Genotype and Environment contributing to the sustainability of dairy cow
production systems through the optimal integration of genomic selection and
novel management protocols based on the development and exploitation of
genomic data and supporting novel phenotyping approaches
GplusE
www.GplusE.eu
GplusE - www.GplusE.eu
• 15 partners
– UCD (coordinator), RVC, AFBI, UGent, AU, CRA, ICBF, HZAU,
S-Eaap, Unifarm, KCA, MU, ULg-Gx & FVM, CRA-W, FBN.
• 6 EU member states (IE, UK, BE, DK, IT, DE); plus US
(Missouri), plus China (HZAU)
• 9 Work packages
• Contract start date 1 January, 2014
• Duration (60 mo); 5 years
• Contract amount €8,997,235.00
• European Union's Seventh Framework Programme
(FP7/2007-2013 grant agreement n° 613689)
WP1
Coordination and management of the G Plus E consortium
Leader: 1 (UCD)
Partners: 2 (RVC), 3 (AFBI), 4 (UGent), 6 (AU), 7 (CRA), 8 (ICBF),
9 (HZAU), 10 (S-EAAP), 11 (Unifarm), 12 (KCA), 13 (MU),
14a (ULg-Gx), 14b (ULg-FVM), 15 (CRA-W), 16 (FBN)
WP2
WP3
WP4
Data harmonization, creation and use of a
database for relevant data from participant
partners
WP Leaders: 4 (UGent), 14a(ULg-Gx)
Partners: 1 (UCD), 2 (RVC),
3 (AFBI), 6 (AU),
7 (CRA), 8 (ICBF),
9 (HZAU), 11 (Unifarm),
13 (MU), 15 (CRA-W),
16 (FBN)
Determination of phenotypic interrelationships between parameters in milk
and physiological status, health, welfare,
fertility, environmental footprint and
production in dairy cows.
WP Leader: 6 (AU), 15 (CRA-W)
Partners: 1 (UCD), 2 (RVC), 3 (AFBI),
4 (UGent), 7 (CRA), 8 (ICBF),
9 (HZAU), 11 (Unifarm),
13 (MU), 14a (ULg-Gx),
14b (ULg-FVM), 16 (FBN)
Genome-wide association study to relate
genotype (DNA SNP) to phenotype (using
predictor phenotypes in milk) for a large
population of dairy cows across management
systems.
WP Leaders: 1 (UCD), 14a (ULg-Gx)
Partners: 2 (RVC), 3 (AFBI),
4 (UGent), 6 (AU), 7 (CRA),
8 (ICBF), 9 (HZAU),
11 (Unifarm), 13 (MU)
WP6
Management strategies at herd and cow
level for improved efficiency, environment,
health and welfare for cows of the future.
WP Leaders: 1 (UCD), 4 (UGent),
6 (AU)
Partners: 8 (ICBF), 11 (Unifarm),
14a (ULg-Gx), 16 (FBN)
WP7
Establishing the most appropriate long term
breeding strategy for the European
population of Holstein Friesian cattle
WP Leader: 8 (ICBF),
Partners: 1 (UCD), 2 (RVC), 7 (CRA),
13 (MU), 14a (ULg-Gx)
WP5
Relationship of some molecular phenotypes
(based on epigenome and Chromatin /
DNA methylation analysis) for key
physiological traits to genome haplotypes
WP Leaders: 2 (RVC), 14b (ULg-FVM)
Partners: 1 (UCD), 4 (UGent), 6 (AU),
13 (MU), 14a (ULg-Gx),
16 (FBN)
WP8
Annotation of bovine, human and other relevant genomes
WP Leader: 13 (MU)
Partners: 1 (UCD), 2 (RVC), 14b (ULg-FVM)
WP9
Producing guidelines and disseminating knowledge
WP Leader: 10 (s-EAAP)
Partners: 1 (UCD), 2 (RVC), 3 (AFBI), 4 (UGent), 6 (AU), 7 (CRA), 8 (ICBF), 9 (HZAU),
11 (Unifarm), 12 (KCA), 13 (MU), 14a (ULg-Gx), 14b (ULg-FVM), 15 (CRA-W), 16 (FBN)
Objectives
1.
to develop and validate new, easily-measured phenotypes that can supplement or correlate
with and replace traditional phenotypes (milk yield and composition, fertility, product quality,
traditional disease and fertility records) (WP 2; WP 3);
2.
to identify novel genomic markers, including causative mutations, for the key phenotypic traits
(productivity, efficiency, environmental footprint, health, fertility and animal welfare) that can be used for GS
(WP2; WP3; WP 4);
3.
to generate ENCODE-like data for the bovine as a public resource that can be used for both
GS in dairy cattle and to increase understanding of genotype/phenotype associations across all species (WP 2;
WP3; WP 4; WP5; WP 8);
4.
to define the key interacting problems that contribute to management of dairy cows under different
systems that will allow the building and validation of an appropriate management blueprint based on Hazard
Analysis & Critical Control Point (HACCP) and Evolutionary Operations (EVOP) principles (WP2; WP3; WP 6);
5.
to develop new breeding and management strategies that incorporates the new genomic
information attaching to the common currency phenotypic data established through the project (WP 2; WP 3;
WP 7);
6.
to disseminate the information widely to producers, consumers and the scientific community and to use
the project to train a new generation of young scientists in the specialism of bio-informatics (All WP; WP 9).
WP 1: Coordination and management
Lead: UCD (32.5 Mo)
Participants (1+14):
Objectives
•
•
•
•
To ensure a successful implementation of the GplusE project.
Effective administrative management.
Overall coordination of the project team.
Seamless co-operation and communication between the partners
(internal), stakeholders/interest groups especially within the dairy
industry and the European Commission (external).
WP 2: Data harmonization, creation and use of a
database for relevant data from participant
partners
Lead: UGent (26 Mo), ULg-Gx (9 Mo)
Participants (2 + 11):
UCD
Mo
11.5
RVC
AFBI
1
7
AU
2
CRA
4.2
ICBF
23.5
HZAU
3
Unifarm
10
MU
5
CRA-W
16
FBN
2
Objectives
• To develop trait ontology of phenotypes of interest based on
literature and on existing data to be collated into the shared project
database.
• Harmonization and organisation of collection of MIR-spectra data.
• To develop draft formats and protocols to enable data transfer from
each partner and rapid loading into the project pooled database.
• To define and to create the databases for relevant data from
participant partners.
WP 3: Determination of phenotypic inter-relationships between parameters
in predominantly milk and blood with physiological status, health, welfare,
fertility, environmental footprint and production in dairy cows.
Lead: AU (40.2 Mo), CRA-W (42 Mo)
UCD
RVC (2 +AFBI
Participants
11): UGent CRA ICBF HZAU Unifarm MU ULg- ULg- FBN
Gx
Mo
22.6
2.7
23
18
29
7.5
12
10
5
FVM
6
Objectives
• To identify milk biomarker phenotypes (MIR spectra, Glycan
profiles, metabolites) for production efficiency, health, physiological
status, fertility, environmental footprint and animal welfare state.
• To provide data on biomarkers, genotypes and tissue samples for
subsequent use in genomic selection (WP4, WP7), epigenetic
studies (WP5) and development of new management strategies
(WP6) to aid development of more robust and environmentally
friendly cows and to promote early detection and prevention of
disease.
9
Challenges and opportunities
• Data intensive projects
– Variety of people
– Variety of data
– Variety of interests
– Variety of interpretation
WP 4: Genome-wide association study to relate genotype (DNA SNP)
to phenotype (using predictor phenotypes in milk) for a large
population of dairy cows across management systems.
Lead: UCD (24.6 Mo), ULg-Gx (24 Mo)
Participants (2 + 9):
RVC
Mo
13.5
AFBI
11
UGent
4
AU
CRA
2
4.6
ICBF
24
HZAU
13.8
Unifarm
10
MU
1
Objectives
•
•
•
•
•
To predict and model environmental impact, welfare and product quality, using traditional and new
biomarker traits and their interactions.
To identify areas of the bovine genome associated with physiological status, environmental
footprint, health, welfare, fertility and production traits identified in WP3 as being commonly
measured on ~10,000 cows.
To investigate the genes occurring in genomic regions identified by SNP analysis for the
physiological status, health, welfare, fertility, environmental footprint and production traits
measured.
To determine associations between candidate genes or quantitative trait loci (QTL) for physiological
status, health (including immunity), welfare, fertility, environmental footprint and production traits.
Provide input information to WP6, WP7 and WP8.
Main challenge and opportunity
• Envolvement of “Industry Partners” crucial
WP 5: Relationship between some molecular phenotypes for key
physiological traits (based on epigenomic and chromatin / DNA
methylation analysis) and genome haplotypes.
Lead: RVC (35.6 Mo), ULg-FVM (34 Mo)
Participants (2 + 7):
UCD
Mo
17.5
AFBI
4
AU
HZAU
2
12
MU
1
ULg-Gx
2
FBN
34
Objectives
The main objective is to exploit and to further implement WGS data and genomic tools for identifying
the genetic components responsible for variation in biological traits in the Holstein-Friesian (HF) dairy
cattle population. Specifically to:
• Generate ENCODE-like data for the bovine (as a public resource) that can be used for genetic
selection using replication of tissues across large numbers of individual cows
• Generate functional genomic data to identify more causative SNPs for comparative genomic
selection.
• Identify epigenomic modifications of chromatin structure and transcription factor binding for
specific phenotypes to determine how specific SNPs relate to phenotype.
• Perform transcriptome analysis from key tissues (liver, blood cells, mammary gland, reproductive
tract) from cows which have been genotyped and phenotyped as part of WP3
• Correlate identified SNPs with innate immune cell function as a phenotypic marker of fitness.
WP 6: Management strategies at herd and cow levels for improved
efficiency, environmental sustainability, health and welfare for cows of
the future.
Lead: UCD (23.3 Mo), UGent (28 Mo), AU (23 Mo)
Participants (3 + 4):
ICBF
Mo
12
Unifarm
10
ULgGx
FBN
4
3
Objectives
•
•
•
•
•
To obtain an accurate data inflow of productive, reproductive and health data from dairy herds across
Europe managed under specified conditions.
To establish a HACCP system at herd level for potential automatic management at cow level to achieve an
assured optimal metabolic, health, fertility and production/efficiency status for current and future dairy
herds within Europe in accordance with the (country) specific management requirements.
To conduct a cost/benefit analysis of the key management decisions addressed in the HACCP systems at
herd and cow level by the means of herd simulation modelling.
To create a web based software tool to allow dairy herd managers and their advisors apply the newly
developed HACCP strategies to their herds.
To validate the implementation of the newly developed system by comparing the data from the users
versus the non-users among the ‘Dairy Datawarehouse’ participants.
WP 7: Developing and evaluating strategies for incorporating the
knowledge derived from WP3, WP4, WP5 and WP6 into breeding
programmes for the dairy cows of the future.
Lead: ICBF (84 Mo)
Participants (1 + 5):
UCD
Mo
5.5
RVC
0.6
CRA
0.8
MU
5
ULg-Gx
4
Objectives
•
•
•
To identify the generic and specific knowledge developments arising in WP3, WP4, WP5 and
WP6, that are relevant to future dairy cattle breeding scheme design and strategy i.e., new
phenotypic and genomic markers.
To establish the most appropriate long term breeding strategy for Holstein-Friesian cattle in
an environment where molecular genetics knowledge is developing rapidly.
To explore a range of options and evaluate each according to the benefits it can deliver in
terms of the sustainability, profitability and environmental impact of dairy production. This
will include benefits in terms of: (i) economic returns to dairy farmers (milk & meat
producers); (ii) genetic changes in important trait groups in the breeding nuclei; (iii)
maintenance of genetic diversity in the breeding nuclei, and (iv) generation of new
knowledge on the genetic mechanisms controlling animal phenotypes and the development
and implementation of tools for exploiting this knowledge on dairy farms.
WP 8: Annotation of bovine, human and other relevant genomes
Lead: MU (72 Mo)
Participants (1 + 3):
UCD
Mo
7.3
RVC
6.3
ULgFVM
8
Objectives
• Integration of genomic variation, epigenetics, expression data and phenotypic
inferences into an improved bovine genomic annotation.
• Linking of bovine, human and other genomes through a synteny-based orthology
inference pipeline.
• Analyses of variation in protein interaction and metabolic networks to discover
pleiotropic interactions between genes with correlated expression, epigenetic or
phenotypic changes.
• Cross-species functional inferences integrating data across >15 mammalian
genomes.
WP 9 Producing guidelines and disseminating knowledge
Lead: S-EAAP (29.5 mo)
Participants (1 + 14):
Mo
UCD
RVC
AFBI
Ugent
AU
CRA
ICBF
HZAU
Unifarm
KCA
16
0.7
1
1.5
5
1
4
0.6
1
9
MU
4.5
ULgGx
ULgFVM
8
CRAW
FBN
1.5
3
Objectives
• Ensure that the vision, activities and results of GplusE become
widely disseminated at a scientific and practical level in the dairy
sector through organization of conferences, meetings, publications
etc.
• Develop and manage a dedicated web site.
• Implementation of research results and new knowledge to the endusers of the dairy sector including farmers, advisors and the
breeding industry by means of specialized training methods.
Timelines
0
WP 1
WP 2
WP 3
WP 4
WP 5
WP 6
WP 7
WP 8
WP 9
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
54
57
60
Acknowledgement
• This research has received funding from the
European Union's Seventh Framework
Programme (FP7/2007-2013) under grant
agreement n° 613689