by species
and geographical regions. It was considered that species experts (see above)
should finalise this table by specifying breeds and countries from which
samples will be collected.
Table 1.1: Number of breeds to be sampled by species and region
Species
Africa
Asia/
Europe/
Latin
North
Pacific
for. USSR
America
America
Near East
TOTAL
Cattle
15
15
10
3
2
5
50
Sheep
15
15
10
2
3
5
50
Goat
10
15
15
3
2
5
50
Pig
3
30
10
3
4
0
50
Buffalo
2
15
2
1
0
0
20
Horse
3
15
20
3
4
5
50
Ass/Donkey
5
5
5
1
2
2
20
Chicken
10
10
10
5
5
10
50
Camel
4
5
--
--
--
11
20
Llamoids
--
--
--
12
--
--
6
Turkey
4
3
9
2
1
1
20
Duck
3
6
8
2
--
1
20
Dom. Goose
2
3
12
2
1
--
20
Rabbit
10
5
10
10
5
10
50
* Banteng, Yak, Mithan, Gaur and Bison will be assayed with cattle also
3
B. COLLECTION OF BREED DATA
6.
Descriptive data for each breed sampled should be collected according to
the existing FAO breed survey questionnaire. This should also include a description
of the production environment and unique indigenous knowledge of the breed.
7.
Photographs should be taken on slide film of typical male and female adult
ani-mals in each region where the breed is sampled. The choice of slide film should
ensure flexibility, in terms of use, reproduction and cost efficiency. A side view of
the animal should be taken with a lens setting of 38mm and at a distance of about 3
metres. The photograph should be taken by the technician in charge of sampling.
Obviously these recommendations would have to be modified when dealing with
smaller animals such as poultry. These breed example photographs should be
duplicated and three copies should be distributed as follows:
- country where breed is sampled
- regional laboratory handling the species
- FAO headquarters - added to DAD-IS Breed Image Database
8.
In addition, an attempt should be made to obtain a photograph of each
animal sampled. These photographs do not have to be of the same quality of the breed
photographs outlined above. In order to eliminate mix-ups and confusion when taking
photographs it is recommended that a programmable camera be used which can place
a date/time stamp plus the sample code on each negative.
C. SELECTION OF ANIMALS WITHIN BREEDS
9.
The following guidelines should be adhered to when selecting animals to
be sampled within a breed:
Criteria for selection of animals within each breed
1. A total of 50 animals (25 of each sex), should be sampled for each breed.
Males may be castrates.
2. These animals should encompass the breed variation whilst taking care to minimise the likelihood of including non-purebred animals.
3. Sampling can be of young stock but must be random within the relationship constraints outlined.
4. The 50 animals should be as unrelated as possible (at least as far as grandparent) where such
information is available.
5. Each sample should be from an animal with a different dam and a diferent sire, and atleast 25
sires and dams hould be represented in the sample of 50. Where pedigree information is not
avaialbe then sampling must be arranged to ensure these numbers are met.
6. In cases where the breed is represented in less than 25 hers, sampling should be stratified by herd
size relative to breed population size with the proviso that representation should include as many
sires as available.
4
7. Where AI or male stud centres are normally used it is essential to establish the policy on usage
over a previous period covering twice the age of sexual maturity of that breed.
8. Males used in AI should not be represented more than other sires within the normal protocol
constraints.
9. Where a single breed is located in more than one country, the sample will be taken from one
country only. The choice of country will be determined by the location of the original breed range,
but will also be influenced by logistics and the cost/ease of sampling. The working group considered possible sampling of such a breed from multiple countries but discounted it from the
standpoint of ownership of samples. The strategy also provide for a superior desing of the second
phase of MoDAD.
10. Only individuals representative of the breed in question should be included. Animals known to
be the result of deliberate, recent cross-breeding should be avoided.
11. Animals displaying obvious symptoms of disease or infection should not be sampled.
D. ESTABLISHING THE STRATEGY FOR COUNTRY/SPECIES
SAMPLING
10.
The heterogenous and dispersed nature of animal production systems
means that the species and breeds to be sampled are distributed across regions (Table
1) and countries within regions. There are two possible options for sampling, these
are: a) sampling by species and organising field missions separately for each species;
or b) sampling by country or region and where possible, sampling the breeds for all
species within a particular region or country. The first option was discounted because
of a projected loss of sampling efficiency, thus leading to increased costs, mainly for
travel and labour. This WG therefore recommended multiple species sampling.
11.
When multiple species sampling is carried out, the choice of breeds
should be not be unduly influenced by the proximity of species/breeds and other
considerations of convenience. This emphasizes the need for independent experts to
also be involved in the choice of breeds within each species and for strict adherence
to the chosen breeds. Additionally, choice of herds/flocks and individual animals to
be sampled should not be made simply on the basis of convenience of multiple
species sampling.
E. COSTING OF FIELD SAMPLING
12.
Costs of field sampling were calculated under the assumption that
qualified technicians will carry out the work. Four options are considered. In the first
3 options, training of technicians on sampling techniques is required on sampling
techniques. In all the options the WG recommended that choice of personnel be made
bearing in mind the need to involve women. Candidates should be selected based on
qualifications and ability without discrimination on gender. Several options for field
sampling were considered - Option A being the one preferred.
5
Option A - Country Focal Point
(a) Identify countries for each species where sampling will be carried out for the
chosen breeds.
(b) Identify a coordinator for each country.
(c) Organise a training course/workshop for those who will be involved in
sampling. One course/workshop for all concerned countries in each region.
(d) Commence sampling using either a single team travelling around the
country or multiple teams assigned to cover zones within country or breeds. It is
assumed that these alternatives will not affect the cost of the project: multiple
teams will cost more per day but will complete the task sooner than a single
team.
(e) Field sampling missions will be coordinated from FAO headquarters.
Training
13.
Training will be required to cover the following:
* Identification of species and breeds
* Collection of phenotypic data on breeds and information on
production systems
* Sampling
* Sample handling and preliminary processing
14.
Training will enhance the quality of samples and data collected and will
also ensure application of uniform standards across all project sites. The working
Group considered the possibility of organising a single course for each region with
all technicians/potential collaborators in attendance. Realising that these courses need
to involve practical demonstrations, the WG recommended that the regional courses
be limited to training of trainers. Each country will nominate one person - possibly
the national contact/coordinator - for the regional course. This person should then
organise a small in-country course for the four or so technicians/collaborators.
15.
It is recommended that the FAO global coordinator be in attendance at
these re-gional training courses to introduce the global programme and to make an
input into the course. This should also provide the coordinator with an opportunity to
get acquainted with those involved in the programme.
Option B - Regional Coordination with Country Focal Point
(a) Identify for each species countries from which sampling will be done to
cover the chosen breeds.
(b) Identify a coordinator for each region.
6
(c) Identify in each country the number of persons to be involved in
sampling. The number chosen will depend on number of breeds to be
sampled within the country.
(d) Contract training course/workshop for entire region.
(e) Sampling coordination to be done at regional level in close coordination
with FAO headquarters.
Option C - Regional Focal Point (Coordination and Sampling)
16.
This option would involve setting up of a team of ten or so persons
assigned to sample all breeds in each region. This approach would require
travelling from country to country within regions. It is considered that local
scientists/technicians would still be required to facilitate the work of the team as it
travels within a country. The ten individuals will travel to different countries in
teams of two or three. These persons would have to be trained. The advantage of
this option would be that samples from a number of countries would have uniform
quality and checking of possible errors would be easier as only a small number of
people will have been involved in sampling. The uniformity of samples may,
however, also represent a disadvantage, eg. same error multiplied on all samples.
This option was discounted by the WG mainly on account of the following disadvantages:
*
The honoraria for members of the regional team at international rates
would represent a substantial cost.
*
Would deny the locals opportunity to be directly involved and for
’ownership’ of the project
*
Would involve more international travel
*
Regional team will not be familiar with the local system and may have
problems with gaining the confidence of the farmers and herders.
*
This option will require more sampling time
Option D - Contract Work
a) Identify individuals (consultants) who have relevant experience in field sample collection.
b) Contract these individuals to travel to the countries from which breeds are to be
sampled and to take desired samples. Teams could be assigned specific regions;
this should not affect overall cost but will affect length of sampling period.
c) Minimal sampling coordination to be done at FAO headquarters.
17.
The obvious advantage of using consultants is the fact that the consultant can be
7
held accountable for the sampling process. Additionally, this option minimises costs of
training and of coordination: only minimum briefing would be required; the
consultants would be expected to draw up a work plan to be approved before they start
the work.
F. COLLECTION OF BIOLOGICAL MATERIAL
18. A sample of approximately 50 animals should be taken from each breed. An
absolute minimum of 25 individuals should be sampled and analyzed. There is a
body of data, from human genetic diversity studies, which suggest that parameter
estimates using 50 individuals (which is equivalent to 100 alleles) are repeatable in
subsequent population samples.
19. Criteria in selection of animals for sampling is described in paragraph 9.
below. Samples should contain both sexes, in as close to equal numbers as
constraints such as herd structure permit. Non-breeding individuals such as young
or castrated males may be included. This is to provide for advanced level assaying
involving gender-specific investigations such as that of Y chromosome diversity.
20. Alternative tissues which have been considered for sampling include: peripheral blood, small skin or ear biopsies, plucked hair samples, bone, feathers, buccal
smears and dried faecal material. The extent of the proposed analysis and the
desirability of long term storage as a resource require that substantial yields of high
quality DNA is obtained. This is possible only with peripheral blood and tissue
biopsies. Blood is most common and convenient source of DNA.
21. From mammals two samples of 10ml should be obtained from each animal.
Smaller samples will suffice for avian species where nucleated red blood cells
ensure a much higher yield per ml of blood.
22. If DNA extraction or storage by freezing of the sample is possible within 36
hours, then the samples should be collected with the addition of an anticoagulant
such as lithium heparin and transported at ambient temperatures. Alternatively,
when a longer delay is envisaged, samples may be preserved by addition of a preservative such as an equal volume of 2 X standard saline citrate which effectively
prevents enzymatic degradation for a period of up to 3 months.
23. Risks inherent in this scheme are: the loss of samples through DNA degradation, mis-labelling of samples, bad laboratory practice and the transmission of
pathogens. Extensive degradation of DNA in blood takes place after approximately
10 days storage at room temperature. This is a longer potential storage time
compared with other tissues and this risk is lessened with the addition of a
preservative as outlined above. Also, even degraded DNA samples of inferior
quality may still be obtained and these will normally suffice for the PCR-based
base-line assays envisaged here.
8
24.
Quality assurance in sampling can be ensured due to the nature of the subsequent analysis. If technicians sample multiple times from the same individual, or from
closely related individuals such as siblings, or even from animals which are from
another, diverse breed, this will become clear based on sample assay, as the
probability of 2 identical samples for 30 microsatellite markers is infinitesimally
small. Sampling technicians will be notified of the ability to monitor adherence to
sampling protocols at the outset.
G. COLLECTION OF FIELD DATA FOR BREEDS SAMPLED
25.
The following are data which may be conveniently collected by the field operatives and which will be either essential or useful in interpretation of the study results.
Basic breed data to be collected during field sampling
- basic pedigree information
- any interesting morphological features
- date sampled
- type of sample
- sex of animal
- precise location of herd, including any recent nomadic history
- size of herd
- name of collector
- sample (and duplicate) number
Additional information (if available)
- local or indigenous knowledge on breed origins
- farming practices
- basic production information
- special features (disease resistance, adaptation to unusual environments etc.)
26.
Photographs of each animal sampled should also be obtained.
H. MONITORING AND ADVISING
27.
Projects executed by FAO have monitoring systems built in as a matter of
course. These include semi-annual reports by, in this case the Global Chief Technical
Advisor to the technical and operational arms in headquarters which are forwarded to
the project donor. Normally there is an evaluation mission by an independent
consultant and in a long-term project of this nature reports at 18 month intervals are
recommended. The technical advisory group established to oversee the project, would
receive reports from the Global Chief Technical Advisor, approve sampling
protocols/breed identification and timetabling of all key project activities. Results of
DNA analysis will be submitted in draft form for technical refereeing by the advisory
group.
28.
The advisory group should be available on a continuous basis during the
life of the project. The advisory group should meet together at a minimum of once a
year.
1
ANNEX 2
DNA EXTRACTION, PURIFICATION, SHIPMENT AND STORAGE
A. DNA EXTRACTION
1.
A number of different options exist for the extraction of DNA from
peripheral blood samples, however most protocols involve the following two
procedures:
(a)
(b)
Concentration of cells containing DNA (most protocols) and
disruption (lysis) of these cells.
Separation of DNA from other cellular constituents, particularly
protein.
2.
The first step may be achieved by buffy coat isolation after whole blood
centrifugation or by differential lysis of red blood cells and subsequent centrifugation.
Nucleated cell lysis is conducted by boiling or chemical disruption. Differential red
blood cell lysis is a clean and efficient technique which uses inexpensive and nonhazardous chemicals.
3.
The second step is conducted through several diverse methods. The
traditional isolation technique involves proteinase digestion, phenol/chloroform
extraction and ethanol precipitation. A variation uses salt precipitation of protein as a
substitute for the use of organic solvents. Furthermore, there are both commercial
methods which use resins or silicates which isolate DNA by preferentially binding
either the nucleic acids or the other blood components.
4.
Commercial kits are rapid and easy to use but, with often produce a
product of low yield and low molecular weight which may be unsuitable for extensive
and varied use. They are also more expensive than the other techniques and their use
is not recommended. Similarly, automated methods now available are not cost
efficient. Salt precipitation is the least expensive, produces good yields of high quality
DNA, and is a convenient method to use. Phenol/chloroform extraction is similar but
involves hazardous chemicals the use of which involves additional safety precautions,
expense, time and waste disposal considerations. However, this is recommended as an
integral part of the isolation process in part because DNA quality and yield is very
good and failure rates are low. Crucially, however, the primary advantage is that
disease-causing pathogens which may be present in the blood samples are most
efficiently eradicated by the harsh chemical treatments in this technique. The steps
involved in this technique are outlined below:
Laboratory protocol for DNA isolation
1) Lysis of red blood cells using an aqueous buffer containing NH4Cl, KHCO3, EDTA:
2) Isolation of white blood cells by centrifugation, followed by lysis and proteinase digestion in a
solution containing Trizma base, EDTA, SDS and proteinase K.
3) Phenol extraction with tris buffer saturated phenol followed by chloroform extraction.
4) DNA isolation by addition of 95% ethanol and manual spooling out of visible, wispy precipitate.
2
5.
Bad laboratory practice can be minimised by ensuring that each extraction
team has at least one experienced molecular biologist present to coordinate the
laboratory phase of the field mission. The serious issue of pathogen transmission is
addressed by using a harsh method of DNA isolation. Cell disruption, protein
degradation, phenol/chloroform extraction and ethanol precipitation are all processes
included which will eliminate potential pathogens. The chance of contaminated DNA
samples leaving a competent laboratory are extremely small and any risk of pathogen
transmission is more likely to be associated with the field sampling and laboratory
personnel themselves. Normal disinfection procedures for these individuals will be
observed. Special care with packaging and transport will be required for any preextracted blood samples that may need to be transferred across national borders within
a region.
B. MATERIALS TRANSFER AGREEMENTS
6.
Since ownership of the biological material will always remain with the country
of origin, clear signed agreements must exist when these materials are transferred from
the country of origin to the FAO global storage laboratory and thence to the regional
laboratories in other countries for assaying and/or storage; and also to the commercial
laboratory if this option is adopted for assay of samples. The documents will specify
the limitations placed on use of the samples by the country owning them and
agreement by the recipient individual and institution to abide by those restrictions.
Precise legal language needs to be developed for the document(s) but it will have to
cover the following points.
(a)
The name and title of the responsible party in the country of origin
and how that party (or designate or successor) can be contacted in the
future. This individual should sign the original agreement when samples
are first sent out of the country.
(b)
The name and title of the FAO post responsible for coordinating
storage and biological analyses of the samples and how that post can be
contacted. FAO should sign the original agreement as the recipient when
samples are first sent out of the country and should sign any subsequent
agreements as the sender when samples are sent from FAO and/or regional
laboratories to specific laboratories for base-line assaying or advanced
assaying.
(c)
The names and titles of the authorized signatory scientist and an
institutional official receiving the samples for assaying and/or storage and
how they (or their successors) can be contacted in the future. These
individuals should sign the agreement.
(d)
Whenever molecular analysis of the samples is involved, the agreement must state precisely what analyses will be performed and the obligations of the scientist/institution performing the analyses:
3
i) The analyses stipulated will be performed in a timely fashion.
ii) No other biological/molecular analyses will be performed
without prior written permission having been obtained by FAO from
the country of origin, usually involving another written document
similar to the present one.
iii) The data collected will be transferred to the FAO MoDAD
Global database in a timely fashion.
iv) Though statistical analyses of the data are not precluded, use of
the data in any publications or other public presentations must
conform to the policy on publication and have prior approval.
v) No part of the samples or derived material (e.g. PCR products)
will be passed on to any other individual/institution without written
instructions from FAO.
vi) The samples remaining after the initial set of
molecular/biological analyses are completed will either be destroyed
or will be maintained in appropriate storage to preserve them for
possible future analyses, depending on the desires of the country of
origin and the country will be advised.
vii) Where necessary, all sample material will be promptly returned
to FAO by an appropriate means on written instructions from FAO.
(e) Copies of the signed documents should be kept on file at FAO and its
entrusted party and copies of all agreements relevant to samples from a
particular country should be sent to that country.
(f) The wording to the effect that the country of origin retains ownership of
the biological material and information, including the specific data
emanating from it, should be included in the agreement. Because of that
ownership, the agreement signed with FAO by countries participating in
MoDAD must include appropriate and specific provisions authorizing use
of the biological material and of information associated with it as detailed
in the MoDAD project description.
C. SUB-SAMPLE ALIQUOTS, DISTRIBUTION AND LABELLING
7.
National or regional centres should be identified that possess the facilities to
prepare and catalogue DNA in accordance with the necessary health regulations.
DNA extraction should be carried out by, or under the supervision of a scientist.
Ideally, this should be the person who was also responsible for field sampling. Centres
should prepare necessary documentation for export of samples. Every effort should be
made to keep DNA samples chilled or frozen at all stages if a preservative has not
been used. Necessary permits, specifying that the DNA extraction protocol satisfies
veterinary requirements for international shipment, should be obtained before the
samples are shipped and the central laboratory should be informed and given the
waybill number of the shipment before it is consigned.
4
8.
Aliquots of samples from subsets of the MoDAD collection will be created by
the national or non-national laboratory performing the extraction. Sample distirubtuin
is described above. Aliquots sent to the primary global repository - which also acts as
the species specific regional research laboratory, will be at full concentration. The
second sample sent to the backup global repository storage site will use 10-fold
dilutions. Distribution should always be via secure express mail services and there
will be no requirement for refrigeration in transit. It will be the responsibility of the
recipient laboratory/global repository to ensure that shipments are in accordance with
national veterinary health and customs procedures. Documentation pertaining to this
should be received by the sample curator before distribution.
Sample tube labelling protocol
One letter species code e.g. ’C’ for Cattle
Two letter Linnean code e.g. ’BT’ for Bos taurus
Two letter breed code e.g. ’FR’ for Friesian
Two letter Internet Protocol (IP) country code e.g. ’NL’ for Netherlands
Individual number
Sex: (’M’ or ’F’)
One letter specifying aliquot identity
An example code would be: C- BT-FR-NL-07-M-A
(Sample number 7 from Dutch Friesian bull, aliquot A)
Alphanumeric labelling is preferred to more sophisticated techniques such as bar coding.
These are not used widely in laboratories and are also unlikely to be suitable for
identifying samples stored in every developing country.
D. DNA STORAGE
9.
The criteria used to establish this strategy were:
Criteria for a strategy for DNA storage
1. The desirability of conducting advanced assays and statistical analyses, particularly for phase II of
MODAD, as additional funds and technology become available. Further work using the same rather
than additional samples will be cost effective.
2. Respect for country of origin sovereignty over genetic resources in accordance with the
Convention on Biological Diversity.
3. The need for duplication of each sample, to insure against accidental destruction.
4. In terms of the MODAD project there is a need for a long term global repository under international control from which laboratories may receive aliquots for assaying. There is a need for centrally
coordinated quality assurance for DNA storage.
5. Long term storage should be planned to satisfy all requirements for a period of 50 years.
10. The four regional research laboratories involved will serve as global repositories.
Each laboratory will have primary responsibility for a specific set species and will serve
as backup storage for a second set of species.
5
11.
Long term storage of DNA may be achieved at minimal cost by dissolving it in
10mM Tris-HCl - 1mM EDTA buffer and keeping it in a -20°C freezer. This buffer
keeps pH constant, preventing acidic/basic damage. It also inhibits nucleases and is
non-hazardous. The presence of EDTA also inhibits bacterial growth. Genetic
material stored thus will be resistant to damage even in the event of prolonged freezer
failure.
12.
While primary ownership of DNA samples will reside within the country of
origin. It is proposed to store DNA from each breed in three locations: one aliquot in
the country of origin, one aliquot in each of two global repositories: where one global
repositiory will also be the species specific regional research laboratory and will serve
as the primary storage site; while the second global repository will serve as backup
storage. These global repositories, will be contracted and supervised by FAO. These
global repositories will be species specific in terms of their primary and secondary
storage functions. A suitable candidate as a global repository would be within the
CGIAR system wide research programme for animal genetic resources lead by ILRI.
Quality control in storage will be coordinated and monitored by FAO to minimise risk
of loss of long-term stores. It will ensure that global inventories are maintained for
each of the stored samples; regularly report to countries on the status of the MODAD
DNA store, ensure proper security and auditing of samples and sub-samples; ensure
that the rules of access are being maintained at all times.
13.
Where extraction has taken place outside the country of origin, samples will be
triplicated and one sample returned immediately to the national body concerned. The
second and third samples sample will be sent one to each of 2 global repositories described in the above paragraph. Security of national sample ownership requires that
non-national laboratories do not retain unassigned aliquots.
14.
The decision on the three storage locations is based on several considerations:
the absolute requirement for at least duplicate storage, the need of each country to hold
a complete set of the samples in has contributed to the global project, the advisability
of one single collection of all samples under the custodianship of FAO, and the added
risks and management problems were samples to be returned from the laboratories
doing the molecular assaying.
1
ANNEX 3
BASE-LINE LABORATORY ASSAYING
A. CHOICE OF LABORATORIES FOR ASSAYING ACTIVITY
1.
A number of criteria are established to in identifying laboratories to participate in
assaying of samples.
(a)
Competence. The laboratories should have a demonstrated
ability to perform assaying to the level required. Preferably this should be
demonstrated in peer-reviewed publications featuring
large-scale
microsatellite surveys. A minimum level will feature published expertise in
general molecular biology techniques, for example PCR, DNA sequencing
and cloning.
(b)
Prior molecular experience. A history of published research into
the molecular analysis of biodiversity will be an advantage. This will
ensure an intellectual familiarity with the scientific issues involved and
some competence in statistical analysis. The most relevant experience will
be DNA-based examination of intraspecific diversity.
(c)
Geography. At least one laboratory must be situated in each of
Africa, Asia and Latin America. Proximity to centres of diversity of
domestic species and an ability to participate in the sampling activity is
desirable.
(d)
International Operations. A history
collaborative international research is desirable.
of
experience
in
(e)
Experience of training, especially in the facilitation of students
achieving Masters and PhD level research projects. A history of interaction
with students and personnel from developing countries is preferable
(f)
Previous Research. Where laboratories possess DNA samples
of the correct quality and provenance and/or substantial data of a form
which may be incorporated into MoDAD their participation should be
encouraged when quality and standardisation is assured.
(g)
Efficacy and Agreement. Should a single or small number of
commercial laboratories be involved price competitiveness, competence and
willingness to enter into the necessary agreements based on the tenders
would be considerations in awarding contracts for sample assaying.
(h)
Longterm Storage. Capability to act a global repository for
longterm storage of DNA samples: primary repository for one set of species
and backup repository for a second species set.
2
B. NUMBER AND TYPES OF LABORATORIES INVOLVED
2.
The options involved in the assignment of institutions to perform the
laboratory assays are as follows:
(a)
Perform assaying where possible in the country of sample origin
and otherwise in a number of laboratories selected per species.
(b)
Conduct all laboratory work in a smaller number of laboratories,
with one or at most two institutions involved in the assaying of a single
species. These could be centres situated in diverse regions of the world and
could also take a major role in sample coordination. These laboratories
would assume responsibility for the following: i) training and coordination
of field sampling for the countries in the region, ii) assaying of samples for
specific sets of species, iii) primary storage for these sets of species ie for
which assaying is carried out on, iv) backup storage for a second set of
speicies, v) quality control for assaying of species set, vi) quality control for
all aspects of field sampling and sample preparation for countries in the
region, vii) data analysis of genetypes for specific set of species.
(c)
Contract the total activity to a single or small number of commercial
laboratories. The regional laboratory acting as primary global repository
for a species set is responsible for creating subsample to be sent to the
commercial laboratory. All other functions of the regional laboratories are
as in (b) with the exception of the assaying function. Additionally, on a
random basis, the regional laboratories would create an additional subsample for use in assay quality control.
3.
Option (a) above was disregarded because of the high costs in equiping,
and sometimes establishing, national laboratories. The remaining two options for
assaying (b) involving the 4 regional laboratories or, (c) involving the 4 regional
laboratories and the commercial laboratory were evaluated using a Multiple Criteria
Analysis (refer to Table 3.1 at end of this section). The major criteria considered
involved in the analysis are: quality assurance; expedinecy with which work carried
out; provision for capacity building; cost effectiveness; and acceptability in terms of
sensitivity to perceptions of sample ownership, the need to reflect the geographical
spread of sample origins. It is important to note that such an analysis depends on the
importance attached to each criterion and the way in which each option is scored
relative to the criteria.
4.
The Multiple Criteria Analysis revealed little difference between the
options. As such, the project funder, as well as the MoDAD participating countries,
should be consulted before a final choice is taken as it may be a particularly sensitive
issue. Advantages of the single commercial laboratory include: (i) speed and quality
control of assaying procedures; (ii) it would be easier to manage and coordinate all
assaying activiities; (iii) it may possibly be slightly cheaper than the four regional
laboratories option. Disadvantages of the commercial laboratory option include: (i) it
would remove the a significant project component the project from the regional
laboratories where the network training, data analysis and DNA long-term storage
would be centred; (ii) it may ingender political sensitivity and misturst over property
3
rights and unauthorized use of genetic material. The latter disadvantage could be
dissipated, but not eliminated, by including in the contractual agreement with the
commercial identity that all DNA samples would be destroyed after assaying.
5.
A number of institutes may act as regional laboratories. Ideally they would
be international laboratories located, one each in Asia, Latin America, Africa and
Central or Eastern Europe. Linkages with laboratories in Western Europe or North
America which have a proven record in research and which may be expected to
interact positively and enrich the project with prior data, species-specific knowledge
and possibly technology transfer should be considered. The advantages of choosing a
relatively small number of centres is that a species may be analyzed in one or very
few laboratories which will facilitate assay standardisation. Centres with a high level
of expertise and with suitable infrastructure may be chosen. Overall costs will be
reduced by the lack of unnecessary duplication of capital equipment expenses. The
linking of the experimental assays with DNA extraction and sampling will be possible
and should be an enhancement of both activities. An advantage of the regional
laboratories option for assaying, and provision of required equipment, serves to
augment research capability. But as in paragraph 2, irregardless of whether these
laboratories are primarily responsible for assaying or serve as quality control in for
assaying at the commercial laboratoy; under both scenarios training will be required on
assaying procedures and necessary equipment provided. Additional training will be
provided for in the analysis of data. Such training is facilitated by both the cultural
and geographical proximity of regional centres to scientists and students from
breed-rich developing countries and also by the planning of substantial bodies of
research in each which may be suitable for Masters and PhD programmes.
6.
The involvement of as many countries as possible in the assaying and
analysis of their own genetic material would be highly desirable as a political
consideration. However if assay of each species were to be spread across a large
number of laboratories this would lead to considerable logistical problems and would
greatly increase costs. Special difficulties of this approach include assay
standardisation and quality assurance. Capital equipment costs would be magnified
and often the amount of work to be performed would fall below a minimum which
merited the management of laboratory setup and importation of techniques and/or
staff.
C. CHOICE OF GENETIC MARKERS FOR BASE-LINE ASSAYS
7.
This discussion focuses on the minimal base-line assays required to achieve
phase I of the primary objective for MoDAD. The commentary is also relevant to considering what advanced assaying could be done. The molecular methodology used
should:
(a)
Afford a level of biological resolution which is suited to the close
relationships between domestic breeds.
(b)
Be DNA based
4
(c)
Be cost efficient
(d)
Involve a rapid assay suited to large numbers
(e)
Not use large amounts of sample and hence should be based on
the polymerase chain reaction (PCR)
(f)
Enable the assay technology to be available for a range of
species, or be possible to develop it at reasonable cost
(g)
Result in data which is reproducible and comparable between
laboratories and be readily coded in a portable and archivable fashion.
8.
A number of alternative methods exist for assaying genetic variation. These
can be categorized as;
1. Classical but unsuitable methods
Morphometric analysis
Immunotechniques
Protein electrophoresis
DNA-DNA hybridisation
2. Single base pair substitution detection
Restriction fragment length polymorphisms (RFLPs)
DNA sequencing
Denaturing gradient gel electrophoresis (DGGE)
Single-strand conformation polymorphism (SSCP)
Amplified fragment length polymorphism (AFLP)
Allele-specific oligonucleotide (ASO)
Randomly amplified polymorphic DNA (RAPD)
Haplotype analysis
(All of the above may be applied (with the exception of RAPD) to different genetic sys
tems: autosomal coding, non-coding, mitochondrial DNA, Y chromosome analysis)
3. Assays of length polymorphisms in repetitive DNA arrays
Minisatellites
MVR-PCR
Microsatellites
9.
Category 1 Methods: The methods listed in the first category are not
recommended. Morphometric analysis employs phenotypic measurements and is
known to be a relatively poor indicator of underlying genetic relationship. Antigenic
crossreactivity and protein electrophoresis share some benefits and limitations. They
are both cheap and use accessible technology. However, they are both limited in the
number of markers which may be produced and these are relatively unpolymorphic
and hence low in information yield. Methods are difficult to standardise between
markers and also between laboratories. Techniques require biological material which
cannot be processed in as rigorously disinfecting procedure as phenol/chloroform
extraction. DNA-DNA hybridisation is more suited to interspecific comparison and is
not a technique of sufficient sensitivity to measure the close relationships present
within domestic species.
5
10.
Category 2 Methods: The basic unit of genetic variation assayed
indirectly by classical techniques above is that of the DNA base-pair substitution. A
range of methods exit which assay DNA sequences in a more direct fashion. RFLPs
utilise variations in the patterns in which DNA is cut by enzymes which act at specific
short sequences which may be created or disrupted by substitution. This technique
may be developed for PCR but is relatively inefficient in both the process of
developing markers and also their typing. More recently methods have been
developed which improve on the efficiency of marker discovery or assay. The most
widely used are: denaturing gradient gel electrophoresis, single strand
conformational polymorphisms and allele-specific oligonucleotide hybridisation. PCR
amplification followed by direct sequencing is a technique which surveys nucleotide
variation at chosen loci in an intensive manner. These methods all have some utility
for the application envisaged in MoDAD. However, the low level of sequence
variation within species, in many of which all breeds will have shared common
ancestry as recent as 10,000 years BP, is a limiting factor in these technologies. This
may be overcome either by assaying a larger number of loci or by examining regions
of organismal DNA which are known to have a higher substitution rate. The former
would be a reduction in efficiency and the latter approach has other drawbacks.
11.
The control region of the mitochondrial chromosome displays a high level
of variability due to the high mutation rate of mitochondrial DNA. It may best be
assayed by sequencing and yields data which has been shown to be informative in
studies of a wide range of different species, including domestic cattle. However,
despite the quality of the data such investigation is limited by the fact that the ancestry
of only one portion of the genome is being accessed and it may not accurately reflect
organismal origins. The population genetics of mtDNA are unusual in a number of
ways. In a study of domestic cattle from three continents Loftus et al. (1994)
illustrated that mtdna sequencing shows utility for illustrating the deeper phylogenetic
relationships but shows none for distinguishing between breeds from the same regions.
12.
Randomly amplified polymorphic DNA (RAPD) is a technique which
samples variation using PCR and randomly chosen short primer sequences. It has the
advantage that novel markers may be developed at low cost but has some
disadvantages which preclude its use in this context. The markers are dominant,
which decrease the quality of information and, most importantly, the technique is
difficult to standardise and reproduce in different laboratories.
13.
Category 3 Methods: Three types of assay based on the high variability
of repeated DNA are currently used. Minisatellites are markers based on tandem arrays
of sequence repeat units of approximately 15 base pairs and greater. MVR-PCR is a
sophisticated development of this technology which utilises small sequence
differences between repeats. Minisatellites usually are not amenable to PCR,
relatively few markers are characterised in domestic species and the cost of de novo
development is high.
14.
The preferred tool for the analysis of genetic variation in closely related
populations involves the use of highly polymorphic microsatellite markers (Litt and
Luty, 1989; Weber and May, 1989; Tautz, 1990). These consist of PCR-amplified
segments of genomic DNA which contain short repeats of mono-, di- or trinucleotides, for example:
6
15.
These repeats have been shown to be ubiquitous throughout vertebrate
genomes and often exhibit substantial variation in the numbers of repeats. Differences
in repeat number can be reliably distinguished, and the variants are inherited as alleles
at a single genetic locus. The polymorphic nature of this type of locus, with variations
many times more common than in non-repetitive sequences, is attributed to slippagebased errors in DNA replication. Microsatellites are the markers of choice for the
intensive gene mapping studies now being done in a number of domestic animal
species, and will provide high resolution discrimination between closely related
populations within the same species.
16.
Microsatellite assay is rapid and cost effective and the technology is widespread. A substantial body of data on microsatellite variation already exists for cattle
and sheep. In the latter, they have proved particularly useful for accurately estimating
admixture between taurine and zebu breeds which has a direct bearing on the
conservation of valuable breeds (Meghen et al. 1994).
17.
Reservations about the suitability of these markers for phylogenetic
analysis focus on the particular mutation process which gives rise to the variation they
utilise and the possibility that alleles which are of identical genotype are non-identical
by descent. However, a substantial body of recent work has concentrated on analytical
techniques for these markers, which takes account of their particular mutational
dynamics (Shriver et al. 1994, Goldstein et al. 1995, Slatkin, 1995) and their utility
has been illustrated in studies in sheep, cattle, canids and humans. An additional
criticism is that mutation rates may vary between loci, but this is not a problem when
the same loci are typed in all breeds of a species. Importantly, mutational effects will
be of minor importance in MoDAD as the crucial distinctions will be between closely
related populations where genetic drift will have been the major differentiating
process. This is also an answer to fears that the high level of microsatellite mutation
will generate noise with the potential to decrease resolution of the parameters to be
estimated.
D. CRITERIA FOR CHOICE OF MICROSATELLITES
18.
In the case of some of the 14 species there will be a panel of
internationally recognised markers for genetic diversity studies. However, for certain
species a set of markers will have to be assembled by reference to the scientific
literature and communication with the laboratories that originally developed the
markers. The International Society of Animal Genetics (ISAG) has resolved to
recommend panels of markers for use in genetic distancing work. Panels of markers
selected by the ISAG will be assembled for a species, the choice will be based on
established criteria and the Barker et al. (1993), these are:
7
Criteria for choice of microsatellites
a) A size range of 4-10 alleles
b) Ability to be robustly amplified via PCR
c) Should display unambiguous allelic banding patterns
d) Ability to be multiplexed (simultaneous amplification with one or more other markers in the
panel)
e) Informative across closely related or sibling-species (eg.. cattle and buffalo)
f) Genomic position (all markers in the panel should be unlinked)
g) Previous use in existing and relevant bodies of data.
h) The markers should not be patented and primer sequences should be freely available in the
public domain
19.
For some species it will be difficult to adhere to these requirements,
however even in these cases every attempt should be made to conform to these criteria
as much as possible.
20.
A perusal of the literature indicates that the following numbers of markers
currently exist in the public domain for each of the 15 species.
Microsatellite markers currently available for the 15 species
Cattle*
Sheep
Pig
Buffalo**
Goats#
Horse
Ass¶
Dromedary§
Bactrian Camel§
Llamoid§
Chicken
Duck
Turkey
Goose
Rabbit
500+
300+
300+
-50+
100+
----100+
-----
* The cattle group also includes the sibling species Banteng, Gaur, Mithan and Yak
** It should be ensured that the markers used for the survey in the cattle group are informative in buffalo also
¶
The markers chosen for the survey of genetic diversity in Horses should be informative in Asses also
#
The markers listed for goats have been largely derived from markers originally developed in sheep and cattle
§
It should be possible to develop a panel of markers which will be informative in both species of camel and also in
the species comprising the llamoid group.
8
E. DEVELOPMENT OF NEW MICROSATELLITE MARKERS
21.
For a certain number of the species (as shown above), there are no suitable
microsatellite markers available at present. In these cases new microsatellite loci will
have to be developed and assessed as genetic markers for genetic diversity studies.
22.
Many methods have been described detailing protocols for isolation of
microsatellite loci. However, the rationale behind the various procedures is similar and
can be outlined as follows.
23.
Genomic libraries will have to be generated for each of the species for which
markers need to be developed. The genomic libraries will then need to be screened
with DNA probes containing dinucleotide repeats (usually (CA)n). Positive clones are
then sequenced using standard methods and PCR primer sequences can be designed to
encompass the dinucleotide repeat region. The newly developed markers would need
to be assessed for polymorphism and considered for inclusion in the species panel
under the criteria outlined above.
24. A post-doctoral level scientist would be required to develop these microsatellite
panels and experience would indicate that new candidate microsatellites could be developed at the rate of about one a week. In order to produce a suitable panel of 30 microsatellites, about 50-70 would need to be initially characterised. It is envisioned that 18
months would be required to carry out this work.
25.
However, it is considered that for the remaining species for which markers are
currently not available, that the timing and impetus of MoDAD will engender activity
in this area of developmental research.
F. LABORATORY ASSAY OF MICROSATELLITE VARIATION
26. The primary criteria required for a rapid-throughput protocol for microsatellite
typing a large number of genomic DNA samples are as follows:
Criteria for a rapid-throughput protocol for microsatellite typing
a) The system should be as automated as possible within the limits of cost-effectiveness.
b) Where possible, the protocol should be simple and straightforward so that in some cases
technicians lacking molecular biology experience may be trained to carry out the procedure.
c) A comprehensive quality control regimen is in place to precisely link all field assaying and
laboratory data, result in accurate, precise and repeatable assaying and reading of assay results
and to track any anomalies in results.
d) Cost-effectively and rapidly process and make all data available for each species.
27. There are numerous options possible with regard to the technical details of
microsatellite typing and many different protocols exist in the molecular biology literature. However a standard protocol can be developed based on the experiences of the
human genome mapping/sequencing community and other scientific groups screening
9
large numbers of microsatellite genotypes.
Polymerase Chain Reaction (PCR) amplification of microsatellites
28.
It is assumed that the optimal PCR variables (MgCl2 concentrations and
thermal-cycling parameters) will have been predetermined by the laboratories where
1
the microsatellite markers were originally developed. Hence, the protocol outlined
here will only be concerned with the actual population typing.
29. It is proposed that all Polymerase Chain Reaction (PCR) reactions for microsatellite
amplification reactions be performed using a 96 microtitre plate system in conjunction
with a 12 channel multi-micropipette for sample dispensing. The PCR-ready stock DNA
samples can also be pre-aliquoted into 96-well microtitre plates for storage and use in the
laboratory. This will greatly speed up and simplify the setup procedures for microsatellite
amplification. It would also dramatically reduce the freezer space required for sample
storage in the assay laboratories. This system will also lend itself to automated robotic
dispensing systems, however the number of genotype screens required for a species in the
first phase (50 animals X 50 breeds X 30 genotypes = 75,000) implies that there would be
no great cost savings if a robotic system was used. A single laboratory technician could
comfortably prepare 10-15 plates an hour if required. DNA samples should be aliquoted
as 1 ml volumes and the aqueous diluent can be evaporated off.
30.
The reaction mixes will contain two synthetic oligonucleotide primers, a
thermostable Taq polymerase enzyme, nucleotides, reaction buffer and a DNA
labelling component (depending on the electrophoretic system, either radiolabelling or
fluorescent-based methods will be used; see later). These dried plates can be stored
indefinitely at -20°C. A repeating incremental dispensing pipette (eg.. Eppendorf)
should be used for dispensing the PCR reaction mix into the microtitre plates. 10 ml of
reaction volume can be added to each well of the plates containing the DNA samples
and these are then overlaid with mineral oil and processed on a PCR machine with a
block capable of holding microtitre plates. These amplified samples are then
electrophoresed using a gel electrophoretic system. With a manual system, two types
of size standards should be used, a) a pre-sequenced DNA ladder, derived from
plasmid DNA, ie. M13 and b) allele ladders derived from individuals of known
genotype. Usually two heterozygotes with four different alleles are combined and run
in a number of wells on the gel (every 12th well etc.). This provides a four-band ladder
and in conjunction with the sequence should allow unambiguous determination of the
genotypes for the samples to be screened. The automated system described below uses
a different method for allele size calibration, but in effect it is just as accurate.
31. There are two options for an electrophoretic system, either an automated datacollection system as described below or a manual entry system. The overall cost of a
single microsatellite genotype using a manual-based genotyping system has been
estimated by various groups and this information was obtained from a number of sources
using the MODAD Internet Reference Panel. The total includes labour, consumables,
durable equipment costs and overheads. A consensus emerged of approximately US$ 4.00
1
This will be the case for most of the major domestic animal species.
10
for each genotype obtained.
32. This cost could be reduced by using a multiplex amplification system, but it provides
a reasonable figure on which to base project costs.
33. As mentioned above, an additional option which was considered by the WG was
should an automated data-collection gel-electrophoretic system be used. The cost of US$
4 per genotype is based on a manual system where data would have to be interpreted
visually and entered by hand into a computer database. An automated system would
simplify the data collection at the end of each electrophoretic run and lessen the workload
for the technicians carrying out the genotyping. The most widely used automated system
is the Applied Biosystems 377 DNA sequencing/typing machine. As outlined below, the
use of these systems would contribute a substantial additional cost to the overall project
and at least four machines would be required, one for each regional laboratory.
Criteria for a rapid-throughput protocol for microsatellite typing
Laser scanning gel electrophoresis system
(including a Macintosh computer)
US$
110,000
Dedicated laser-transmissible gel plates
US$
8,000
GeneScan data collection software
US$
10,500
Annual cost of consumables
(assuming machine is running continuously)
US$
40,000
34. The additional cost that these machines would add to the overall project lead the
WG not to recommend their use in the MODAD project. The throughput of genotypes
required (75,000 for species with 50 breeds) would not justify their use and anyway, a
single technician could comfortably enter and validate 1,000 genotypes a day if required.
In addition, in the experience of the WG, the complexities of these machines, which were
originally designed for automated DNA sequencing and not microsatellite genotyping
would give rise to many technical problems.
G. ADVANCED ASSAYING
35.
The information collected from a survey of 30 microsatellites in each
species will provide a solid body of data from which rational decisions can be made in
relation to the management of Domestic Animal Diversity. The Working Group
recommended advanced assaying to be carried out on other genomic regions.
Advanced assays are by nature not required as a crutial part of the base-line assaying
discussed above but are of importance because they will enhance and supplement
results obtained from surveys of variation at microsatellite loci. In particular it is
recommended that small-scale surveys of mitochondrial D-loop variation are conducted and also where possible variation at the male-specific Y-chromosome (Z
chromosome in birds). These markers would provide useful information about the
relative depth of divergence between distantly related groups and also highlight any
sex-mediated gene flow among and between various groups. Mitochondrial DNA in
11
particular will reveal any islands of "cryptic" or hidden genetic variation within a
species which can be confirmed by microsatellite analysis.
12
Table 3.1 Multiple Criteria Analysis of sample assaying options: regional laboratories or
regional laboratories complemented by commercial laboratory for sample assaying. Each
criterion assigned a relative emphasis score (out of 100%). Options evaluated for each
criterion on a scale of 1 to 5 (1=very low, 2=low, 3=medium, 4=high, 5=very high rating
with respect to each criterion.
Criteria may not be completely mutually exclusive (ie
decreased CAPACITY BUILDING may contribute to reduced ACCEPTANCE).
Criteria
Regional Laboratories conduct sample
assaying
Commercial Laboratory contracted to
conduct sample assaying + Regional
Laboratories responsible for quality
control
Quality Control
3 - Greater opportunity for laboratory
failures such as problems with reagents,
variable standards between labs, equipment failure and human error.
5 - high quality assured due to highly
evolved production line function,
micorsatellite assay optimization, automated sample tracking, data collection and
archive (use of genescanning equipment)
3 - assaying carried out over 2.5 years
5 - assaying completed within one year.
4 - Regional labs receive training in field
sampling, storage, data base management
and analysis of data.
5 - This option similar to alternative
with the exception that regional labs
only carry out the quality control
assays.
15%
Speed of Assaying
10%
Capacity building
15%
Equipment provided for quality control
and base-line assaying of samples.
Training in field sampling techniques,
storage and database management for
nationals conducted by regional labs.
Encourages assumption of Phase II
where significant breed variation
detected.
Regional labs receive training in field
sampling, storage, data base management
and analysis of data and quality control.
Training in field sampling techniques,
storage and database management for
nationals conducted by regional labs.
Regional
labs
gain
added
opportunity to interact with a major
commercial operation.
If Phase II required built in reliance on
centralized lab unless at onset of Phase II
countries receive required training and
equipment.
Acceptance
5- prior input from countries to selection
of regional laboratories guarantees
cooperation and acceptance.
1 - Putting in place transfer protocols in
terms ownership potentially more difficult
(intellectual property rights issues).
Agreements for DNA stroage and
assaying required with FAO and
countries involved.
Agreements must also include the
commercial laboratory.
3 - Less cost-effective than alternative.
5 - Regional laboratories are equally
involved but more are effective and
absolute costs are the same.
40%
Cost effectiveness
20%
1
ANNEX 4
STATISTICAL ANALYSIS AND DATA STORAGE
A. BASE-LINE ANALYSIS OF GENETIC STRUCTURE WITHIN BREEDS
Calculation of allele frequencies and estimation of heterozygosities
1.
The data on all the markers will be summarized in tables of genotype
frequencies for each population or breed. Allele frequency estimates at each locus
will be calculated by simple gene counting and binomial standard errors will be calculated for each allele. These allele frequency distributions can be most be readily
visualised in the form of histograms and any major differences among populations
will be immediately evident. Observed heterozygosity can be estimated directly
from the raw genotypic data and this quantity when condensed over all loci can
reveal any major past episodes of inbreeding or population bottlenecks.
Deviations from Hardy-Weinberg Equilibrium (HWE)
2.
The difference between the observed heterozygosity and the expected
heterozygosity calculated from allele frequencies under the assumption of HardyWeinberg Equilibrium (HWE) can be used as a crude method for detecting
perturbations in the population structure of breeds. However a much more accurate
method is to test the observed genotype distributions versus the expected
distributions under Hardy-Weinberg Equilibrium. Any significant deviations would
indicate that the breed is actually sub-divided, is undergoing significant inbreeding
or is experiencing substantial gene flow from another population. This will be
examined using an exact test or a likelihood ratio procedure using one or more of
several already existing programs available at no cost. The programs required for
analysis of Hardy-Weinberg Equilibrium (HWE) will need to be able to perform
permutative allele-shuffling or Markov chain procedures in order to calculate exact
probabilities (Hammond et al. 1994). These capabilities are required because the
large number of alleles at microsatellite loci means that the number of possible
genotypes is very high. Without these computational aids, much larger sample sizes
would be required to detect subtle deviations from HWE. Overall significance
levels will need to take account of the multiple markers being studied for each
population.
If significant deviation from Hardy-Weinberg proportions is observed or
suspected, additional analyses considering all loci will be undertaken. For example, if
several loci have fewer heterozygotes than expected, it may be possible to obtain a
meaningful estimate of the current level of inbreeding for the breed. The nature of the
deviations at the various loci will dictate the types of analyses that are possible and
meaningful. Such analyses have the immediate benefit of identifying aspects of breed
structure (such as inbreeding) that might not have been suspected but could have
importance for future breed management. Moreover, the analyses are quite inexpensive
to conduct once the genetic marker data are in the MoDAD database. The risk of not
2
conducting such analyses is less knowledge about breed structure and the possibility of
missing a significant level of inbreeding that may be affecting production.
B. ANALYSIS OF GENETIC STRUCTURE AMONG BREEDS
4.
As complete data on sets of breeds become available, the following analyses
will be performed. Several such analyses will be conducted for each species: initial
analyses as data are complete for meaningful groups of breeds (level 1 analyses) with
a final set of analyses of the entire set of data when marker typing is complete for all
breeds in the species (level 2 analyses). The general approach to data analysis will
involve the calculation of genetic distances among breeds based on gene frequency
data, followed by analyses of relationships and genetic distinction. Level 1 analyses
will be carried out by scientists at the various laboratories; level 2 analyses will be the
responsibility of FAO.
Calculation of various genetic distance measures
5.
Using breeds as the Operational Taxonomic Units (OTUs) and the allele
frequencies at all loci, matrices of pairwise genetic distances will be calculated. There
is no general consensus as to which of the many genetic distance measures would be
best for analysis of within-species populations such as domestic animal breeds.
However, the correlations among various distance measures have been found to be
generally very high (Nei et al. 1983), particularly when applied to local populations
within a species, such as livestock breeds.Nei’s (1972) standard genetic distance has
been used most commonly in studies of natural populations in evolutionary genetics.
However, distance measures based on Wright’s FST statistic (see above) (e.g. Reynolds
et al., 1983) may be more appropriate for short-term evolution such as the divergence
between livestock breeds, especially if effective population sizes have varied through
time and among breeds. Also, as with measures of population sub-division, newer
measures of genetic distance have been developed which incorporate the mutational
mechanisms governing the evolution of microsatellite alleles. These measures
incorporate the Stepwise Mutation Model (SMM) and have been found to be more
appropriate for microsatellite loci under most circumstances (Goldstein, 1995). These
newer measures should also be used as estimators of genetic distance during the
analysis stage of MoDAD.
6.
As the mathematical properties and biological base of the various measures
do differ, it is conceivable that different distance measures could lead to different
interpretations of the phylogenetic relationships among a set of breeds, with no way of
determining the ’best’ phylogeny, i.e., the one closest to the true phylogeny. In effect,
every method makes some assumptions about the data and evolutionary processes that
generated them; often it is impossible to know whether the populations sampled meet
those assumptions and if they do not how much they deviate from those assumptions.
7.
In usual practice, two or more different genetic distance measures will be
calculated and the similarities/differences among those measures will be examined for
each set of breeds being analyzed to determine the degree to which conclusions might
be dependent on choice of genetic distance measure. The risk of not doing this is not
3
knowing how robust the conclusions are to some of the assumptions made by any
single distance measure. The added cost of doing multiple distance calculations is
simply the additional time of the data analyst, which is not great for these virtually
automatable analyses.
Clustering/Phylogenetic representation of breed relationships
8.
Though the genetic distance matrix contains all of the information on breed
relationships provided by the genetic markers studied, it is difficult to interpret without
additional analyses. Therefore, the distance estimates will be used in a variety of
clustering and representational analyses. The objective will be to facilitate
interpretation of the breed relationships that are represented by the genetic distance
matrix.
9.
One approach will be construction of tree diagrams, usually involving
methods that allow for unequal rates of evolution. An important consideration is that
a tree diagram can be interpreted as a phylogenetic tree if certain assumptions are met;
however, even if a phylogenetic interpretation is not possible, a tree diagram is a
graphical representation of a clustering analysis and is useful in representing the existing genetic relationships among breeds/populations however they may have arisen.
The distinction needs to be made between the tree produced by a specific algorithm
(e.g., the neighbor-joining method of Saitou and Nei, 1987) and the best possible tree
representation of a distance matrix according to some criterion (e.g., additivity as
measured by least squares as discussed in Cavalli-Sforza and Edwards, 1967,
Felsenstein, 1973). Since it may never be possible to know when the best tree is
found, and since "best" is dependent on unprovable assumptions, a variety of genetic
distance measures and tree building approaches will be used. The PHYLIP package is
available free of cost and provides several options (Felsenstein, 1993). Computer
programs such as the DISPAN package (T. Ota, Institute of Molecular Evolutionary
Genetics, Pennsylvania State University) or BIOSYS-1 (Swofford and Selander, 1989)
may also be used to assist in calculation of distance, heterozygosity, and similarity
trees.
10.
Bootstrap analysis provides a different and statistically preferable measure
of the robustness of a result but is time consuming and is probably best left until the
final series of analyses. It will not be possible to try bootstrap analysis for all possible
genetic distances or all possible tree building/evaluating algorithms but programs exist
for bootstrap analysis of some combinations of distance measure and tree building
algorithm (e.g. the DISPAN package of programs, T. Ota, Institute of Molecular
Evolutionary Genetics, Pennsylvania State University).
11.
Principal Components Analysis (PCA) of a distance matrix allows a
completely different representation of the genetic similarities among breeds.
Depending on the results of a specific analysis, the great majority of the information in
a distance matrix can usually be preserved in a small number of synthetic variables. A
visually interpretable plot (in two dimensions) of the populations in a three
dimensional "genetic" space, defined by the first three components, will usually
preserve sufficient information to be extremely valuable; often the first two principal
components preserve more than half of the information allowing even simpler
graphical representations of the relationships.
4
12.
The level of phylogenetic distinction of each breed is a measure of the evolutionary distance between it and other breeds, tempered by the number of closely
related forms. For example, a breed that has a large evolutionary distance between it
and other breeds, and has no closely related breeds, has greater distinction than one of
similar distance but which also has several closely related forms (Crozier, 1992; May,
1990). Analysis of genetic distances has to tempered with a note of caution in relation
to admixture or gene flow between breeds. If there has been significant admixture
among breeds, the genetic distance estimates become meaningless in terms of the
actual evolutionary divergence between the original populations.
Clustering analyses using individual animals as OTUs
13.
Analyses can be done to determine whether individuals sampled from
several breeds cluster into the breed groups that were the basis of sampling. Such
analyses would evaluate the tendency of animals to cluster together into populations.
A finding that animals sampled from the same breed did cluster together would
provide support for the use of the breeds as the basis for future analyses. A finding that
little clustering occurred or that some animals did not cluster with their breed would
suggest the possibility of problems in breed definition or sampling. This analysis
would be done with individuals as the operational taxonomic units (OTUs) and an
allele-sharing algorithm to produce a matrix of pairwise distances between individuals
(e.g., Bowcock et al., 1994, Nature). A variety of analytic programs to draw trees or
other representations of the distance matrix for individuals could be used to visualise
the clustering and make subjective interpretations. Rigorous statistical testing of the
clustering may not be possible nor is it necessary at this level of analysis.
C. ADDITIONAL ANALYSES
Calculation of Wright’s Fixation Indices
14.
Other analyses of population structure that could be carried out include
calculation of Wright’s fixation indices (FST, FIT and FIS) (Wright, 1951). These
measures give an insight into the level of within breed diversity as compared to the
level of between breed diversity. Many different approaches have been developed to
calculate these quantities. However, recently a number of new methods have been
developed which take into account the mutational mechanisms governing the
evolution of microsatellite loci (Slatkin, 1995). The WG recommends that these new
measures should also be estimated in conjunction with the classical approaches.
Other population-level parameters
15.
It is possible to estimate the effective population size for a particular breed
using the data generated from a survey of molecular variation. This parameter gives an
indication of the "genetic health" of a particular population in terms of the effective
numbers of breeding females and males. This is particularly relevant for surveys
among endangered populations or breeds. An estimate of the effective population size
5
can be derived from the expected heterozygosity, the mutation rate at each locus and
the observed number of alleles.
16.
Another important genetic parameter which should be estimated for certain
populations is the proportion of admixture. This quantity reflects genetic contributions
from two or more parental or source populations. Microsatellite data has been used
effectively in calculating levels of admixture in African taurine/zebu hybrid cattle
populations. This type of analysis has allowed quantification of the level of zebu genetic introgression or gene flow into the trypanotolerant taurine populations of West
Africa (Meghen et al. 1994). These analyses can be performed quickly in those
situations where it is suspected that some breeds represent hybrid populations formed
due to gene flow between two or more distinct parental or source breeds.
17.
All of the analyses described above could be readily programmed as
ancillary functions of the database used for storage of the raw genotypic data. Hence,
this would make these analyses essentially automated and there would be no marginal
costs or significant personnel time required. The individuals entering the marker
typing data will perform these analyses and make them available, electronically or as
hard copy, to appropriate individuals in the relevant countries, at FAO, and in
collaborating laboratories.
18.
These additional analyses can be undertaken by anyone given access to the
data with minimal marginal costs other than the time of the analyst. Most statistical
packages that might be used are broadly available, some may be made available
through FAO’s DADIS. If specific analytic programs need to be written, a PC is
perfectly sufficient. Results of these exploratory analyses will be made available to
the responsible FAO official who will see that they are shared with all appropriate
individuals, as above.
D. COSTS OF STATISTICAL ANALYSIS
19. All of the analyses described above would be carried out at the regional research
laboratories and may be performed by anyone with a good knowledge of population
and evolutionary genetics and access to the data. Computer programs for practically all
of the possible analyses exist and should be available at no cost (or at most a modest
fee to cover distribution costs). Some standard statistical/graphic packages may be
useful and are widely available. Some programs may require computers larger than
IBM-compatible PCs and there may be access/use fees if analyses are done on local
institutional machines. Such access costs should be minimal (US$ 100) for each set
of animals analyzed (usually a total species). Alternatively, MoDAD could acquire and
make available most of the relevant analytic programs at some overall cost savings
compared to each group acquiring its own set of analytic programs. Whichever
approach is followed, the major cost will be the time of the analyst, these analyses can
be time-consuming and may take several days to perform and interpret. Results of
these analyses will be made available to the responsible FAO official who will see that
they are shared with all appropriate individuals. Results may be publishable in
themselves and the policy on publication will apply.
6
E. DATA MANAGEMENT AND DATABASE SYSTEMS
20.
There are two main stages to the management of data generated from the
MoDAD Project. Initially, a uniform database system will need to be implemented for
the management of the raw genotypic data generated from the genotypic surveys in the
various species. The second stage of the system will be required once the data from the
surveys are analyzed and the resulting information needs to be disseminated both to
the participating countries and to the scientific community in general. Both of these
systems will be based primarily around the Internet. These databases can most costeffectively be implemented as modules of DAD-IS.
Management of the raw genotypic data from each species
21.
It is proposed that management of the raw genotypic data will involve
three components:
(a)
Assaying Laboratories: The laboratories responsible for doing the
actual genotype screening in the various species will need to maintain and
update a flexible and uniform database for entry and validation of raw
genotypic data. This database should also have the capacity to generate
reports containing basic summary genetic statistics such as allele
frequencies, heterozygosities, gene diversities and results from preliminary
tests for Hardy-Weinberg Equilibrium etc.
(b)
FAO Project Coordination: The MoDAD Project Coordinator will
maintain the MoDAD database containing field survey data generated by
the regional laboratories. The regional laboratories will connect to this
database via the Internet to provide regular updates as they produce the
survey data. The central FAO database should also contain relational links
to information about the microsatellite markers used for the various species
including assay conditions, chromosomal locations, allele sizes etc. Any
supplementary databases must be accessible via the Internet by the various
laboratories. This will facilitate consistent laboratory procedures and ensure
that up-to-date information is always available to the scientists in the
regional laboratory.
(c) Participating Countries: The relevant scientists in the countries where
the samples originate should be able to connect to the FAO DAD-IS
database in FAO via the Internet and have access to the raw genotypic data
from breeds which were surveyed in their countries. If full Internet access is
unavailable (as will be the case for many countries), the data should be
available via e-mail or in the form of diskettes which can be dispatched by
secure mail.
22.
The database infrastructure required to achieve this should consist of the
following:
7
1. One central database designed as a client-server system. This will be a
component of DADIS. A powerful commercial database system such as
SYBASE or ORACLE is essential for the central server since the amount of
data will be very large and the issues of data integrity and security can be dealt
with well by such systems. This database should be fully integrated into the
main Domestic Animal Diversity Information System (DAD-IS).
2. Access to that database by all participating laboratories via the Internet.
There should be two modes of access to this database. It should be accessible via
the World Wide Web (WWW) with a secure interface so that only the four
regional laboratories can access it fully. The relevant scientists from
participating countries should be able to access all of the information pertaining
to the breeds collected in their country. There should be an access mode which
does not rely on the WWW so that laboratories and scientists without WWW
facilities can log on using standard Telnet-based packages.
3. Local stand-alone PC versions of the database for participating
laboratories to enter and validate the data as the marker information accumulates for each species. As each breed is completed the information can then
either be uploaded via File Transfer Protocol (FTP) for validation and updating
by the staff of the Animal Genetics Resource Group in FAO. The data could
also be sent to Rome using secure courier services in standard diskette form if
required.
4. A management information system would be developed to facilitate the coordination and operation of MoDAD at national, regional, and global levels.
Standard procedures and protocols would be defined and integrated in the system
to manage the flow of work at various levels. The system would also provide a
time frame for the various activities depending on the volume of data involved at
each laboratory.
Access to summary information and published interpretative data
23.
When data has been validated, analyzed according to the recommendations
in the previous section and published, it should be made available to the general
scientific community. The most convenient method to do this is again via the Internet
and where necessary by resorting to postal dispatch of diskettes.
24.
The WWW is ideally suited to the distribution of the information generated
by the MoDAD project. In most cases, the resulting information will be highly
graphical (phylogenetic trees, histograms, principal components diagrams, gene flow
maps etc.). This will lend itself perfectly to a WWW interface and this method will
provide the best method for rapid dissemination of the material to the scientific
community and to the decision-making bodies responsible for management of animal
genetic resources. A flexible form-based WWW interface should be available to the
database containing all of this information and the user should be able to structure
their queries on the basis of country, species, breed etc. It should also be possible to
retrieve the original files via FTP in Postscript or Adobe Acrobat format.
8
25.
The database containing the information for the MoDAD project should
also be fully integrated with the main DAD-IS database and the user should be able to
link seamlessly to the other component databases in the DAD-IS system.
26.
There should be a capacity for users to receive the information in other
forms also. If required, the end-user should be able to request information using email. For example, if somebody wanted all the phylogenetic data for goat breeds
available in the system, they should be able to send an e-mail message with the
following structure:
To:
From:
Subject:
Message:
[email protected]
[email protected]
INFO
Goat
Phylogenetics
27.
The system should be flexible to deal with requests by breed, country,
species etc. also. Again if required, the user should be able to receive the required
information by ordinary mail.
28.
The main database should be developed using existing databases and
experience as models. For example, a database designed for human genetic diversity
studies already exists at Yale University in the U.S. and has design components that
might be used with little modification. Other components of that database design
would need modification, but the types of information being stored will still serve as
useful models.
29.
Where possible, the database should integrate existing data on breeds and
genetic markers for a MoDAD species, even if those breeds and markers are not a formal part of MoDAD survey. Existing data is very sparse for most species included in
the MoDAD project, with the exception of cattle, sheep, pigs, chickens and horses.
However where possible, every attempt should be made to include pre-existing data.
When such data cannot themselves be incorporated into the database, at least notation
of their existence should be included in the database. Any published references should
be detailed and an abstract should be available from one of the many on-line
bibliographic databases. Such data will add to the interpretation of MoDAD data.
Costs for the computerisation of the MoDAD data retrieval system
30.
A centralised workstation, probably UNIX-based, is needed for the server
based in Rome. A Sun SPARCStation or a Digital ALPHA AXP are examples of the
type of hardware required. A large enough computer with adequate disk storage and
computing power may need to be purchased for the MoDAD database. This could be
on the DAD-IS central computer but rapidly the MoDAD database may be sufficiently
large to require dedicated machines or a larger machine. Of course, all DADIS
computers will be interconnected on the Internet and the initial machine could still be
useful as the DADIS program increases incrementally. US$ 30,000.00 should be
9
sufficient for the initial machine and a dedicated MoDAD database machine. Ongoing
hardware maintenance fees and licensing fees for the operating system, etc., can run to
15% of the purchase price each year.
31.
The commercial database system may be expensive but is essential. Only
the large commercial database systems have the data protection and data integrity
functions that are essential for the project. With current educational discounts, annual
licensing fees can run to $10,000.00 and more, depending on the size of the computer
system. (Larger systems have higher fees because the software can be used for more
applications by more individuals.)
32.
Initially a full-time database programmer will be required. Once the design
of the database is finished and implementation is nearly complete, a full-time database
manager will be required and at least a half-time database programmer for ongoing
maintenance and updating of the MoDAD database. This could be one of the
activities of a full-time programmer working on DADIS or shared among several
DADIS staff. The important point to emphasize is that one cannot just design a
database and assume that it can be used with no other effort. The computer operating
systems are updated, the database management software will be updated, and users
will have new requirements as knowledge increases and omissions in the initial design
are recognised. All of these require the continued involvement of programmers
familiar with the database to make the necessary changes; without those changes the
database will cease to function!
Comparisons between the Yale database and the requirements for MoDAD
1. The current client software at Yale is 4th Dimension on a Macintosh. 4th
Dimension may soon be available under Windows, but that is not certain.
MoDAD must have a client that operates under Windows. However, even if
the client interface needed to be translated from 4th Dimension to, say, Access,
it may still be easier to translate an existing functional system than design a
very similar system from scratch.
2. The Yale database exists only as client-server; there is no stand-alone
version. MoDAD must have a stand-alone version as well as the client server
version of essentially the same database. The WG realises from experience
with a previous stand-alone prototype of the Yale database that a stand-alone
version would work well for a database limited to 50 breeds of one species
using existing PC hardware (e.g., a Pentium-based machine). The stand-alone
version will not contain all the functionality of the Internet version, though it
will be designed to use the same basic interface and to present data which is
identical in form and content to that available on the server.
3. The Yale genetic diversity database does not yet have a WWW query
interface but other databases at Yale, designed using the same basic clientserver architecture and software, do have WWW interfaces for querying
selected data that are deemed "public". A WWW interface, however, will not
provide for every type of query and data input and editing that are required in
MoDAD. However as described above, it does offer an ideal way to make the
10
data available to a large number of researchers.
F. PUBLICATION AND REPORTING
33.
Data and analytic results from the project must be made generally available to
FAO, to governments, and to the world community in a timely fashion while protecting
the legitimate desires of the investigators in the project for recognition of their efforts.
For each species two levels of results could be relevant to deciding how to achieve these
objectives: (1) results and analyses of a subset of the breeds being studied for a species
and (2) the analyses and interpretations of the total dataset for a species.
34.
The first level will involve the raw gene frequency data for sets of breeds and
may or may not involve extensive analyses. Those frequency data are valuable for the
overall project but may not, in any particular subset, make a major scientific contribution. In any case, the realities of modern scientific publication make it extremely
unlikely that any journal will publish extensive tables of gene frequencies. Therefore,
alternatives to conventional scientific publication need to be considered. A minimum
cost means that retains recognition could be a refereed electronic journal, possibly titled MoDAD Studies managed under the auspices of FAO. Articles submitted to the
journal would have to be refereed, for example by members of the MoDAD Expert
Advisory Group, so that the journal would have scientific credibility and
thereby assure professional recognition to the investigators. Such a journal would not
preclude publication elsewhere, subject to project policies, but would provide a means
of publication for specific results that might otherwise be unpublishable irrespective of
their high intrinsic value. Costs of the journal would be minimal: some time for the
editor and secretarial assistance since articles would be managed electronically from
submission, through review and revision, to publication. Less desirable alternatives,
in situations where scientific/professional recognition is not important would be (1)
publication in FAO technical reports and (2) simply making data and results available
in electronic form accessible over the Internet. However, once data has either been
published in electronic form via MoDAD Studies or in conventional form, it must be
made available electronically for all researchers as detailed previously.
35.
The primary objective of this project requires a second level of results: a
global set of analyses on the total dataset for each species. It will be the responsibility
of FAO to conduct these analyses and to provide the initial interpretation to the
MoDAD Expert Advisory Group. The results may be included in a scientific
publication but will be incorporated into an FAO report to be considered for
acceptance by the Intergovernmental Commission on Genetic Resources for Food and
Agriculture, for increasing the effectiveness and efficiency of the Global Programme
for the Management of Farm Animal Genetic Resources.
36.
Authorship and contents of scientific papers, especially at first level of
results, will be determined by consensus of the relevant individuals: (1) a
representative of each country with a breed involved in the publication, (2) the scientists in the laboratories doing the genetic marker typing included in the publication,
(3) the scientists performing the statistical analyses, and (4) the appropriate MoDAD
coordinator(s) at FAO. The MoDAD Expert Advisory Group will oversee decisions
on publications and arbitrate disagreements. Publication of the global analysis in the
11
scientific literature is advisable, but questions of authorship are more complicated
since many more individuals are involved. A precedent in human genetics might be a
model that could be followed: authorship listed as "The (disease name) Collaborative
Research Group" with a footnote or appendix giving all investigators grouped by
institution with institutions listed alphabetically and individuals listed alphabetically
under each institution. This has worked and is accepted for large multi-institutional
projects with over 50 researchers. The suggested parallel for this project would be
"The MoDAD Collaborative Group for (species name)".
37.
As data are generated by this project, they will be stored in the MoDAD database component of FAO’s Domestic Animal Diversity Information System under the
authority of FAO in trust for all humankind. Access to the data for a species will be
open to all participants in the global project for that species but access will not carry any
rights to distribution of the data or publication of the data. Of course, raw data in FAO’s
databank remains the property of the respective countries from which each of the breed
samples was obtained. Published data and analytic results, whether in MoDAD Studies
(the proposed electronic journal) or a conventional scientific journal, are in the public
domain and FAO, governments, individuals and NGOs involved in the project will have
no control over what further statistical analyses, with resulting publication, may be done
by individuals not associated with the project.
However, to avoid serious
misunderstandings, individuals already associated with the project (for whatever species)
should still be considered bound by the requirement that consensus of the relevant
individuals (as specified above) must be obtained on any publication.
1
ANNEX 5
Economic Analysis
A. BACKGROUND
The Importance of Global Animal Genetic Resources
Livestock and livestock products play a crucial role in world agriculture, and animal
genetic resources are essential for supporting the contribution that domestic livestock
make to global food production. FAO has estimated that livestock and their products
may account for as much as 30% of the value of total world food production, although
formal estimates of this figure are not routinely compiled. Even a simple calculation
using published data for the most important livestock products traded internationally
(meat, dairy products, fibre, hides, skins and eggs), and average world prices, gives
annual production values close to $U.S. 500 billion. However, the contribution of
animals includes not only the value of livestock products (meat, dairy products, fibre,
hides, skins and eggs) but also the substantial transport, draught power, dung supply and
store of wealth functions associated with domestic animals. Thus, the true value is liable
to be even higher. Many species (sheep, for example) make use of resources from areas
such as grasslands which could not otherwise contribute to world food production.
Animal genetic resources (AnGR) support the contribution made by domestic animals to
world food production by serving as a storehouse for the wide range of desirable
production traits associated with domestic animals. Clearly, breeding improvements and
responses to changing demand conditions cannot proceed without the wealth of genetic
variation embodied in the 4000 or so breeds of livestock, representing some 40+ species.
Within breed variation is crucial for continued survival and improvement of a breed.
Many examples exist of the use of between-breed variation through cross-breeding
programmes which were able to tap useful alleles present in certain breeds. More
dramatic are the sudden disease epidemics or changing livestock management conditions
which have required emergency programmes to protect existing breeds from these new
threats.
Compared to initiatives for plant genetic resources, which began in the 1960s,
conservation issues related to domestic livestock have only recently come to the
forefront. There are many similarities between animal and plant genetic resources in
terms of genetic principals and gene action. Also for both, the vast majority of breeds or
varieties are found in developing countries. However, because plant genetic resources
are simpler to collect, conserve and preserve, different strategies for conservation are
warranted. Countries in the North and South may perceive problems involving the two
types of genetic resources differently, even though both face some measure of threat due
to reliance on one or a few breeds or varieties. Hermitte (1990) argues that there may be
greater urgency with respect to AnGRs. Plant genetic resources transferred to the North
represent a loss of control for the developing countries of the South over their indigenous
resources, but no irreversible harm is typically done. With AnGRs, the flow is the
reverse and the threats are more serious: the importation of northern breeds of domestic
livestock into the South serves to weaken and threaten the indigenous genetic base.
Ensuring the crucial breeds of livestock and their genetic information are properly
characterized and conserved is therefore imperative. This is one of the key rationales for
2
the MoDAD project vis-a-vis the conservation status of plant genetic resources.
Special Problems of Animal Genetic Resources
Hall and Ruane (1993) state that "of the 3831 breeds or breed varieties of ass, buffalo,
cattle, goat, horse, pig and sheep believed to exist or to have existed this century, 618
(16%) are estimated to have become extinct." Still, few if any species themselves have
been lost. Thus, the situation may not seem alarming when compared with estimates for
non-domestic species losses, which Barbier et al. (1994) cite as ranging from 1% to 11%
per decade, on the basis of estimates from seven different researchers. We can further
ask whether these losses of domestic livestock breeds are simply the breeds no longer
considered commercially interesting. But even so, based on present market conditions
alone, can we be sure these lost breeds are unlikely to contain some as yet unappreciated
trait or allele which might suddenly be found desirable in the future? Is it not more
realistic to assume some degree of randomness in the loss of existing breeds such that
currently desirable genetic characteristics worth conserving are inadvertently
disappearing and cannot be recovered using present technology? These questions are
pertinent to the economic evaluation of a project concerned with the study of genetic
variation, although they are made more complex in that some traits not considered
valuable now may become so in the future.
Several attributes characterize genetic resources and make the application of standard
economic analysis methodologies problematic. For instance, such resources have some
of the qualities of a public good; that is, the information they contain can be made
available to an individual breeder or country without diminishing its availability to
someone else and in some cases access to this information may be difficult to regulate.
The potential benefits associated with breed distinctiveness may not be appropriable by a
single herd owner (or country) where they do not control the sole source of genetic
material. Livestock breeds are characterized by their wide spatial dispersion, often
crossing many national boundaries; domestic animal genetic resources can therefore be
characterized as international or global resources. Thus, there is scope for what
economists' describe as “market failure”: there is likely to be a sub-optimal amount of
genetic information conserved in the absence of coordinated international efforts to deal
with the issue.
It is difficult to quantify the potential benefits associated with better information about
genetic variability with any certainty. In fact, there is liable to be a high degree of
uncertainty involved, since the potential benefits from exploiting breed distinctiveness
are of unknown size, although liable to be large, given our knowledge of previous case
study situations. We have years of experience and data from livestock breeding
programmes so that some aspects of the importance of AnGR may be estimable in
financial terms. A further consideration is that once the genetic variation unique to a
species or breed is lost, as a result of extinction, it cannot realistically be retrieved, so
there is an irreversible loss of potential value. In the absence of genetic variation
information which can help ensure efficient conservation choices (thereby avoiding an
irreversible loss of important genetic resources), conservation decisions may be made for
political and other institutional reasons, sometimes resulting in inefficiencies. These
attributes and problems characterize many environmental resources and help to explain
why they are not managed and distributed effectively by private markets (allocated
"efficiently" in economists' terms).
3
It may be tempting to think of domestic livestock as a purely commercial resource,
having little importance outside of its commercial uses. This would simplify the analysis
of genetic resource conservation in comparison to, say, wild resources, which may be
valued for many reasons completely unrelated to their genetic value. But there are
several reasons why a purely commercial perspective may be inadequate. For
instance, approximately 25% of the well-known (but poorly understood) Greenhouse
Effect is apparently attributable to methane releases into the atmosphere. Domestic
livestock are alleged to account for about 20% of these releases. Thus, breeding
improvements which might reduce methane releases would have a possible global
benefit, although not one of commercial interest. Similarly, many wild species are
progenitors of domesticated species and still represent important repositories of genetic
information which could be beneficial for livestock breed improvement (Oldfield, 1984),
If these were to be included under MoDAD eventually, then some of the thorny issues
related to the conservation of wild genetic resources may apply. It is also incorrect to
assume that domestic livestock have no cultural or traditional values outside of their
ability to contribute to world food production. Many pastoral societies cling to their
traditional grazing way of life, even though they may be under great pressure to modify
their practices, and it may be financially attractive to do so. We should also keep in mind
that domestic livestock have become integrated into the natural world around us and can
no longer be considered as somehow external to nature. Such realizations are
fundamental to the agro-ecological approaches for managing agricultural systems, and
argues in favour of avoiding sudden and dramatic changes in livestock numbers and
management.
Moreover, large-scale losses of production due to chance occurences, extinctions or
irreversible shifts in productivity may have more than just a commercial dimension if
human welfare is seriously threatened over large areas of the globe. To this we can add
that increases in livestock product consumption are likely to be concentrated in poorer
countries in the future, so that there may be a greater weight placed upon livestock
production improvements which encourage this process, and these would not be wholly
reflected in commercial or financial gains. Thus, animal genetic resource conservation
programmes may involve more than just a desire to protect food production but may
include many other objectives as well (some of which may be important in providing a
stronger rationale for GEF involvement). While these considerations are distinct from
the desire to conserve livestock breeds for their genetic diversity, they are critical in
supporting the overall rationale for global conservation efforts.
MoDAD and the Global Conservation of Animal Genetic Resources
For the proper evaluation of the project, its relationship with the broader effort to
conserve livestock genetic diversity must be clarified. For instance, what is the role of
this project within the wider GAGRMP programme? What alternatives to the project
exist to meet its objectives, or those of GAGRMP? These alternatives are perhaps more
deserving of economic evaluation than the many options noted in the background
documents for field sampling, storage and other project activities. There is still a need to
approach the economic evaluation of the project in this way, even though it may already
have been decided how to tackle the problem technically. The proposed studies of
genetic variation and particularly genetic distances under the project must still be
rationalized. As a result, the project needs to be carefully considered within the overall
4
context and costs of the global conservation of animal genetic resources. This suggests a
three-tiered structure as follows:
MoDAD: This is the project level and represents the focus for the evaluation
(see the description of objectives, activities and outputs below).
GAGRMP: This is the programme level within which MoDAD constitutes
one element or component. The FAO constituted programme has a broad
objective for
promoting the better management and conservation of AGRs but would not
itself undertake physical conservation.
Overall Global Conservation Effort: This is the level enveloping all
national and international conservation programmes and includes the
physical conservation of semen, embryos/ova, and in situ and ex situ live
breeding stock. The major costs of conservation are most likely to be
concentrated at this level and are to be guided by efforts at the previous two
levels.
The economic evaluation must analyse only the benefits and costs of MoDAD and not
confuse these with the benefits and costs at the other two levels described above. For
instance, MoDAD itself would not undertake conservation of germplasm, but only
provide information on genetic diversity to help in targeting conservation efforts, thus
increasing their efficiency. The overall benefits liable to accrue as a result of global
conservation efforts should not be attributed to MoDAD alone. Indeed, a wide range of
analyses can be undertaken relating to the economics of conserving AGRs, as cited in a
recent FAO publication concerned with the implications of the Convention on Biological
Diversity for the conservation of animal genetic resources (Strauss, 1994), but few if any
of these are relevant for an analysis of MoDAD on its own.
Before proceeding with the economic evaluation of the project, a more detailed review
of its objectives, activities and outputs would be useful. The project would attempt to
measure the genetic diversity existing within each of the 14 most important domestic
animal species and to estimate the relative genetic contribution of individual breeds to
1
the species. This information would then be used to develop national and global
strategies for managing the genetic resources of each species. The main activities of the
project involve the field-sampling of a selected number of breeds within each species (at
most 50 breeds), followed by assaying of the samples, detailed statistical analyses of the
results, publication of the findings and long term storage of the samples. The proposed
outputs of the project would include:
analyses of the genetic distances between populations and breeds for each
species, the genetic structure within breeds and breed groups, the rates of
geneflow between populations and individual-level genetic variation;
a baseline set of information on the breeds sampled in terms of various
1
These 15 species are contained within the groups: pigs, goats, sheep, cattle, buffalo, asses, camels,
horses, rabbits, lamoids, chickens, turkeys, ducks, geese.
5
assays and analyses including phenotypic performance data and
photographs;
a series of DNA stores for the breeds sampled which would be owned by the
country providing the samples but which, by signed agreement, could be
used for further research and development; and,
an increase in the number of trained personnel, especially in developing
countries, for the research and analysis of animal genetic resources and
provision of published research results via a dedicated electronic
network known as DAD-IS (Domestic Animal Diversity Information
System).
It would also be useful to clarify how the outputs of the project would be used or could
contribute to the global conservation effort. Project outputs would result in better
prediction of the potential "heterosis" or hybrid vigour arising from crosses between
breed groups, increasing the probability of immediately realizable production benefits
and permitting improved management of active breeding programmes. Better
understanding of the genetic relationships among breeds and levels of inbreeding will
similarly allow for better breeding programme management but also assist with
rationalizing breed definitions and reducing the numbers of breeds to be preserved. Such
knowledge would also aid in identifying and targeting those MoDAD and endangered
1
breeds which are most in need of conservation assistance. Finally, by enabling national
conservation programmes to recognize those breeds harbouring the greatest genetic
diversity, a buffer is provided against future environmental challenges (see the
discussion of this topic below).
One important output, pairwise distance estimates for individual breeds, could assist
with conservation programme planning and improving active breeding programmes by
allowing estimation of "diversity functions". These can be a important component in the
development of optimal conservation programmes, where maintenance of the greatest
diversity is one of the objectives. Many authors have modelled such functions, some
seeking to place a probability of extinction or value on the diversity preserved, rather
than assuming it should be simply maximized without qualification (see papers by
Weitzman, 1993; Polasky et al., 1993; Eiswerth and Haney, 1992). These approaches
may be important in providing a methodology for using genetic distance information
stemming from the project, and thereby provide a basis for analysing its potential
2
benefits. In a related sense, it is often argued that funding for global conservation of
genetic resources is likely to be constrained, so that realistically not all breeds could be
preserved, even if this were deemed desirable. Thus, conservation is liable to involve
choices among alternative species or breeds as to which can be conserved or protected
1
An example is the threatened Kuri cattle breed of West Africa, which is characterized by its unusal
adaptation to travel through flooded areas assisted by its thick, buoyant horns. Genetic studies, however,
have demonstrated that the breed is no longer pure having been subjected to a lengthy period of crossbreeding, rendering it less likely to be a respository of unique genes. As a relic breed, it is of less interest
from the point of view of conserving animal genetic resources than earlier thought.
2
There is probably a wealth of such research centred in the biological and genetics fields, not to
mention animal production science. These references, however, are taken from the economics literature.
6
(whether ex situ or in situ) and which must be left to become extinct, if necessary. Data
from MoDAD, together with information on phenotypic diversity (as an indicator of
genotypic diversity), can assist in making these decisions.
Limits to the usefulness of the information forthcoming from the project should not be
ignored in the desire to see MoDAD as a panacea for addressing genetic erosion. An
understanding of specific gene effects within breeds would not be obtained as an output
of the project, for example. Similarly, genetic distance information cannot be the sole
criterion for evaluating breed value, as this must be supplemented with efforts to identify
specific genes and markers and their chromosomal location. Finally, many of the
proposed benefits stemming from the project are liable to be indirect. Economically
important traits cannot be analysed as a component of genetic diversity studies directly.
Instead, genetic distance information allows the targeting of crosses more likely to
result in heterosis, since heterosis is correlated with greater diversity in the parents.
Moreover, heterosis itself does not guarantee non-additive improvements in productive
traits (it has no impact on purely additive traits), but is a necessary condition for these to
occur.
Conserving Animal Genetic Diversity and the Precautionary Principle
Economists have developed alternatives to the standard cost-benefit analysis (CBA)
approach, used in the evaluation of most investment projects, for situations where there
is uncertainty involved in making decisions about the preservation or loss of
biodiversity. Such techniques recognize that we are not fully knowledgeable about the
potential benefits from adopting the project, nor of their probabilities of occurence.
Although such information might be forthcoming as time passes, it is not available now,
and yet important decisions about the preservation or extinction of wild and
domesticated animal genetic resources must be made in the interim. Preference for a
risk-averse decision rule (erring on the side of caution) in such a situation suggests
1
application of the Precautionary Principle. Related to this notion is that of Option
2
Value, which suggests that society may be willing to pay a premium for the
conservation of resources whose full value may not yet be known or appreciated, in the
same sense that we purchase insurance protection as individuals. In this case, society
may wish to take the steps necessary to preserve genetic resources as long as the cost or
"premium" is not too high. Determining just what this limit might be is not easy but is
liable to involve a least-cost perspective. These concepts are well-developed within the
environmental economics field and are pertinent for the evaluation of projects like
MoDAD. For this reason, it is recommended that the project’s overall justification be tied
to the adoption of a Precautionary Principle for the conservation of animal genetic
resources.
1
Formally, application of the Precautionary Principle is defined as taking action before uncertainty
over possible environmental harm or losses can be resolved. Its use is evident in such international
agreements as the Montreal Protocol on substances likely to damage the ozone layer or the Declaration of
the Third Ministerial Conference on the North Sea with respect to the dumping of potentially toxic
materials (see O’Riordan and Cameron, 1994 for a thorough treatment of the subject).
2
More precisely, economists refer to this situation as a special case of option value referred to as
"quasi-option" value.
7
The argument for applying a Precautionary Principle hinges on the dilemna that at
present we do not know the risks or magnitudes of potential losses from doing nothing.
We can guess that these may be quite large, and that we might miss out on significant
benefits (through transgenesis, cloning, etc.) or incur severe losses (from disease) if
MoDAD were not undertaken and instead conservation proceeded on an ad hoc basis.
Thus, it is argued that the burden of proof should be shifted to those who would argue
against a safe minimum level of conservation of genetic diversity and, by extension,
against projects such as MoDAD which are critical for determining what this safe
minimum level is. As stated above, we could then characterize the costs of the project as
part of the insurance premium which we would be willing to pay to preserve the
necessary genetic variation for the future.
There are several implications of adopting the Precautionary Principle.
First, no rate of return would be calculated, because of our inability to
quantify the uncertainty or risk involved at this time and as a matter of
principle related to a shifting of the burden of proof. This is not to argue
that such analysis cannot nor should not be attempted. Indeed, such
analyses can contribute useful information to decion-making. Efforts are
underway to analyse AnGRs using standard project appraisal techniques
but are limited by the absence of key data required for the analysis Evenson,
R.E., “Establishing the Value of Animal Genetic Resources” (unpublished
paper, Yale University, undated), data which in contrast is avavailable for
the analysis of plant genetic resource conservation programmes. Even if the
necessary parameters were available for AnGR analyses, the problem of
distinguishing the benefits of MoDAD alone from the wider benefits of
1
conservation of AnGRs would remain. Similarly, Smith (1984) presents a
method for calculating the benefits of conserving AnGRs, but for assessing
MoDAD this approach would face the same obstacles as discussed for
2
Evenson’s technique.
Second, all project add-ons (those activities not essential to meeting the
above Precautionary Principle) would need to be costed and considered as
1
Evenson (undated) disaggregates the sources of growth in rice yields to show the proportion
originating from the development and maintenance of genetic resource collections (GRCs), demonstrating
that these produce benefits of about $US 200 million annually, compared to annual costs for GRC
maintenance of $US 10 million. Studies of the sources of growth in livestock production are not available
and while he attempts to measure the benefits of AnGR conservation using rice parameters, together with
the much higher accession costs for AnGRs, he is forced to concede that differences in the way in which
rare breed information is used by plant and animal breeders renders the analysis of questionable value.
However, he provides useful advice on the design and scope of the studies needed to fill the gaps.
2
Smith proposes an algorithm for calculating conservation benefits as follows:
B = P (R-Ro) - nC
where B is benefits, P is the probability a conserved stock has a higher performance of return R than
the original stock (Ro) and nC is the number of stcks conserved and unit conservation costs,
respectively (Smith 1984). Isolating the impact of MoDAD from other conservation expenditures
and obtaining the necessary parameters would be difficult.
8
distinct from the core elements of the project. For example, the collection of
semen or embryos simultaneous with DNA sample gathering, was
considered as a possible project activity. However, this would add
substantial costs to the project as well as presenting certain logistical
difficulties, and therefore was dropped. No other add-ons have subsequently
been considered.
Third, it is still necessary to demonstrate that MoDAD is the best means for
ensuring important AnGRs are conserved, that its costs constitute the least
costs for identifying these unique resources and that these costs are not too
large. Some of the necessary justification has already been provided. More
specific discussion of this aspect of the economic evaluation is provided
below.
Considerations in an Economic Evaluation of MoDAD
It has been argued so far that the Precautionary Principle should serve as the basic
economic rationale for the global conservation of animal genetic resources and, by
inference, for the project. MoDAD would assist global conservation by providing the
information necessary to ensure conservation is targeted efficiently and confined to at
least those breeds which are most likely to retain diverse genetic information, thus
reducing the global costs of conserving a minimum acceptable amount of genetic
variation. By helping to reduce the global costs of conservation and increase their
effectiveness, MoDAD would help ensure that the Precautionary Principle is adopted at
costs which are acceptable to the nations concerned. To demonstrate MoDAD’s
importance, a partial economic analysis of the project is possible and indeed necessary,
although no one technique can capture all the diverse elements of the project (thus, the
need to adopt a "partial" perspective).
Analysis of the genetic variation within or among species, breed groups or breeds is a
complex, technical undertaking. The costing and partial economic evaluation of such a
programme is likewise challenging. However, economists are developing approaches for
tackling such problems and these are liable to be useful for analysing a project such as
MoDAD. Tisdell (1990) argues that the major options for evaluating projects involving
genetic resource conservation are cost-benefit analysis (CBA), safe minimum standard
(SMS) techniques using game theory or mixed approaches. We will adopt a mixed
approach, making use of CBA and the SMS in evaluating aspects of the project.
One area not subjected to economic analysis was the evaluation of the options for
carrying out several of the project activities. For example, decisions were required as to
the most appropriate configurations for assaying and analysis of the DNA samples,
whether to be undertaken by a central lab or in a more dispersed fashion. These, along
with the other options to be assessed, were deemed to be primarily a technical concern
and it was agreed that while cost-effectiveness was an important criterion, the technical
1
experts were best suited to making recommendations.
1
For example, there is a body of evidence from human diversity studies that a minimum number of 50
individuals is required for sampling in order for the parameter estimates to be repeatable in subsequent
population samples. For this reason, the project adopted 50 as its sample size per breed and economics
9
A. Partial Economic Evaluation of MoDAD
The mixed approach adopted for evaluating the project incorporates more conservative
analytical techniques (the SMS) within a more conventional, but informal CBA
framework. The CBA technique is well known and can be described as an attempt to
quantify a project’s important benefits and costs using market prices, where these exist,
or using various valuation techniques where they do not, and to construct a benefit-cost
ratio, net present value or rate of return as an indicator of the economic viability of the
project. It is not the intention here to provide a full description of the technique, since
many of these already exist (see, for example, Hanley and Spash, 1993).
CBA used in isolation has less applicability in situations of uncertainty than in
situations where risk is involved, since in the latter case an expected or weighted value
1
for benefits or costs can be derived and used within the CBA framework. With
reference to wild genetic resource conservation, its use would not be advised or advised
only in association with other decison-making tools (as we are proposing here). As
discussed earlier, there may be some advantages to applying CBA principles to animal
genetic resource conservation problems, since these resources have an important
commercial aspect for which there are relatively good data and experience from
historical breeding programmes. Eventually, it might be possible to develop a set of
hypothetical benefits, costs and associated probabilities for use in a formal CBA, but this
will take much time and resources. Thus, only a representative or partial analysis,
making use of additional techniques (such as the SMS), and which excludes estimation
of any overall indicator of project viability, is attempted here. In effect, the analysis
constitutes more a “thought experiment” than a traditional investment project appraisal.
An economic evaluation should compare the situation with the proposed project to one
or more "without project" scenarios. This is possible in analysing MoDAD but requires
the definition of these without project situations. For instance, one hypothetical
alternative might be simply preventing all breeds from disappearing. This would achieve
the goal of ensuring no important genetic information was lost and make the costly
researching of genetic diversity unnecessary from a conservation point of view. There
are obviously numerous counterarguments -- improved breeding possibilities with the
availability of breed characterization information would be lost, the costs of conserving
all breeds would be excessive, etc. -- and these would need to be considered in a proper
analysis, thereby helping to justify the project approach adopted.
Alternatively, if we assume the global budget for conservation expenditures is limited,
then some other criteria, such as expected commercial importance, or the number of
endangered breeds in a country, could be used as a basis for making conservation
decisions about individual breeds, instead of using genetic variation information. Such
played no role in selecting this figure.
1
Risk can be described as the situation where both the magnitude of potential benefits or costs are
known, as well as their probabilities of occurrence, whereas uncertainty refers to the case where only one
or neither is known.
10
an situation is obviously vulnerable to political and other influences liable to increase the
inefficiency of the selection process, but would have lower costs associated with
targeting breeds. In contrast, MoDAD provides a consisttent and logical (though not
exclusive) information basis on which to make conservation decisions.
Finally, Oldfield (1984) points out that many of the benefits of genetic improvements
have been obtained more cheaply by increasing expenditures on antibiotics, veterinary
care, pesticides and more intensive management. This approach enables narrowly bred,
highly productive livestock breeds to be maintained, at least in the short term, without
extensive crossbreeding to introduce traits from more adapted, indigenous breeds. She
then goes on to point out the problems with this approach, including its unsustainability
and the exclusion of any of the ancillary benefits of genetic diversity studies, but it again
represents a hypothetical alternative for achieving certain objectives of the proposed
project and might be considered in a more formal CBA.
More realistically, the analysis here concentrates on two possible "without project"
scenarios, one which assumes the current situation and level of conservation effort is
more-or-less maintained and a second one assuming that an all out effort is made
to conserve the most endangered breeds from extinction and thereby ensure conservation
of some arbitrarily acceptable safe minimum level of genetic variation. Alternative
scenarios could be imagined but the two presented below are thought to capture a range
of alternatives. Both without project situations are described initially in more detail
below, and then these are used as the basis for the ensuing partial economic analysis of
the project:
(a)
Business as Usual Scenario - Conservation activities continue
more-or-less as at present, with continuing breed loss, despite the
existence of national and international (GAGRMP) conservation
programmes. It is assumed that the total resources available for
AnGR conservation activities (as distinct from investment in
MoDAD) remain essentially whether or not the project is
undertaken. Research on adaptive traits and genetic variation
continues in an uncoordinated way, with gains being made but
some opportunities lost. We also run some -- albeit small -- risk of
large losses at a national, regional or global level because valuable
genes or alleles are lost inadvertently.
(b)
Conservation of Threatened Breeds Scenario - In the absence of
MoDAD, this alternative assumes that a significantly larger
conservation effort is undertaken to conserve most threatened
livestock breeds to ensure that a safe minimum acceptable level of
genetic variation is preserved. In the absence of the information to
be provided by MoDAD, it is assumed the conservation effort
required would be much larger than if MoDAD were undertaken.
Thus, there is an implicit tradeoff between devoting resources to
MoDAD and reducing the number of breeds to be conserved, and
devoting these funds (and perhaps additional ones) to an expanded
but less targeted conservation programme. This extreme case is
intended to present an alternative to MoDAD where the global
conservation objectives are similar, but the costs differ.
11
Business as Usual Scenario
Three important benefits can be analysed in comparing the situation with the project to
one where current and planned conservation programmes proceed without the genetic
diversity information expected to emerge from the project.
First, the project would constitute a form of insurance against
unforseeable, and perhaps catastrophic, production losses which
might arise in the future as a result of disease or genetic
vulnerability. Similarly, by providing useful information about the
relationships among breeds, MoDAD could result in production
benefits, as breeders are better able to respond to changing
livestock management conditions or shifts in consumer demand.
The emphasis here is responding to the unknown, where potentially
large production values are at stake and where it is not possible to
reliably quantify these values or their probabilities of occurrence at
this time.
Second, the project should lead to more conventional production
benefits relating to known traits of economic importance by
increasing the efficiency of active breeding programmes by
increasing the amount of information available to breeders seeking
favourable crossbreeding opportunities. Experience from prior
breeding programme successes allow quantification of the typical
gains to be realized but the increased probability of these gains
being achieved, as a result of the project, cannot be estimated.
Third, a reduction in costs for active breeding programmes and
genetic research activities is liable to occur with the project, once
breed information becomes more centrally coordinated and
duplication and other inefficiences can be avoided. Little
quantification of such a benefit is possible, although some
representative savings can be cited.
MoDAD as an Insurance Premium: Application of a Safe Minimum Standard
(SMS)
Since we do not know the likelihood or magnitude of losses associated with either a
potential catastrophic event involving national or global livestock production or a
missed opportunity to exploit some hitherto unknown economic trait, we must seek
alternatives to the standard CBA approach discussed earlier. One particular approach
under the general framework of the Precautionary Principle is the Safe Minimum
Standard (SMS) of conservation, originating with Ciriacy-Wantrup (1952). The term
originally referred to a conservation strategy applicable to wild species with a critical
threshold size below which populations could not recover; its aim was to ensure at least
this minimum population size was maintained. Such an approach could equally apply
here, to livestock genetic resources. The SMS is usually presented as a decision
12
technique making use of game theory, which adapts easily to situations where the
probabilities of gains and losses are not known. Game theory, therefore, provides a
useful framework for analysing decision problems involving the Precautionary Principle.
In effect, the SMS would pit the known and relatively low costs of maintaining a safe
minimum supply of genetic variation against the uncertain but potentially large costs of
not ensuring adequate genetic variation is preserved. The SMS, therefore, would be the
preferred strategy providing the costs of implementing the it are acceptable. While it is
not the intention to describe the approach in detail here, an example derived from Smith
(1984), who effectively used this approach without calling it such, may serve to illustrate
its usefulness for the problem at hand. Smith was concerned about conserving livestock
genetic resources in the U.K. over a 20 year period. He indicated annual production
values of about £5.5 billion for the livestock products industry and annual conservation
costs for cattle, sheep, pigs and chickens vary according to the technique employed. The
following three conservation options were costed at the following rates (£ 1984) :
-
live breeding stock: ........................ £620,000 per year;
frozen semen: ...............................
£102,000 per year;
frozen embryos (cattle and sheep)....... £230,000 per year.
He compares these conservation costs to a potential catastrophic event resulting in losses
of an arbitrary one percent of the total annual production value, on the assumption the
proposed conservation programme would prevent these losses occurring. He then argues
that if such benefits are liable to be achieved via conservation, the costs of conservation
would be easily covered. To place this within an SMS framework, we create a loss
matrix, which shows the potential losses incurred under various states of nature. For
ease of illustration, let us assume that there are two potential states, one involving a
major new disease which begins reducing the productivity of a key livestock breed at a
rate equal to one percent of the total annual value of U.K. livestock production.
However, the disease can be combatted through selection of a resistant gene available
from a genetically unique breed which was targeted for conservation as a result of the
project.
To Smith's conservation costs we must add an allowance for the project costs
attributable to the U.K., which would lead to better targeting of the conservation effort
and, therefore, greater assurance that the most genetically unique breeds were
maintained. Adjusting for the year of expenditure, the U.K.'s share of global domestic
livestock breeds (5%), and taking account of MoDAD's approximate present value cost
1
of about $U.S. 9 million, this would result in added expenses of about £60,000 per year.
The loss matrix, using Smith's data, is presented below.
1
The values are calculated as follows: England, Scotland and Wales contain 159 of the 3,213 extant
livestock breeds recorded in the FAO database (Hall and Ruane, 1993); assuming the project cost is
annualized at a 12% discount rate over 20 years, the resulting cost attributable to the U.K. would be about
,60,000 per year. No adjustments have been made to the present value project costs used in the annex to
convert these to economic terms. However, it is believed such an adjustment would not change the results
much.
13
Loss Matrix for U.K. Livestock Genetic Resource Conservation (£
thousands/year)
Strategy
SMS
No SMS (extinction)
Maximum Loss
State A
No Disease
State B
Disease Epidemic
£162 - £680
£162 - £680
£680
0
£55,000
£55,000
Source: Smith, 1984
The decision rule applied under this type of game is referred to as minimax loss, since
we select the strategy which minimizes our maximum loss. In this case, the maximum
loss is associated with not selecting the SMS and is valued at £55 million annually.
Thus, without specifying the probabilities involved, we have arrived at a hypothetical
1
decision to conserve the necessary genetic resources by formally applying the SMS. The
minimax strategy is considered very risk averse but then this is likely to be best suited to
the conservation of genetic resources.
Application of the minimax loss strategy is problematic if we are dealing with potential
windfall gains arising from, say, selection of a trait which brings a large productivity
improvement, made possible only by undertaking the project. This is more like a
"lottery" game (since we pay the premium in hopes of a large possible gain), in contrast
to the "insurance" game presented above. If lottery type situations are liable to be
important (and one would expect they might be in this case), then a revised strategy,
2
known as minimax regret can be used.
Extending the above national example to the global level at which MoDAD needs to be
considered is relatively simple, although the data needed for achieving this are sparse.
The present value costs of MoDAD, estimated at about $U.S. 9 million are added to the
global costs for animal genetic resource conservation, which are presently unknown but
3
liable to range from $U.S. 20 to 50 million in present value terms. If a conservative
combined cost for appropriate national and global conservation programmes, together
with MoDAD, should cost $U.S. 50 million, these costs would represent about 0.01% of
the very conservative estimate for the annual global value of selected livestock products
1
Formally, this mathematical technique is referred to as game theory, for which there is a wide range of
applications beyond that indicated here.
2
This game strategy involves specifying the possible gains or losses from not selecting a particular
strategy and terms these "regret". When applied to both the lottery and insurance type games, the minimax
regret strategy results in selection of the SMS.
3
Such a calculation is obviously problematic. Here we have assumed a global present value cost for a
mixed strategy of cryogenic preservation of semen combined with live breeding animals averaging $U.S.
100,000 per breed (using a standard project discount rate of 12% and a time horizon of 20 years). The
number of breeds conserved in this way is assumed to be from 200 to 500, but other ranges could equally
be considered without changing the results substantially. Sources for the estimates are provided in a later
section.
14
calculated earlier ($U.S. 500 billion per year). If MoDAD alone were to result in the
avoidance of a single catastrophic event, this event would need to entail losses of $U.S.
1.2 million per year for 20 years (using a discount rate of 12%), for the project to pay for
itself. This averted "loss" works out to 0.00024% of the annual global production value
referred to above.
To help illustrate the applicability of an SMS approach, a few examples can be cited.
Catastrophes can and have occurred in the global livestock industry and retaining
sufficient genetic diversity is an important aid in combatting such occurences. One of the
most significant historical examples of an unforseen catastrophe is the rhinderpest
epidemic in Africa at the turn of the century. Introduced from Asia in cattle brought to
Ethiopia by Italian soldiers, rhinderpest almost wiped out Africa’s indigenous cattle
population, although exotic zebu breeds were resistant to the disease. A similar
occurence in the future could be potentially avoided with the assistance of the genetic
information stemming from the project. Ironically, some of the same indigenous breeds
(such as the West African shorthorns) are highly resistant to trypanosomiasis, or
"sleeping sickness", while the popular, introduced zebu breeds are not. Thus, there may
be opportunities in the future to breed this resistance into the exotic cattle population,
and information provided by MoDAD could be helpful. Further, prospects for global
climate change may mean that new adaptations may be needed for livestock to withstand
greater extremes of temperature and rainfall, again requiring that a diversity of genetic
resources be available. As a final example, recent changes in the laws governing the pig
industry in the U.K., in response to consumer demands, have required that pig farmers
shift from indoor production systems to outdoor ones. This modification in the
production system requires new digestive adaptations in pig breeds to accommodate
grass feeding and the ability to partition more nutrients to fat will be needed for
weathering colder temperatures. Other examples could be cited, but the above should
serve to illustrate the point that we must retain sufficient animal genetic variation not just
to avoid catastrophes but to allow breeders to respond to unexpected shifts in the
demand for desirable production traits.
The main difference between the CBA and SMS approaches is in placement of the
burden of proof, as discussed earlier. In the CBA approach, this lies with the
conservation project: it must be demonstrated that preservation of genetic resources
pays. Under the SMS, the burden of proof instead rests with those opposing conservation
to demonstrate that the costs of preserving a safe minimum level of genetic variation are
intolerably high. The evidence presented in the previous paragraphs suggests that these
costs are not very high in relation to the production values being safeguarded.
Conventional Production Benefits: An Example from Crossbreeding of Dairy
Cattle
MoDAD would produce information about breed diversity which would assist breeding
programmes with identifying suitable matches for cross-breeding, thereby increasing the
prospects for heterosis. While the magnitude of potential benefits, across the full range
of globally important species and production traits, would be impossible to quantify
precisely, an example from the dairy industry in the tropics could be regarded as
representative. Cunningham and Syrstad (FAO, 1987) provide an extensive review of the
literature concerning crossbreeding of Bos taurus and Bos indicus species of cattle for
milk production. Using crossbreeding results from a range of countries in Asia, Africa
15
and Latin America, the authors show that the gains from crossbreeding have averaged
about 1,000 litres per lactation, representing an increase of about 100% in comparison to
average indigenous breed production. Typically, milk is not an internationally traded
commodity in its raw form, but FAO collects local milk prices and these can be used to
value the milk production benefits associated with these crossbreeding programmes.
Producer price information is presented below, along with the approximate value of
benefits in U.S. dollars per lactation. The costs of producing, collecting, transporting and
distributing incremental milk production are not known, but an arbitrary figure of 50%
of the price is deducted to take account of these costs.
Hypothetical Production Benefits from Crossbreeding Dairy Cattle Species
Countries
Producer Price
for Milk
"Net" Producer
Price for Milk
(U.S. cents/litre)
Production Gain
from
Crossbreeding
(litres/lactation)
Hypothetical
Production
Benefit
($U.S./lactation)
(U.S. cents/litre)
India
18.2
9.1
1,000
91
Indonesia
20.2
10.1
1,000
101
Philippines
30.4
15.2
1,000
152
Thailand
30.0
15.0
1,000
150
Nigeria
25.0
12.5
1,000
125
Source: FAO, personal communication
The global benefits from dairy cattle crossbreeding programmes are not known, as the
total number of crossbred animals would be difficult to estimate. Actual on-farm milk
production benefits are similarly liable to be difficult to calculate since
management and genetic characteristics are likely to be highly variable. Nonetheless, a
rough estimate of the potential global benefits from crossbreeding of Bos taurus and Bos
indicus cattle can be attempted, using proposed cross-breeding targets for India, since
this country alone dominates efforts in this area. Cunningham and Syrstad (1987) cite a
proposal to increase the number of crossbred dairy cattle in India to 20 million, which
might more realistically serve as a conservative global target (total world dairy cattle
numbers exceed 100 million). Adjusting this figure to exclude non-lactating females and
males (say, by reducing it 50%), and assuming a conservative benefit from crossbreeding
of $US 50 per lactation (to represent farm-level conditions and take account of
crossbreeding programme costs), the potential benefit could be as much as $U.S. 500
million per year. It should be emphasized that such an estimate is extremely crude, but
even if it is correct on an order of magnitude basis, it is clear that production benefits
from crossbreeding programmes could be quite substantial in the dairy industry.
Comparing such benefits to the project costs for MoDAD ($US 9 million), suggest that
the project need make only a small contribution to the benefits of current active breeding
programmes (certainly less than 1%) to generate benefits which would offset its costs.
16
Benefits from Greater Efficiency and Reduced Costs in Active Breeding and
Research
Benefits may not just accrue from newly realized production gains, as described in the
previous section, but from reduced costs for achieving the production benefits of ongoing breeding programmes. By improving the dissemination of breed characterization
information and by reducing duplication and the other inefficiencies associated with
highly decentralized, uncoordinated crossbreeding research programmes, the project
would reduce the costs of achieving a given improvement in a production trait. Thus,
production improvements liable to be achieved regardless of the project would be
obtained at lower cost. This benefit is therefore distinct from and additive with the
benefits described above.
While it is impossible to quantify the potential benefits associated with these cost
savings, some idea of the magnitudes involved can be highlighted. For instance, progeny
testing of bulls is required to assess their breeding value for improved milk production.
In the absence of information about genetic distinctness, active breeding programmes
may need to carry out additional progeny testing of bulls. Each test costs approximately
$US 80,000, so that the potential savings from reducing the number of tests carried out
globally could be quite substantial. This argument, of course, ignores any other potential
cost savings likely to accrue to active breeding programmes as a result of the project.
Nonetheless, considering this one cost element alone, it would only require a savings of
about 15 progeny tests per year to fully offset the $US 9 million present value cost of the
project.
Conservation of Threatened Breeds Scenario
There is a consensus among researchers concerned about the world V DQLPDO JHQHWLF
resources that good management of these resources is not possible under present
conditions for cost and logistic reasons. With a global total of some 4,000 breeds or so,
global and national conservation efforts simply cannot cope. As a result, there is a need
to reduce the total, from the perspective of maintaining adequate genetic variation, to
something like 800 to 1,000 breeds. The project would simplify and reduce the costs of
global and national livestock genetic resource conservation by providing information
which would help identify the most genetically diverse breeds. Recognizing this
situation, this "without project" scenario assumes that the necessary efforts to conserve
all important livestock genetic resources proceeds without the information about genetic
1
variation stemming from the project. It would require that a much larger global
conservation programme be funded than would be necessary were MoDAD undertaken;
yet in either case virtually all critical genetic variation would be assumed to be retained
for posterity. Here we abstract from the additional benefits associated with the project
and focus instead on whether the project, together with a much smaller global
conservation effort, presents the least cost alternative for conserving a minimum
acceptable level of animal genetic resources.
1
While we have referred to this as an alternative "without project" scenario, we could equally have
considered it as an alternative to the project, both options being measured against the first "without project"
scenario.
17
The above discussion implies that with MoDAD we could maintain essentially all the
important genetic variation with a much smaller number of breeds, potentially resulting
in reduced total AnGR conservation costs. However, at this stage we do not know how
much smaller this number of breeds would be and therefore a sensitivity analysis of a
range of possibilities would be appropriate. A notional benefit could be approximated by
comparing the costs of global conservation for a number of combinations of breeds
conserved under the two alternatives. The cost savings accruing to the project would
depend upon how many fewer breeds need be conserved.
The first step in undertaking the analysis is calculation of average conservation costs per
breed. Estimating such a figure is inevitably challenging and open to criticism. A review
of conservation programme costs for Germany (Lömker and Simon, 1994), Italy (EAAP,
personal communication), the U.K. (Smith, 1984) and Canada (FAO, personal
communication), using a combined approach of cryogenic preservation of semen and
live animals (in situ), suggests these would range from $US 150,000 to 200,000 per
breed in present value terms, using a discount rate of 12% over a 20 year period. These
costs include collection, storage and reactivation costs for semen, along with incentive
payments required for in situ live animals to compensate for the lower production
revenues associated with conserved breeds. Conservation costs in developing countries
were not available, but discussions with Working Group members knowledgeable of
conservation in developing countries indicated these would be lower, by perhaps onehalf to two-thirds. This range suggests present value conservation costs in developing
countries of approximately $US 50,000 to 75,000 per breed. To arrive at an
appropriately weighted global cost figure, the distribution of livestock breeds by zone
(developed versus developing) were used. Since the world's livestock breeds are split
approximately equally between the two zones, a rounded figure of $US 100,000 for the
1
average present value cost per breed was selected.
Even should MoDAD not be undertaken, it is not realistic to assume that all livestock
breeds would be conserved under a concerted global conservation programme. Instead, it
is assumed here that such efforts would concentrate on MoDAD and threatened breeds,
which FAO estimates at more than 700 breeds based upon the incomplete, preliminary
information available in their global databank. Using this figure as a median for the
number of breeds actively conserved under "without project" conditions, alternative
sensitivity cases of 500 and 1,000 were also considered. Assuming the numbers of
breeds requiring active conservation would be lower with the project undertaken,
sensitivity cases of 200, 350 and 500 were analysed. It should be emphasized that these
figures are hypothetical and could be refined with sufficient input from experts in the
area of animal breeding and conservation. Nonetheless, the important consideration is
not the absolute numbers of breeds conserved, but the fewer number of breeds requiring
conservation as a result of the information provided by MoDAD. The notional costs for
each hypothetical number of breeds actively conserved, whether under a MoDAD or No
MoDAD scenario, are presented in the table below.
1
A more desirable weight might be the distribution of threatened or MoDAD breeds by zone. However
the information on such breeds is incomplete and the numbers of known MoDAD and endangered breeds
are highly skewed towards the developed countries where data are more available.
18
Notional Costs for Global Conservation of Threatened and MoDAD Livestock
Breeds Under MoDAD and an Alternative Conservation Scenario (No MoDAD)
(Present Value Terms, $US million, 1995)
Project
Alternative
200 Breeds
350 Breeds
500 Breeds
700 Breeds
1000 Breeds
9
9
9
-
-
- conservation
costs
20
35
50
-
-
- total costs
29
44
59
-
-
No MoDAD
- total costs
-
-
50
70
100
MoDAD
- project cost
Source: see text
Taking the notional costs provided in the table above and presenting these in a matrix
form showing global conservation cost differences for each pairwise comparison of the
number of breeds conserved, results in the following table. The figures shown below can
be interpreted as indicative "net" benefits of the project, based upon the numerous
assumptions made.
Indicative Net Project Benefits based upon Sensitivity Analysis of the
Number of Breeds Conserved ($US million, 1995)
Project Alternatives
No MoDAD
500 Breeds
No MoDAD
700 Breeds
No MoDAD
1000 Breeds
MoDAD
- 200 Breeds
21
41
71
- 350 Breeds
6
26
56
- 500 Breeds
(9)
11
41
Source: see table above
The results indicated in the table above suggest that from a least-cost perspective, and
only taking account of the objective of conserving a safe minimum acceptable amount of
animal genetic resources, the project is liable to generate substantial benefits. That is, it
would appear to be the preferred route for achieving this objective as long as it results in
a modest reduction in the number of breeds requiring active conservation and therefore
generates savings in notional global conservation costs. At minimum, the costs used
above ($US 100,000 per breed) suggest that if MoDAD can bring about a reduction of at
least 12 breeds per year in the number targeted for active conservation efforts, then the
19
project will have paid for itself.
There is another dimension to the comparison of the two alternative scenarios considered
(MoDAD versus No MoDAD). Without objective criteria to guide global conservation,
there is no guarantee that conservation programmes worldwide will actually target the
right breeds or be undertaken at all. FAO, for example, is often besieged by requests for
last minute assistance to save endangered breeds in various countries, for which the main
justification may be unrelated to the breeds distinctness or importance in global diversity
terms. Many countries may be forced to undertake expensive breed conservation
programmes for political and other reasons, and because they have no objective basis to
allocate their scarce conservation funds. Other countries may find it easy to neglect
AnGR conservation activities altogether because of the lack of objective criteria with
which to target breeds and thereby justify the expenditure. MoDAD would assist in
providing these criteria.
Economic Evaluation of MoDAD and GEF Criteria
A further point relating to the preliminary economic evaluation should be made with
respect to GEF criteria. The methodology adopted above, while consistent with standard
investment project assessment techniques, requires some modification for GEF funding
consideration. GEF is principally concerned with the financing of projects having a net
positive global benefit, but which are not viable at a national level. A failure of many
environmental projects to generate benefits which can be captured by the source country,
because these benefits may be global public goods or be dissipated internationally and
unappropriable, accounts for how such situations may arise. Thus, it makes good sense
for GEF to help finance such projects by, in effect, compensating countries for the global
environmental benefits they cannot capture, thereby encouraging the undertaking of the
project in question. A diverse literature has sprung up to help clarify the conditions under
which GEF-type funding is appropriate and especially for the treatment of so-called
"incremental costs", which refer to the added domestic project costs which the country
would not be willing to pay given the limited benefits it would be able to capture (Brown
et al., 1993).
This analytical framework does not wholly apply to the MoDAD case, since MoDAD
would be undertaken as an international project in support of member countries’ own
conservation efforts. However, the GEF criteria can be readily applied to MoDAD by
focusing on the potential savings liable to accrue to individual countries (of the order
demonstrated in previous sections) and the global "public good" benefits of the project.
Clearly, few countries would be inclined to undertake the genetic diversity studies
comprising MoDAD on their own, both for cost, public good (see the discussion of this
problem earlier) and scale reasons. Even if they do, their efforts are liable to be
inefficient and uncoordinated from a global perspective, and to result in pressure on
international agencies to provide conservation assistance in an ad hoc manner.
Moreover, possible extra-national or global benefits from a coordinated effort would be
lost if each nation were to go it alone. Instead, such an effort is best situated at the
international level, which internalizes all livestock breeds and achieves substantial
"economies of scale" (for example, there is no need to duplicate breed analyses simply
because they occur simultaneously in different countries).
A carefully considered analysis to meet GEF conditions might compare the global
20
programme (GAGRMP combined with MoDAD) to the situation where national
livestock genetic resource conservation programmes are pursued in isolation.This would
involve estimating the incremental global benefits available to countries participating in
GAGRMP (with MoDAD), together with the aforementioned cost savings. While not
attempted here, the results of this analysis would clearly demonstrate the global net
benefits accruing to the project and would aid in defining an appropriate share of the
costs to be supported by GEF. Using the strict GEF criteria of financing incremental
costs, its share would be the costs attributable to individual nations of participating in
MoDAD, less the immediately realizable domestic benefits. The latter would exclude the
global public good-type benefits from the international sharing of information stemming
from the project which cannot be captured by any single nation.
Distributional and Incentives Issues
Evaluation of the production and related benefits of MoDAD represent only one area in
considering the its desirability and potential success. For example, there may be issues
surrounding the intellectual property rights associated with the information compiled
by MoDAD and important political considerations respecting access to this information.
This problem of property rights associated with biodiversity (however defined) is well
known, whether that of property rights over the pharmaceutical value of MoDAD plants
with important medicinal properties or whether non-residents of tropical areas have
rights with respect to the buildup of atmospheric gases due to tropical deforestation.
These issues are critically important and must be treated in the project evaluation.
Similarly, the distribution of benefits and costs of the project must be carefully
analyzed and it is certain that this exercise will highlight the potential incentives for
countries to participate in the project and be related to any discussion of the property
rights question.
Addressing the distributional issue first, we can consider the contrasting cases where
countries have either large or small animal genetic resource endowments. On this basis,
one might expect the benefits of the project to be unevenly distributed, favouring the
latter; countries with fewer distinct livestock breeds (assuming the presence of a much
larger number of less distinct breeds) would stand to save substantially since they could
target a much smaller number of breeds to be conserved than otherwise anticipated. In
the former case, participation in the project would presumably result in few savings,
since fewer indistinct breeds could be screened out. However, this view misses an
important benefit available to countries having greater genetic diversity in their livestock
breeds: they would benefit from the project proportionately more from domestic
breeding applications and be able to market their breeds internationally with more
certainty of their desirable genetic properties. This rationale may be important in
convincing some countries to participate in the project, depending on the share of DNA
field collection and storage costs to be borne by individual countries. Obviously, those
countries having a greater number of breeds would incur higher collection and storage
costs, and might wish to benefit commensurately from the project, if these costs are
financed by the countries themselves. In contrast, core project costs, which could be
allocated more flexibly, might take the potential distribution of benefits into account; the
above discussion implies that this could proceed on a relatively equitable basis if the
project benefits are not likely to be skewed significantly, or could be allocated so as to
offset an imbalance in collection and storage costs.
21
Participants in the project would not just benefit in terms of their immediate domestic
breed improvement programmes but would have access to the global database (DAD-IS)
to supplement those benefits (the so-called "global public good" benefits). Many
countries, particularly in the developing world, would also benefit from the transfer of
technology and from training stemming from the use of local teams in the sampling,
assaying and analysis of the DNA samples. Such benefits would help to alleviate any
concerns that the project was simply "robbing" developing nations of their genetic
patrimony, or otherwise interfering with their intellectual property rights, as may have
taken place with some plant genetic resources. Incorporating local expertise would not
only lower project costs but provide important distributional benefits as well.
Incentives to participate in the project may be a critical determinant of its success,
regardless of the economic arguments which might be marshalled in its defence. There is
liable to be a mixed set of incentives facing many countries. Some may have vested
interests in the promotion of certain breeds and may not be willing to accept the results
of genetic studies which undermine a breed’s perceived importance for conservation.
Similarly, countries may be reluctant to contribute genetic material to a global
programme, despite the legal safeguards that might be established. In contrast, some
nations might view participation in the project as an opportunity to obtain useful breed
characterization information originating in other countries, without making any
contribution themselves. This latter incentive is known as free-riding and is often
associated with situations involving public goods.
One area of related concern is the selection of species and the inclusion or exclusion of
geographically specialized species, such as the lamoids and yaks. These species are of
great regional importance in areas such as South America and the Central Asian
highlands, but of relatively little significance globally. The extent to which such species
are included under MoDAD (both those cited would be) may be an important
determinant of the distribution of the project’s benefits on a regional or even national
basis and have a bearing on the incentive to participate in the project for some countries.
The incentives to participate in and support the project may also have a temporal
dimension. Immediately realizable benefits are likely to be associated with
improvements in on-going active breeding programmes and adaptations to pressing
environmental and demand conditions. These would be short-term benefits and would
presumably be the main attraction of the project for many countries, liable to be
concerned with immediate, pragmatic benefits rather than long-term, speculative ones.
By the latter, we might refer to prospects for microbiological advances, such as
transgenesis and other forms of genetic engineering. Lacking the means to conceptualize
such benefits liable to arise sometime in the future with varying degrees of uncertainty,
many countries may undervalue the benefits of participating in the project. It will be
important to "sell" these benefits and assist countries with understanding how they might
one day benefit from technological advances in genetic engineering.
22
D. PROJECT RISKS
Much was made in earlier sections about uncertainty and its potential costs if the project
is not undertaken. In a balanced economic evaluation it is also necessary to consider the
risks associated with the project itself. While these are likely to be substantially less than
the uncertainty relating to not managing and preserving animal genetic resources
appropriately, they should not be ignored. For instance, the effort required to organize,
consolidate, store and disseminate the results of the project’s analyses is immense. There
is some risk that such a global organizational effort might founder, for reasons of scale
or if participating countries are not able to agree on protocols governing key procedures.
As pointed out above, individual countries face mixed incentives for participating in the
project and despite best efforts, it may be difficult to overcome some of the
disincentives, regardless of the organizational prowess of the project staff.
There may also be technological risks. The use of microsatellite markers as a means of
characterizing breeds is still a reasonably new technology and difficulties with the
technique (for instance, locating markers in some of the species not yet tested), must be
addressed. However, considering that MoDAD will require some time to be
implemented, advances are likely to be made in the development of the microsatellite
marker technique. The species for which markers still need to be developed may be
addressed following the completion of assaying on the species for which markers are
currently available. Other potential limitations of the proposed project analyses or
outputs were cited earlier.
E. FOLLOW UP ANALYSES AND DATA REQUIREMENTS
Data
The economic evaluation of MoDAD contained in this annex was constrained by limited
data and time so that the analyses presented are necessarily preliminary. Better data and
further consultation with livestock industry experts could be expected to improve them.
The main areas for enhancement related to data availability would be the following:
Preparation of a more credible estimate of the value of livestock production
globally would assist not only with raising the profile of the industry with
prospective project funders, but would be useful for the application of a
Safe Minimum Standard (SMS) and for placing the project costs within the
overall context of the industry’s importance. Any estimate should try to
include not only commercially-traded livestock products but subsistence
production and non-tradeables such as dung, transport and draught power.
Conservation programme costs, both national and global, are critical for
assessing the potential benefits of the project. While the figures used are
expected to be reasonably reliable, a more thorough review of such costs,
especially for developing countries, would be useful.
Very crude estimates of the immediately realizable production gains and
breeding programme cost savings were offered. These estimates would
benefit from additional information about such gains and savings (Are these
representative? What are the likelihoods of achieving such benefits? What
23
other related benefits might be obtained and what is their value?).
Some of the analyses related to the GEF criteria might be undertaken,
especially an assessment of the possible national versus global benefits, to
assist in estimating the "incremental costs" associated with the project.
The first two sets of estimates could be undertaken as a short consulting contract and be
completed within a relatively short period of time. Some data mentioned under the third
and fourth points may be available in existing documents or in the literature, or
discussions with animal breeding experts may suffice. The final point should be
reviewed with GEF and would be integral to an application for funding under the
programme.
Formal Cost-benefit Analysis
A full, formal cost-benefit analysis (CBA) involving estimation of a rate of return (ROR)
was not recommended for MoDAD, for reasons cited earlier. Yet should it be deemed
necessary, a highly generalized evaluation approach using CBA might be attempted
using the methodology proposed by Evenson (undated), which was described earlier.
Such an approach would require large amounts of information not presently available
and so would necessarily involve many simplifying assumptions. For this reason, and
because there exists a growing consensus that global environmental problems involving
large amounts of uncertainty not be analysed in this way, such an effort would be
subjected to criticism and might be controversial.
Alternative Methodologies
An alternative analytical approach, one which is suitable if several project alternatives
are identified, is Multicriteria Analysis (MCA). This technique is best suited when
there are a number of recognized criteria, besides monetary benefits and costs, to be
considered in evaluating the proposed project and its alternatives. Some authors (Van
Pelt, 1993 and Munda et al., 1994), would argue that MCA is a more effective tool than
CBA or cost-effectiveness analysis, since it can cope with unquantifiables in project
planning and is better suited to situations where political or other non-economic criteria
are important. Van Pelt, for instance, is especially keen to apply it to situations where
sustainability is a big factor, since standard CBA may not properly account for it.
MCA relies on there being a set of project or activity alternatives (options), which must
be evaluated on the basis of a range of criteria. Often, the most important criterium is an
economic or financial one, but it is supplemented by a number of other criteria. Planners
must decide on a range of questions in order to carry out an MCA analysis. These
include:
-
the alternatives and criteria to be applied, as discussed above;
a grading scale for the non-quantifiable criteria;
a set of weights which would be applied to the various criteria;
an acceptable aggregation and decision procedure.
The evaluation of MoDAD lends itself in some ways to the use of MCA since it could be
24
construed as involving more than one alternative for achieving the same objective (see
the economic evaluation) and there is a readily available network of knowledgeable
experts already in place (the MoDAD reference group as well as the Working Group
members). The latter is important because the use of a focal group setting is ideal for
applying MCA, and this is possible using electronic mail. An initial effort was made to
use the technique for selecting and ranking the domestic species to be included in the
project by the Working Group during its meeting in Rome. The methodology used is
reported elsewhere in the report.
References
Barbier, E., Burgess, J.C. and Folke, C. 1994. Paradise Lost?. Earthscan, London.
Barker, J.S., Bradley, D.G., Fries, R., Hill, W.G., Nei, M. and Wayne, R.K. 1993. "An
Integrated Global Programme to Establish the Genetic Relationships Among the
Breeds of Each Domestic Animal Species". Animal Health and Production Division,
FAO, Rome.
Brown, K., Pearce, D., Perrings, C. and Swanson, T. 1993. Economics and the
Conservation of Biodiversity. Working Paper 2. Global Environment Facility, The
World Bank, Washington.
Ciriacy-Wantrup, S.V. 1952. Resource Conservation: Economics and
Policies.Division of Agricultural Sciences, University of California, Berkeley.
Cunningham, E.P. and Syrstad, O. 1987. Crossbreeding Bos indicusand Bos taurus for
Milk Production in the Tropics. FAO Animal Production and Health Paper 68. FAO,
Rome.
Eiswerth, M.E. and Haney, J.C. 1992. "Allocating Conservation Expenditures:
Accounting for Inter-Species Genetic Distinctiveness". Ecological Economics. 5:235249.
FAO. 1995. "Global Project for Research on Animal Genetic Resources". Draft
Identification Report. Rome.
Fitzhugh, H.A. 1990. "Institutional and Legal Aspects: Recent Developments and
Future Prospects". In Animal Genetic Resources: A Global Programme for Sustainable
Development. FAO Animal Production and Health Paper 80. FAO, Rome.
Hall, S.J. and Ruane, J. 1993. "Livestock Breeds and their Conservation: A Global
Overview". Conservation Biology. 7 (4): 815-825.
Hanley, N. and Spash, C. 1993. Cost-Benefit Analysis and the Environment. Edward
Elgar, Brookfield, Vermont.
Hermitte, M.A. 1990 "Legal Questions Relating to the Preservation and Use of Animal
Genetic Resources". In Animal Genetic Resources: A Global Programme for
Sustainable Development. FAO Animal Production and Health Paper 80. FAO, Rome.
25
Lömker, R. and Simon, D.L. 1994. "Costs of Inbreeding in Conservation Strategies for
Endangered Breeds of Cattle". In Proceedings of the 5th World congress on Genetics
Applied to Livestock Production. Vol. 21. University of Guelph, Guelph, Ontario.
Munda, G., Nijkamp, P. and Rietveld, P. 1994. "Qualitative Multicriteria Evaluation
for Environmental Management". Ecological Economics. 10: 97-112.
Oldfield, M.L. 1984. The Value of Conserving Genetic Resources. National Park
Service, U.S.D.I.. Washington, D.C.
O'Riordan, T. and Cameron, J. 1994. Interpreting the Precautionary Principle.
Earthscan, London.
Polasky, S., Solow, A. and Broadus, J. 1993. "Searching for Uncertain Benefits and
the conservation of Biological Diversity". Environmental and Resource Economics. 3:
171-181.
Smith, C., 1984. "Economic Benefits of Conserving Animal Genetic Resources".
Animal Genetic Resources Information. 3: 10-14.
Smith, C., 1984. “Genetic Aspects of Conservation in Farm Livestock”, Livestock
Production Science, 11(1984) 37-48.
Strauss, M.S. 1994. Implications of the Convention on Biological Diversity. Animal
Production and Health Division. FAO, Rome.
Tisdell, C. 1990. "Economics and the Debate about Preservation of Species, Crop
Varieties and Genetic Diversity". Ecological Economics. 2: 77-90.
Van Pelt, M.J. 1993. "Ecologically Sustainable Development and Project Appraisal in
Developing Countries". Ecological Economics. 7: 19-42.
Weitzman, M.L. 1993. "What to Preserve? An Application of Diversity Theory to
Crane Conservation". QJE. February: 157-183.
1
ANNEX 6
Estimated Project Costs
2
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Expenditure Accounts Project Cost Summary
Local
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
Total Recurrent Costs
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
(US$ ’000)
Foreign
Total
Local
(US$ ’000)
Foreign
Total
%
% Total
Foreign
Base
Exchange Costs
262.0
66.9
196.0
524.9
1,047.8
1,299.9
84.0
2,431.7
1,309.8
1,366.8
280.0
2,956.6
262.0
66.9
196.0
524.9
1,047.8
1,299.9
84.0
2,431.7
1,309.8
1,366.8
280.0
2,956.6
80
95
30
82
16
17
3
37
1,644.4
76.2
582.0
28.6
717.0
34.0
879.7
3,961.8
4,486.7
448.7
1,381.9
6,317.3
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
1,644.4
76.2
582.0
28.6
717.0
34.0
879.7
3,961.8
4,486.7
448.7
1,381.9
6,317.3
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
100
85
50
15
20
23
45
45
16
40
20
1
1
7
2
18
14
63
100
10
20
130
3
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Expenditure Accounts by Years -- Totals Including Contingencies
(US$ ’000)
1995
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
Total Recurrent Costs
Total PROJECT COSTS
Totals Including Contingencies
1996
1997
1998
Total
596.9
500.5
172.5
1,269.8
606.1
474.6
107.0
1,187.7
253.3
488.6
85.4
827.3
132.1
159.1
291.3
1,588.4
1,622.9
364.9
3,576.1
548.6
17.8
63.8
585.1
145.8
581.6
12.5
359.0
2,314.2
3,584.1
832.5
18.3
36.2
169.8
78.0
598.1
13.6
517.6
2,264.1
3,451.8
616.9
18.7
415.8
14.9
419.8
1,486.0
2,313.3
364.7
19.2
265.8
16.2
228.3
894.2
1,185.5
2,362.6
74.0
100.1
754.9
223.8
1,861.3
57.2
1,524.6
6,958.5
10,534.7
4
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Expenditure Accounts by Years -- Base Costs
(US$ ’000)
1995
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
Total Recurrent Costs
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
Taxes
Foreign Exchange
1996
Base Cost
1997
1998
Total
Foreign Exchange
%
Amount
511.3
436.0
140.0
1,087.3
498.6
401.8
80.5
980.9
199.9
401.8
59.5
661.2
100.0
127.2
227.2
1,309.8
1,366.8
280.0
2,956.6
80.0
95.1
30.0
82.2
1,047.8
1,299.9
84.0
2,431.7
431.8
15.6
50.2
460.5
125.6
482.3
10.0
288.4
1,864.4
2,951.7
295.2
337.2
3,584.1
595.7
15.6
25.9
121.5
64.8
465.9
10.0
382.8
1,682.2
2,663.0
266.3
522.5
3,451.8
401.3
15.6
303.9
10.0
285.6
1,016.3
1,677.6
167.8
468.0
2,313.3
215.6
15.6
182.1
10.0
142.8
566.1
793.3
79.3
312.9
1,185.5
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
100.0
85.0
50.0
15.0
20.0
22.8
44.5
44.5
15.8
40.0
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,470.7
1,388.7
942.7
415.4
4,217.4
-
-
5
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Components Project Cost Summary
Local
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
Subtotal Project Coordination
H. Long-term DNA Repositories
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
(US$ ’000)
Foreign
Total
Local
(US$ ’000)
Foreign
Total
%
% Total
Foreign
Base
Exchange Costs
863.0
750.4
425.0
1,956.4
12.0
454.8
621.6
175.0
899.6
48.0
1,317.8
1,372.0
600.0
2,856.0
60.0
863.0
750.4
425.0
1,956.4
12.0
454.8
621.6
175.0
899.6
48.0
1,317.8
1,372.0
600.0
2,856.0
60.0
35
45
29
32
80
16
17
7
35
1
1.5
2.2
197.7
26.6
228.0
27.6
42.2
116.7
505.4
691.8
29.0
44.4
314.4
532.0
919.8
1.5
2.2
197.7
26.6
228.0
27.6
42.2
116.7
505.4
691.8
29.0
44.4
314.4
532.0
919.8
95
95
37
95
75
1
4
7
11
178.0
178.0
74.0
4,486.7
448.7
1,381.9
6,317.3
462.0
91.2
553.2
154.8
3,598.9
359.9
258.6
4,217.4
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
178.0
178.0
74.0
4,486.7
448.7
1,381.9
6,317.3
462.0
91.2
553.2
154.8
3,598.9
359.9
258.6
4,217.4
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
72
100
76
68
45
45
16
40
8
1
9
3
100
10
20
130
6
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Expenditure Accounts Project Cost Summary
Local
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
Total Recurrent Costs
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
(US$ ’000)
Foreign
Total
Local
(US$ ’000)
Foreign
Total
%
% Total
Foreign
Base
Exchange Costs
262.0
66.9
196.0
524.9
1,047.8
1,299.9
84.0
2,431.7
1,309.8
1,366.8
280.0
2,956.6
262.0
66.9
196.0
524.9
1,047.8
1,299.9
84.0
2,431.7
1,309.8
1,366.8
280.0
2,956.6
80
95
30
82
16
17
3
37
1,644.4
76.2
582.0
28.6
717.0
34.0
879.7
3,961.8
4,486.7
448.7
1,381.9
6,317.3
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
1,644.4
76.2
582.0
28.6
717.0
34.0
879.7
3,961.8
4,486.7
448.7
1,381.9
6,317.3
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
100
85
50
15
20
23
45
45
16
40
20
1
1
7
2
18
14
63
100
10
20
130
7
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Project Components by Year -- Base Costs
(US$ ’000)
1995
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
Subtotal Project Coordination
H. Long-term DNA Repositories
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
Taxes
Foreign Exchange
1996
Base Cost
1997
1998
Total
943.5
905.5
600.0
60.0
374.2
466.5
1,142.4
-
1,142.4
-
571.2
-
1,317.8
1,372.0
600.0
2,856.0
60.0
29.0
44.4
157.2
230.6
89.1
266.0
355.1
68.1
266.0
334.1
-
29.0
44.4
314.4
532.0
919.8
160.0
22.8
182.8
29.3
2,951.7
295.2
337.2
3,584.1
160.0
22.8
182.8
142.0
2,663.0
266.3
522.5
3,451.8
160.0
22.8
182.8
18.3
1,677.6
167.8
468.0
2,313.3
160.0
22.8
182.8
39.3
793.3
79.3
312.9
1,185.5
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
1,470.7
1,388.7
942.7
415.4
4,217.4
8
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Project Components by Year -- Totals Including Contingencies
(US$ ’000)
1995
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
Subtotal Project Coordination
H. Long-term DNA Repositories
Total PROJECT COSTS
Totals Including Contingencies
1996
1997
1998
Total
1,151.0
1,097.5
739.7
70.0
503.8
603.9
1,514.7
-
1,634.6
-
882.9
-
1,654.8
1,701.5
739.7
4,032.2
70.0
33.3
51.0
192.2
276.5
117.2
314.3
431.5
95.9
323.5
419.4
-
33.3
51.0
405.3
637.8
1,127.3
188.4
26.0
214.4
34.9
3,584.1
197.3
26.7
224.0
173.9
3,451.8
206.9
27.3
234.3
25.0
2,313.3
217.2
28.0
245.3
57.3
1,185.5
809.9
108.1
918.0
291.1
10,534.7
9
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Project Components by Year -- Base Costs
(US$ ’000)
1995
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
Subtotal Project Coordination
H. Long-term DNA Repositories
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
Taxes
Foreign Exchange
1996
Base Cost
1997
1998
Total
943.5
905.5
600.0
60.0
374.2
466.5
1,142.4
-
1,142.4
-
571.2
-
1,317.8
1,372.0
600.0
2,856.0
60.0
29.0
44.4
157.2
230.6
89.1
266.0
355.1
68.1
266.0
334.1
-
29.0
44.4
314.4
532.0
919.8
160.0
22.8
182.8
29.3
2,951.7
295.2
337.2
3,584.1
160.0
22.8
182.8
142.0
2,663.0
266.3
522.5
3,451.8
160.0
22.8
182.8
18.3
1,677.6
167.8
468.0
2,313.3
160.0
22.8
182.8
39.3
793.3
79.3
312.9
1,185.5
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
1,470.7
1,388.7
942.7
415.4
4,217.4
10
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Expenditure Accounts by Years -- Base Costs
(US$ ’000)
1995
I. Investment Costs
A. Equipment
B. TA and Training
C. Quality Control
Total Investment Costs
II. Recurrent Costs
A. Travel and Field Allowances
B. International air-travel
D. Vehicle Hire
E. Labour
F. Sampling Consumables
G. Laboratory consumables and operating costs
H. Incremental office costs
J. Overheads and miscellaneous
Total Recurrent Costs
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
Taxes
Foreign Exchange
1996
Base Cost
1997
1998
Total
Foreign Exchange
%
Amount
511.3
436.0
140.0
1,087.3
498.6
401.8
80.5
980.9
199.9
401.8
59.5
661.2
100.0
127.2
227.2
1,309.8
1,366.8
280.0
2,956.6
80.0
95.1
30.0
82.2
1,047.8
1,299.9
84.0
2,431.7
431.8
15.6
50.2
460.5
125.6
482.3
10.0
288.4
1,864.4
2,951.7
295.2
337.2
3,584.1
595.7
15.6
25.9
121.5
64.8
465.9
10.0
382.8
1,682.2
2,663.0
266.3
522.5
3,451.8
401.3
15.6
303.9
10.0
285.6
1,016.3
1,677.6
167.8
468.0
2,313.3
215.6
15.6
182.1
10.0
142.8
566.1
793.3
79.3
312.9
1,185.5
1,644.4
62.4
76.2
582.0
190.4
1,434.0
40.0
1,099.6
5,129.0
8,085.6
808.6
1,640.6
10,534.7
100.0
85.0
50.0
15.0
20.0
22.8
44.5
44.5
15.8
40.0
62.4
161.8
717.0
6.0
219.9
1,167.2
3,598.9
359.9
258.6
4,217.4
1,470.7
1,388.7
942.7
415.4
4,217.4
-
-
11
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Components Project Cost Summary
Local
A. Field Sampling
B. DNA Extraction
C. Microsatellite Markers
D. Assaying
E. Data Storage and Analysis
F. Technical Assistance and Training
TA for Field sampling
TA for Laboratory assaying analysis
Quality control
Training
Subtotal Technical Assistance and Training
G. Project Coordination
Project Coordinator
Expert Advisory Group
Subtotal Project Coordination
H. Long-term DNA Repositories
Total BASELINE COSTS
Physical Contingencies
Price Contingencies
Total PROJECT COSTS
(US$ ’000)
Foreign
Total
Local
(US$ ’000)
Foreign
Total
%
% Total
Foreign
Base
Exchange Costs
863.0
750.4
425.0
1,956.4
12.0
454.8
621.6
175.0
899.6
48.0
1,317.8
1,372.0
600.0
2,856.0
60.0
863.0
750.4
425.0
1,956.4
12.0
454.8
621.6
175.0
899.6
48.0
1,317.8
1,372.0
600.0
2,856.0
60.0
35
45
29
32
80
16
17
7
35
1
1.5
2.2
197.7
26.6
228.0
27.6
42.2
116.7
505.4
691.8
29.0
44.4
314.4
532.0
919.8
1.5
2.2
197.7
26.6
228.0
27.6
42.2
116.7
505.4
691.8
29.0
44.4
314.4
532.0
919.8
95
95
37
95
75
1
4
7
11
178.0
178.0
74.0
4,486.7
448.7
1,381.9
6,317.3
462.0
91.2
553.2
154.8
3,598.9
359.9
258.6
4,217.4
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
178.0
178.0
74.0
4,486.7
448.7
1,381.9
6,317.3
462.0
91.2
553.2
154.8
3,598.9
359.9
258.6
4,217.4
640.0
91.2
731.2
228.8
8,085.6
808.6
1,640.6
10,534.7
72
100
76
68
45
45
16
40
8
1
9
3
100
10
20
130
12
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 1. Field Sampling
Detailed Costs
(US$)
Unit
I. Investment Costs /a
A. Photography
Total Investment Costs
II. Recurrent Costs
A. Sampling consumables /b
B. Travel and field allowances
Technicians /c
C. Vehicle hire /d
D. Labour /e
E. Postage /f
Total Recurrent Costs
Total
1995
1996
Quantities
1997
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
breed
314
162
-
-
476
200.0
62.8
62.8
32.4
32.4
-
-
95.2
95.2
breed
314
162
-
-
476
400.0
125.6
64.8
-
-
190.4
breed
breed.
breed
breed
314
314
314
314
162
162
162
162
-
-
476
476
476
476
1,200.0
160.0
250.0
100.0
376.8
50.2
78.5
31.4
662.5
725.3
194.4
25.9
40.5
16.2
341.8
374.2
-
-
571.2
76.2
119.0
47.6
1,004.4
1,099.6
_________________________________
\a Costs are per breed (50 animals).
\b Tubes, needles, anticoagulant, vet. supplies.
\c Two technicians : 3 days travelling plus 5 days sampling at $75/day each.
\d 400 km. at $0.40/km.
\e Two labourers for 5 days each at $25/day each.
\f Of blood samples to country laboratories.
13
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 2. DNA Extraction
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Equipment
Centrifuge (3000 g)
Refrigerator/freezer
Water bath
Total Investment Costs
II. Recurrent Costs
A. Laboratory consumables
Plastic ware
Chemicals
Enzymes
Glassware
Waste disposal
Subtotal Laboratory consumables
B. Labour
C. Overhead and miscellaneous
Total Recurrent Costs
Total
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
Labo.
Labo.
Labo.
37
37
37
19
19
19
-
-
56
56
56
6,000.0
1,000.0
500.0
222.0
37.0
18.5
277.5
114.0
19.0
9.5
142.5
-
-
336.0
56.0
28.0
420.0
breed
breed
breed
breed
breed
314
314
314
314
314
162
162
162
162
162
-
-
476
476
476
476
476
100.0
600.0
100.0
100.0
100.0
breed
breed
314
314
162
162
-
-
476
476
500.0
500.0
31.4
188.4
31.4
31.4
31.4
314.0
157.0
157.0
628.0
905.5
16.2
97.2
16.2
16.2
16.2
162.0
81.0
81.0
324.0
466.5
-
-
47.6
285.6
47.6
47.6
47.6
476.0
238.0
238.0
952.0
1,372.0
14
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 3. Microsatellite Marker Development
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Equipment
Total Investment Costs
II. Recurrent Costs
A. Labour /a
B. Laboratory consumables
C. Travel
D. Overheads and miscellaneous
Total Recurrent Costs
Total
_________________________________
\a 1 post-doc. and 1 post-graduate.
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
species
5
-
-
-
5
20,000.0
100.0
100.0
-
-
-
100.0
100.0
species
species
species
species
5
5
5
5
-
-
-
5
5
5
5
45,000.0
30,000.0
5,000.0
20,000.0
225.0
150.0
25.0
100.0
500.0
600.0
-
-
-
225.0
150.0
25.0
100.0
500.0
600.0
15
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 4. Laboratory Assaying /a
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Equipment /b
Total Investment Costs
II. Recurrent Costs
A. Laboratory consumables
B. Personnel
C. Miscellaneous & overheads
Total
1995
Quantities
1997
1996
1998
Unit
Cost
Total
1995
1996
Base Cost (’000)
1997
1998
Total
phasing
1
-
-
-
1
0.7
-
199.9
199.9
199.9
199.9
100.0
100.0
499.8
499.8
marker
marker
marker
-
285,600
285,600
285,600
285,600
285,600
285,600
142,800
142,800
142,800
714,000
714,000
714,000
1.0
1.3
1.0
-
285.6
371.3
285.6
1,142.4
285.6
371.3
285.6
1,142.4
142.8
185.6
142.8
571.2
714.0
928.2
714.0
2,856.0
_________________________________
\a Assumptions: 30 markers per animal; 50 animals per breed; 476 breeds.
\b -6896 1. Equipment at 1 marker each.
16
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 5. Data Storage and Analysis
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Equipment
Computers, equip., software and ancillary
Total
Labo.
1995
Quantities
1997
1996
4
-
-
1998
Total
-
Unit Cost
4
15,000.0
1995
60.0
60.0
Base Cost (’000)
1996
1997
1998
-
-
Total
-
60.0
60.0
17
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 6. Training Technical Assistance
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Field Sampling
Fees /a
DSA /b
Travel /c
Subtotal Field Sampling
B. Laboratory Assaying and Analysis
1. Training
Fees /d
DSA /e
Travel
Subtotal Training
Total
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
phasing
phasing
phasing
1
1
1
-
-
-
1
1
1
4,500.0
750.0
2,000.0
18.0
3.0
8.0
29.0
-
-
-
18.0
3.0
8.0
29.0
workshop
workshop
workshop
4
4
4
-
-
-
4
4
4
7,000.0
2,100.0
2,000.0
28.0
8.4
8.0
44.4
73.4
-
-
-
28.0
8.4
8.0
44.4
73.4
_________________________________
\a 9 days travel/workshop presentation at $500/day. 4 Fees at 1 workshop each.
\b 5 days at $150/day. 4 DSA at 1 workshop each.
\c Airfares 4 Travel at 1 workshop each.
\d 14 days $500/day.
\e 14 days at $150/day.
18
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 7. Quality Control Technical Assistance
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Field Sampling Laboratories /a
1. Regional Laboratories
DSA /b
Airfares /c
Subtotal Regional Laboratories
2. Country Focal Points
DSA /d
Airfares/vehicle hire /e
Subtotal Country Focal Points
Subtotal Field Sampling Laboratories
B. Assaying (regional laboratories)
Consultants fees /f
DSA /g
Airfares
Subtotal Assaying (regional laboratories)
Total
_________________________________
\a Regional Laboratories and National focal points.
\b 30 days at $120/day.
\c Airfares.
\d 30 days at $75/day.
\e Airfares/vehicle hire.
\f 5 days at $500/day/visit for 2 visits/laboratory
\g 5 days at $150/day/visit for 2 visits/laboratory
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
Labo.
Labo.
2
2
1
1
1
1
-
4
4
3,600.0
5,000.0
7.2
10.0
17.2
3.6
5.0
8.6
3.6
5.0
8.6
-
14.4
20.0
34.4
pers/day
Foc. point
28
28
14
14
14
14
-
56
56
2,250.0
2,000.0
63.0
56.0
119.0
136.2
31.5
28.0
59.5
68.1
31.5
28.0
59.5
68.1
-
126.0
112.0
238.0
272.4
Labo.
Labo.
Labo.
4
4
4
4
4
4
-
-
8
8
8
2,500.0
750.0
2,000.0
10.0
3.0
8.0
21.0
157.2
10.0
3.0
8.0
21.0
89.1
68.1
-
20.0
6.0
16.0
42.0
314.4
19
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 8. Field Sampling Training
Detailed Costs
(US$)
Unit
I. Investment Costs
A. In-Country Field Training
Travel /a
DSA /b
Training Materials
Subtotal In-Country Field Training
B. Regional Field Sampling Training
Travel /c
DSA /d
Training Materials
Subtotal Regional Field Sampling Training
Total
_________________________________
\a 2 days travel at $200.
\b 2 days DSA at $75/day
\c $1000 per trainee.
\d 3 days per trainee at $75/day.
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
trainee
trainee
trainee
224
224
224
-
-
-
224
224
224
400.0
150.0
100.0
89.6
33.6
22.4
145.6
-
-
-
89.6
33.6
22.4
145.6
Region
Region
Region
4
4
4
-
-
-
4
4
4
3,150.0
14,000.0
1,000.0
12.6
56.0
4.0
72.6
218.2
-
-
-
12.6
56.0
4.0
72.6
218.2
20
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 9. Regional Network Training /a
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Regional Training
DSA /b
Travel /c
Miscellaneous /d
Total
trainee
trainee
trainee
_________________________________
\a Assumes total of 112 trainees.
\b 30 days per trainee at $75/day.
\c $2000 per trainee
\d Training materials, internal transport, etc.
1995
Quantities
1997
1996
-
56
56
56
56
56
56
1998
Total
-
112
112
112
Unit Cost
2,250.0
2,000.0
500.0
Base Cost (’000)
1996
1997
1998
1995
-
126.0
112.0
28.0
266.0
126.0
112.0
28.0
266.0
Total
-
252.0
224.0
56.0
532.0
21
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 10. Project Coordination
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Project Coordinator (FAO)
Salary & Allowances
Total Investment Costs
II. Recurrent Costs
A. Travel
DSA
Airfares
Subtotal Travel
B. Incremental Office Costs
Total Recurrent Costs
Total
man/year
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
1
1
1
1
4
120,000.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
480.0
480.0
days
value
100
1
100
1
100
1
100
1
400
4
150.0
15,000.0
value
1
1
1
1
4
10,000.0
15.0
15.0
30.0
10.0
40.0
160.0
15.0
15.0
30.0
10.0
40.0
160.0
15.0
15.0
30.0
10.0
40.0
160.0
15.0
15.0
30.0
10.0
40.0
160.0
60.0
60.0
120.0
40.0
160.0
640.0
22
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 11. Project Coordination
Expert Advisory Group /a
Detailed Costs
(US$)
Unit
I. Investment Costs
A. Honoraria
Total Investment Costs
II. Recurrent Costs
A. Travel
DSA
Airfares
Total Recurrent Costs
Total
1995
Quantities
1997
1996
1998
Total
Unit Cost
1995
Base Cost (’000)
1996
1997
1998
Total
person/day
24
24
24
24
96
300.0
7.2
7.2
7.2
7.2
7.2
7.2
7.2
7.2
28.8
28.8
person//days
persons
24
6
24
6
24
6
24
6
96
24
150.0
2,000.0
3.6
12.0
15.6
22.8
3.6
12.0
15.6
22.8
3.6
12.0
15.6
22.8
3.6
12.0
15.6
22.8
14.4
48.0
62.4
91.2
_________________________________
\a Assumes 6 members meeting once per year for 4 days over 4 years.
23
MoDAD
Global Project for the Maintenance of Domestic Animal Genetic Diversity
Table 12. Long Term DNA Repositories
Detailed Costs
(US$)
Unit
I. Investment Costs
A. National Laboratories
1. Freezer /a
2. Storage trays and tubes
Subtotal National Laboratories
B. Regional Laboratories
1. Freezer /b
2. Replacement & op. costs
Replacements /c
Operational lump sum /d
Subtotal Replacement & op. costs
3. Storage trays and tubes
Subtotal Regional Laboratories
C. Global Repository
1. Global Repository
Total Investment Costs
II. Recurrent Costs
A. Electricity & Maintenance
National Laboratories
B. Global Repository
Electricity
Scientist Supervision
Technician
Materials & Supplies
Subtotal Global Repository
Total Recurrent Costs
Total
_________________________________
\a Assuming 50 breeds/freezer
\b Assuming 50 breeds/freezer
\c To cover freezer replacement after 10 years
\d Operational costs over 10 years
1995
Quantities
1997
1996
1998
Total
Unit Cost
Base Cost (’000)
1996
1997
1998
1995
Total
breeds
breeds
-
476
476
-
-
476
476
20.0
50.0
-
9.5
23.8
33.3
-
-
9.5
23.8
33.3
breeds
-
476
-
-
476
20.0
-
9.5
-
-
9.5
breeds
breeds
-
476
476
-
-
476
476
20.0
100.0
breeds
-
476
-
-
476
50.0
-
9.5
47.6
57.1
23.8
90.4
-
-
9.5
47.6
57.1
23.8
90.4
Labo.
1
-
-
-
1
11,000.0
11.0
11.0
123.8
-
-
11.0
134.8
breeds
476
476
476
476
1,904
10.0
4.8
4.8
4.8
4.8
19.0
1
1
1
1
1
1
1
1
1
1
1
1
7
1
7
7
10
4
10
10
2,000.0
10,000.0
1,000.0
500.0
2.0
10.0
1.0
0.5
13.5
18.3
29.3
2.0
10.0
1.0
0.5
13.5
18.3
142.0
2.0
10.0
1.0
0.5
13.5
18.3
18.3
14.0
10.0
7.0
3.5
34.5
39.3
39.3
20.0
40.0
10.0
5.0
75.0
94.0
228.8
value
value
value
value
1
ANNEX 7
PRIMARY STRATEGY AND ACTIVITIES
1.
MoDAD represents the only option for cost effective management
programs to be developed both nationally and globally for maintenance of domestic
animal diversity. Substantial financial, human and animal genetic resources will be
wasted within each country and globally in both the short and longer term if the key
structural, logistical and coordination activities comprising MoDAD are not realised at
an early date.
2.
MoDAD offers governments the opportunity to negotiate and effectively
participate in a global effort which provides for capacity building and benefit sharing.
3.
Limited and fragmented studies on genetic analysis of varination are ongoing
in a few developed countries for a few species (cattle, sheep and pigs). These
initiatives cannot produce results of praticular and combined value represented by
MoDAD through the essential storage, access, use and matenance of diversity.
4.
Project MoDAD is directed specifically at enabling and improving the
management of an essential sector of agrobiodiversity, both in-country and globally.
Hence, all governments must be given the opportunity to be involved in this project; to
review progess with and the base-line and advanced results for each animal species
included, and to negotiate guiding principles for access to their samples in the
Database and DNA Repositories. This can be most effectively achieved through
FAO’s Intergovernmental Commission on Genetic Resources for Food and
Agriculture.
5.
FAO’s Centre for Domestic Animal Diversity will provide the necessary global
technical coordination for Project MoDAD, the responsible operative within CDAD
being its specialist Animal Production Officer for Genetic Resources Monitoring and
Characterisation. This coordination covers the following primary activities globally
(also refer to Figure 1 for the essential linkages amongst these activities):
•
Assist countries to be properly involved and link this involvement to
achieve the level of coordination essential for each species of animal to
be monitored.
•
Serve the MoDAD Expert Advisory Group in its development and
review all protocols and procedures required for the operation of the
range of essential technical activities, in the coordination and review of
global results, and in the preparation of reports for consideration by
FAO and the countries and other parties involved.
•
Sequence, specify and monitor all necessary selection of species and of
breeds to sample, and all essential sampling operations required for the
operation of MoDAD throughout the world in accordance with
established protocols.
•
Monitor globally the transport of samples and sub-samples, and also of
2
associated
data
in
accordance
with
established
protocols.
•
Assist countries involved, with the development of their National
MoDAD Repositories for DNA and Data and overview the
establishment and maintenance of the supporting Global MoDAD
Repositories for each of the species involved.
•
Sequence, monitor and coordinate globally the base-line and advanced
assaying required, according to established procedures and protocols.
•
Sequence, monitor and coordinate globally the range of base-line and
advanced statistical analyses required, according to established
procedures and protocols.
•
Monitor and regularly report on the use of pre-established quality
controls at the field sampling, short and long-term sample storage, and
base-line and advanced assay and analytical points, to ensure highest
level of integrity achieved in all aspects of the project.
•
Maintain the MoDAD Global Databank for all species involved, as an
integral component of the Domestic Animal Diversity Information
System (DAD-IS), ensuring that the established data security and
access protocols are applied at all times.
•
Under the guidance of the MoDAD Expert Advisory Group, establish
and maintain within DAD-IS the refereed electronic journal MoDAD
Studies to achieve: the necessary global integration of results with
evaluation and development of the range of procedures being used in
the Project and; capacity building in the Developing Countries
involved.
•
Assist with the establishment and coordination of the activities of the
MoDAD Regional Research and Training Networks in their:
- preparation of (sub-)Project funding proposals
- (sub-)Project management
- base-line and advanced analyses
- research aimed at further understanding the characteristics of, and
advancing the range of sampling, storage, assaying and analytical
procedures required for the conduct of Project MoDAD
- conduct of a range of training activities to maximise the
effectiveness and efficiency of MoDAD and to further enable
capacity building in the countries involved and their regions
•
•
To prepare and progress the necessary funding proposals required to
realise Project MoDAD at the global level; and to implement maintain and
report on these additional globally enabling activities.
To otherwise monitor and coordinate the total Project.
3
6.
This coordination and assistance is essential globally: (1) if the efficacy and
efficiency of the results for each species are to be realised, and at low cost,
without delay; (2) to promote further evaluation and development of the range
of procedures and protocols required; and (3) to ensure all countries involved
achieve maximum benefit from the range of capacity building activities which
must be associated with Project MoDAD.
4
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