“Know Your Genes”
An Update on DNA Technology for the Seedstock Producer
DNA Technology
and the
Wagyu Producer
Beef Genetics Education Projects
Southern Beef Technology Services
Workshop Program
9.30 am Welcome
9.35 am Applying DNA Technology in Your Herd
10.05 am Improving Production Traits using DNA Technology
10.35 am Morning Tea
11.05 am How Useful are the Current Gene Markers?
12.15 pm Getting the Most from DNA Technology
12.30 pm Closing Remarks & General Discussion
Applying DNA
Technology in
Your Herd
Presented by Christian Duff
How can DNA Technology be
Used by Cattle Producers?
Current Uses for DNA Technology
1. Parent Verification
2. Genetic Disease Management
3. Genetic Management of Type Traits
(e.g. horn/poll, black/red coat colour)
4. Genetic Improvement of Production Traits
(e.g. Tenderness, Retail Beef Yield)
Parent Verification – Uses?
•
Reduce pedigree errors caused by “natural” errors (e.g.
human error, bull jumping the fence, cross mothering)
•
Identify actual sire from multiple sire matings
•
Identify sires & dams from artificial breeding programs
(e.g. AI or backup bull, IVF)
•
Mother-up calves
Parent Verification – Society Regulations
Regulation
Breed(s)
All registered calves to be DNA parent verified.
Wagyu, Lowline, Dexter
All sires & donor dams DNA fingerprinted. Every nth (e.g.
500th) calf is subject to sire verification
Angus, Limousin, Charolais
All sires & donor dams of registered calves DNA fingerprinted
Shorthorn, Red Angus,
Simmental, Gelbvieh
All AI sires and/or donor dams DNA fingerprinted
Brahman, Brangus,
Droughtmaster,
Hereford, South Devon,
Blondes, Salers
Society/Council may request DNA fingerprint for parentage
verification
Santa Gertrudis,
Parent Verification
¾ Companies:
• University of Queensland, Animals Genetics Lab
• Pfizer Animal Genetics
¾ Indicative Cost – $20 to $40 per sample
¾ Individual Breed Societies may have contracts with one
or both companies.
¾ Other companies based outside Australia also offer this
service such as IGENITY.
Genetic Disease Management - Uses
•
Identify visually normal animals that are “carriers” of
genetic defects (deleterious genes)
•
Effective for diseases that are caused by simple
genetic defects (e.g. base pair deletions)
•
Majority of genetic defects are recessive
Genetic Disease Management Defects
Genetic Defect
Breed(s)
Alpha – Mannosidosis
Angus, Red Angus, Murray Grey, Galloway
Beta-Mannosidosis
Salers
Cardiomyopathy & woolly haircoat syndrome (CWH)
Poll Hereford
Factor VII Deficiency
Hereford
Inherited Congenital Myoclonus (ICM)
Poll Hereford
Maple Syrup Urine Disease (MSUD)
Hereford, Poll Hereford, Shorthorn
Congenital Myasthenic Syndrome (CMS)
Brahman
Pompes Disease
Brahman, Shorthorn
Protoporphyria
Limousin, Blonde d’Aquitaine
Myophosphorylase Deficiency
Charolais
Arthrogryposis Multiplex (AM)
Angus
Neuropathic Hydrocephalus (NH)
Angus
¾ Some Breed Societies have regulations based on genetic disease and known
carriers.
Genetic Disease Management
¾Companies:
•University of Queensland, Animal Genetics Lab
ƒ All in conjunction with EMAI
•Elizabeth Macarthur Agricultural Institute (EMAI)
ƒ All in conjunction with UQ
•Pfizer Animal Genetics
• AM & NH
¾Indicative Cost – $30 to $40 per sample
¾Individual Breed Societies may have contracts with
one or both companies.
¾Other companies based outside Australia also offer
this service such as IGENITY
Genetic Management of Type Traits - Uses
•
Identify animals that carry both copies (homozygote)
of the preferred type trait
•
Horn/Poll
•
Black/Red Coat Colour
Genetic Management of Type Traits Companies
¾ Companies:
• UQ Animal Genetics Lab or EMAI
ƒ Black/Red coat colour
• Pfizer Animal Genetics
ƒ GeneSTAR Black
• IGENITY (USA)
ƒ Black/Red coat colour
ƒ Horned/Polled (breed specific – Limousin, Hereford, Simmental,
Gelbvieh, Shorthorn, Charolais & Angus ). No test for scurs or African horn
gene.
• Metamorphix or MMI (USA)
ƒTru-CoatColour
ƒTru-Polled (breed specific - Charolais, Gelbvieh, Hereford, Limousin,
Salers and Simmental). No test for scurs or African horn gene
¾Indicative Cost – $40 to $125 per sample
Genetic
Improvement of
Production Traits
using DNA
Presented by Andrew Byrne
In this session, we will :
¾ Discuss the use of DNA technology to make genetic
improvement for production traits
(eg. marbling, tenderness, feed efficiency)
¾ Outline what DNA tests for production traits are
commercially available today
¾ After morning tea, we will discuss how useful these tests
may be for improving genetic improvement
1
DNA Tests Available for Production Traits
Company
Tests
University of Queensland, Animal Genetics Lab or
Elizabeth Macarthur Agricultural Institute (EMAI)
Myostatin* : 7 variants
Pfizer Animal Genetics
(MVPs)
GeneSTAR Tenderness
GeneSTAR Marbling
GeneSTAR Feed Efficiency
IGENITY (Merial)
(MBVs & 1-10 score)
Carcase Composition (3)
Carcase Quality (3)
Female Traits (3)
Average Daily Gain (1)
Feed Efficiency (1)
Docility (1)
Myostatin* : 9 variants
METAMORPHIX
(MGVs)
Tru-Marbling
Tru-Tenderness
¾ Indicative Cost – $30 to $90
¾* Myostatin – Both Disruptive (e.g. Double Muscle) & Missence Variants (e.g.F94L)
DNA Tests Offered (Pfizer Animal Genetics)
¾ Molecular Value Predictions (MVPs) have replaced “STARS”
¾ An MVP is effectively an EBV generated from gene marker
information only (uses a 56 SNP panel)
¾ MVPs available for feed efficiency, marbling and tenderness
2
Molecular Value Predictions (MVPs)
¾ MVP expressed on a +/- scale from 0
0 = average of the 7000 animals tested in discovery & validation
¾ Reported in units of measurement for the trait:
• FE: Net Feed Intake in kg
• Marb: AUSMEAT Marble score
• Tend: Shear Force in kg
¾ Percentile rank of each animal provided by trait
(Angus, Brahman, Charolais, Santa Gertrudis and Wagyu)
Molecular Value Predictions (MVPs)
¾ Reliability value is similar to “accuracy” provided by
BREEDPLAN
¾ Based on Pfizer’s prediction of the amount of genetic
variance explained by the MVPs
3
DNA Tests Offered (Igenity/Merial)
¾ DNA Tests Available for a range of traits covering:
•
•
•
•
•
•
Carcass Composition (Yield, Rib Eye Area, Back Fat Thickness)
Carcass Quality (Marbling, Tenderness, %Choice)
Female Traits (Stayability, Pregnancy Rate, Calving Ease)
Average Daily Gain
Feed Efficiency
Docility
¾ Results reported both as Molecular Breeding Values (MBVs)
and using a 1 to 10 score system.
¾ As with an MVP, an MBV is essentially an EBV generated
from gene marker information only (using a SNP panel)
4
Take Home Messages
¾ One of the potential uses of DNA Technology is for genetic
improvement of economically important production traits
¾ Only tests commercially available in Australia at the moment
are offered by Pfizer Animal Genetics
¾ Several other organisations around the world offer DNA tests
for production traits (ranging from universities to subsidiaries
of pharmaceutical companies).
¾ More companies are likely to enter the Australian market
shortly.
Genetic Improvement of Production Traits
- Uses
¾ Identify animals that carry “favorable” genes for an
economically important production trait
¾ In contrast to type traits, few production traits are controlled
by simple single genes with large effects
¾ Most are controlled by hundreds, if not thousands of genes,
with each gene having a small effect
5
Validation of
Current Gene
Markers
Presented by Christian Duff
Forms of Validation
1. Discovery – Undertaken by research organizations
or the genomics company
2. Internal Validation – Undertaken by the genomics
company
3. Independent Assessment – Undertaken by
“independent” research organisations
Independent Assessment
1. SmartGene for Beef (STARS)
2. Beef CRC Independent Assessment (MVPs)
SmartGene for Beef
¾
Collaborative project aiming to:
1)
Develop methods to combine DNA marker test results, performance
information and pedigree to produce marker-assisted EBVs (EBVM)
2)
Generate Trial EBVMs through BREEDPLAN
¾
Research utilised the DNA markers (STARS) commercialised by
Pfizer Animal Genetics (formally known as Catapult or Genetic
Solutions)
¾
4 x Tenderness, 4 x Marbling, 4 x Feed Efficiency
SmartGene for Beef - Population
Number of Phenotypes
Genotypes
Tenderness
IMF%
NFI
Brahman
2915
1743
1810
815
Santa Gertrudis
1248
1127
1228
248
Belmont Red
1491
1341
1458
304
Tropical Composite
2400
1187
1197
783
Angus
1761
1605
1676
731
Hereford
1023
901
1027
241
Murray Grey
433
369
427
87
Shorthorn
Total
774
447
695
278
12045
8720
9518
3487
SmartGene for Beef - Results
Based on the populations tested (n=12,045):
1) The Tenderness Markers had a small effect in British (T1 & T2) –
and Tropical breeds (T1, T2, T3 – 8%).
2) The Marbling Markers did not have a statistically significant effect
(individually or combined) on either IMF, MSA marble score or
AUSMEAT marble score.
3) The Feed Efficiency Markers were only significant in the population
in which they were discovered (CRCI temperate animals).
Full results available at: http://agbu.une.edu.au/smartgene.php
SmartGene for Beef - Results
Gene Frequency N2
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
AA
TC
B
S
B
B
S
S
H
M
A
C
CR A PT G C H CR H CR H D u B CR B CR G CR R CR
RC
rh a
C- RCCCCCCCII
I
I
-I
I
I
I
I
I
I
m
SmartGene for Beef - Results
M1 in Temperate Breed Datasets
7
6
IMF %
5
Zero
4
one
3
two
2
1
0
AA
MG
HH
Temperate Breed Datasets
SH
SH_DR
SmartGene for Beef - Results
T3 in Tropical Breed Datasets
6
LD Shear Force Kg
5
4
Zero
3
One
Two
2
1
0
SG
BR
BM1
TC
BM2
Tropical Breed Da tasets
SmartGene for Beef - Results
Information used to calculate Trial Shear Force EBVMs
Trial
Shear Force
EBVMs
SmartGene for Beef - Results
Trial Shear Force EBVMs
¾ Provide estimates of genetic differences between animals in
meat tenderness.
¾ Expressed as differences in the kilograms of shear force that
are required to pull a mechanical blade through a piece of meat.
Can be likened to the effort required to chew a piece of steak.
¾ Lower, more negative EBVs are more favorable
SmartGene for Beef - Results
Information source and EBVM accuracy
SmartGene for Beef - Results
Example Brahman Trial Shear Force EBVMs (Kg SF)
http://www.beefcrc.com.au/Aus-Beef-DNA-results
Beef CRC Independent Assessment Populations
¾ Population 1 – Angus, Hereford, Murray Grey, Shorthorn
¾ Population 2 – Brahman, Santa Gertrudis, Belmont Red
Beef CRC Independent Assessment –
Data Analysed
Beef CRC Independent Assessment –
Results
For every 1 unit difference in MVP what is the
difference in phenotype ?
Population
Marbling
Tenderness
Feed efficiency
IMF%
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
0.26
0.22
0.24
0.30
2. Bos indicus
0.23
0.17
0.66
0.37
Statistically Significant (P<0.05)
Beef CRC Independent Assessment –
Results
What difference in performance would we expect
between the “best” and “worst” MVP animal?
Tenderness
Feed efficiency
IMF%
Marbling
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
0.34
0.29
0.22
0.63
2. Bos indicus
0.33
0.24
0.77
0.63
Population
Beef CRC Independent Assessment –
Results
What difference in performance would we expect
between the best half and worst half of the mob?
Marbling
Population
Tenderness
Feed efficiency
IMF%
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
0.08
0.07
0.05
0.13
2. Bos Indicus
0.06
0.04
0.19
0.14
Beef CRC Independent Assessment –
Results
How much phenotypic variation is explained by
the MVP?
Population
Tenderness
Feed efficiency
IMF%
Marbling
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
0.1%
0.6%
0.2%
0.8%
2. Bos indicus
0.1%
0.3%
2.4%
1.1%
Beef CRC Independent Assessment –
Results
How much genetic variation is explained by the
MVP?
Population
Marbling
Tenderness
Feed efficiency
IMF%
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
0.3%
1.7%
2.9%
6.2%
2. Bos indicus
0.4%
0.9%
8.0%
5.4%
Beef CRC Independent Assessment –
Results
What accuracy, relative to an EBV, would be
generated from the MVP alone?
Population
Tenderness
Feed efficiency
IMF%
Marbling
Marble Score
SF (kg)
NFI (kg)
1. Bos taurus
5%
13%
17%
24%
2. Bos indicus
6%
10%
28%
23%
What Have We Learnt?
1. Most gene markers only have a small effect (%
genetic variation) on the target trait
2. Current MBVs account for <10% genetic variation
(at best)
3. Size and direction of effect are population (e.g.
breed, country) and production system specific
4. Independent validation processes are in place
5. Methodology has been developed to combine
gene marker results into EBVs (MBVs?)
Getting the Most
from
DNA Technology
Presented by Andrew Byrne
How can you get the
most from DNA
technology?
1
Current Tool for Genetic Improvement
BREEDPLAN
Calculates
ESTIMATED BREEDING
VALUES
using pedigree and
performance data supplied by
breeders
EBV
Most Beneficial Application of DNA Technology
Pedigree
Phenotypes
DNA tests
Phenotypes
DNA tests
BREEDPLAN
Marker
Assisted
EBVMs
Phenotypes
Progeny
DNA tests
2
Making Genetic Improvement for Marbling
1. Join Wagyu GROUP BREEDPLAN
2. Employ an accredited scanner to measure animals
3. Collect abattoir information for marbling
4. Select animals using BREEDPLAN IMF% EBVs
5. Consider what DNA tests are available?
- Enhance accuracy of selection
- Measure early in life
Questions to Ask?
1. How big of an effect (phenotypic & genetic) does the MBV
have on the trait of interest (in Wagyu cattle)?
2. Does the effect provide a cost-benefit?
3. What level of accuracy will the MBV provide (relative to an
EBV)?
4. Has the effect of the MBV been independently validated and
published?
5. Has the MBV information been incorporated into
BREEDPLAN EBVs?
3
How will Wagyu
producers be able to
answer these questions?
What is BIN?
¾ Beef Information Nucleus
¾ Part of the CRC/MLA Strategic plan for DNA Marker
Commercialisation
¾ Provides for the systematic collection of accurate phenotypic
information from all sectors of the beef industry
¾ Facilitates the independent validation of DNA markers
relative to Australian breeds and production systems
4
What is BIN?
Breed Society Involvement:
¾ Structured progeny test to measure BREEDPLAN traits, plus
optional NFI, EQ and lifetime female reproduction
¾ DNA collected on all animals
¾ Significant commitment and resources needed
¾ MLA Donor Company 50:50 funding
Final Thought
“DNA Technology will be part of the
future seedstock producers tool kit for
increasing the rate of genetic
progress”
The challenge as cattle breeders is to
get the most from this new technology
5