John B. Cole
Animal Improvement Programs Laboratory
Agricultural Research Service, USDA
Beltsville, MD 20705-2350, USA
joh...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (2) Cole
Introduction
 Genomic selection increases selection
response.
 ...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (3) Cole
Many animals have been genotyped
Evaluation Date (YYMM)
Genotypes...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (4) Cole
Why are good decisions important?
0
0.5
1
1.5
2
2.5
3
1 2 3 4 5 6...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (5) Cole
How does genetic selection work?
 ΔG = genetic gain each year
 ...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (6) Cole
Can I afford genomic testing?
Number of SNP 9K 50K 800K
U.S. Pric...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (7) Cole
Four ways to use use genomics
 Animal ID and parentage verificat...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (8) Cole
…if the missing relative has been genotyped:
92%
Animal
Missing
M...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (9) Cole
0%
10%
20%
30%
40%
50%
60%
0-2
months
3-15
months
16-23
months
2 ...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (10) Cole
Now we know which heifer is best
The best has
a PTA NM$ of
+868 ...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (11) Cole
You know nothing about their Genetic
Merit for lifetime profitab...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (12) Cole
Change in Genetic Merit for NM$ after
genotyping
-600
-400
-200
...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (13) Cole
If we cull the lowest 10
Average of the remaining ones is
+$99.2...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (14) Cole
How should you select mates?
 Selected 3 Jersey herds from the ...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (15) Cole
Comparison to actual matings
 Three strategies tested in simula...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (16) Cole
What bulls were available?
Bullsusedinherd
Cows in herd
Genotype...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (17) Cole
Actual DGV and inbreeding
Similar distribution of direct
genomic...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (18) Cole
What did we learn about mating?
 Each of the 3 herds could have...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (19) Cole
Identify your elite animals
 When you genotype your
cows you wi...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (20) Cole
Conclusions
 Genotyping can increase
rates of genetic gain
 Pe...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (21) Cole
Acknowledgments
Tom Lawlor
Holstein Association USA
Brattleboro,...
ANAFI Workshop, Cremona, Italy, 7 February 2013 (22) Cole
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The use and economic value of genomic testing for calves on dairy farms

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My invited talk from the 2013 ANAFI workshop in Cremona, Italy.

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The use and economic value of genomic testing for calves on dairy farms

  1. 1. John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350, USA john.cole@ars.usda.gov The use and economic value of genomic testing for calves on dairy farms
  2. 2. ANAFI Workshop, Cremona, Italy, 7 February 2013 (2) Cole Introduction  Genomic selection increases selection response.  Bulls were genotyped first due to cost.  Many more cows than bulls have now been genotyped.  How can you use genomics to make better decisions on your farm?
  3. 3. ANAFI Workshop, Cremona, Italy, 7 February 2013 (3) Cole Many animals have been genotyped Evaluation Date (YYMM) Genotypes 0 50000 100000 150000 200000 250000 1004 1008 1012 1104 1108 1112 1204 1208 1212 Bulls Cows 335,929 genotyped animals
  4. 4. ANAFI Workshop, Cremona, Italy, 7 February 2013 (4) Cole Why are good decisions important? 0 0.5 1 1.5 2 2.5 3 1 2 3 4 5 6 7 8 9 10 11 12 2010 2011 2012 M:FP = price of 1 kg of milk / price of 1 kg of a 16% protein ration Month Milk:FeedPriceRatio July 2012 Grain Costs Soybeans: $15.60/bu (€0.46/kg) Corn: $ 7.36/bu (€0.23/kg)
  5. 5. ANAFI Workshop, Cremona, Italy, 7 February 2013 (5) Cole How does genetic selection work?  ΔG = genetic gain each year  reliability = how certain we are about our estimate of an animal’s genetic merit (genomics )  selection intensity = how “picky” we are when making mating decisions (management can )  genetic variance = variation in the population due to genetics (we can’t really change this)  generation interval = time between generations (genomics )
  6. 6. ANAFI Workshop, Cremona, Italy, 7 February 2013 (6) Cole Can I afford genomic testing? Number of SNP 9K 50K 800K U.S. Price €32 €92 €184 International Price €41 €100 €192
  7. 7. ANAFI Workshop, Cremona, Italy, 7 February 2013 (7) Cole Four ways to use use genomics  Animal ID and parentage verification  Is this the animal that I think it is?  Early culling decisions  Am I raising the right animals?  Mate selection  How do I produce the best calves?  Identification of elite cows
  8. 8. ANAFI Workshop, Cremona, Italy, 7 February 2013 (8) Cole …if the missing relative has been genotyped: 92% Animal Missing Missing 98% 100% If a missing parent is genotyped, we will find it!
  9. 9. ANAFI Workshop, Cremona, Italy, 7 February 2013 (9) Cole 0% 10% 20% 30% 40% 50% 60% 0-2 months 3-15 months 16-23 months 2 yr- olds 3 yr- olds 4 yr- olds 5 yr- olds 6 yr- olds 7 & older 73% of genotyped US Holsteins are < 15 mo old! Genotyped heifers in the US
  10. 10. ANAFI Workshop, Cremona, Italy, 7 February 2013 (10) Cole Now we know which heifer is best The best has a PTA NM$ of +868 and a REL of 73%. The worst has a PTA NM$ of +48 and a REL of 68%. PLANET has 3,783 genotyped daughters – which one do you want in your herd?
  11. 11. ANAFI Workshop, Cremona, Italy, 7 February 2013 (11) Cole You know nothing about their Genetic Merit for lifetime profitability (NM$) -600 -400 -200 0 200 400 600 Without any pedigree information, they all appear the same! GeneticMeritforNM$ 46 US Holsteins – unknown parents
  12. 12. ANAFI Workshop, Cremona, Italy, 7 February 2013 (12) Cole Change in Genetic Merit for NM$ after genotyping -600 -400 -200 0 200 400 600 GeneticMeritforNM$46 US Holsteins – genotyped
  13. 13. ANAFI Workshop, Cremona, Italy, 7 February 2013 (13) Cole If we cull the lowest 10 Average of the remaining ones is +$99.2 higher -600 -400 -200 0 200 400 600 GeneticMeritforNM$The poorest animals can be culled
  14. 14. ANAFI Workshop, Cremona, Italy, 7 February 2013 (14) Cole How should you select mates?  Selected 3 Jersey herds from the US  Compared actual matings with other possible choices  Could the herd manager have selected better mate pairs?  Data included 220 actual matings from 142 mate pairs
  15. 15. ANAFI Workshop, Cremona, Italy, 7 February 2013 (15) Cole Comparison to actual matings  Three strategies tested in simulation  Mating plans using traditional and genomic PTA as in Pryce et al. (2012)  Selection of mate pairs with greatest mean DGV  Bulls limited to 10 matings
  16. 16. ANAFI Workshop, Cremona, Italy, 7 February 2013 (16) Cole What bulls were available? Bullsusedinherd Cows in herd Genotyped calves Consider each bull as a mate for each cow using different strategies. Actual calves born to these parents. Simulated calves
  17. 17. ANAFI Workshop, Cremona, Italy, 7 February 2013 (17) Cole Actual DGV and inbreeding Similar distribution of direct genomic values (DGV) Different distribution of relation- ships – different sire portfolios
  18. 18. ANAFI Workshop, Cremona, Italy, 7 February 2013 (18) Cole What did we learn about mating?  Each of the 3 herds could have made better mating decisions  Differences between the methods were moderate  Inbreeding continues to be a concern  In the US, many farmers do not use mating programs!
  19. 19. ANAFI Workshop, Cremona, Italy, 7 February 2013 (19) Cole Identify your elite animals  When you genotype your cows you will know which animals to contract as bull dams  You will also know which embryos from a flush are the good ones and bad ones  The sale of elite genetics can supplement your income from milk sales http://vet.tufts.edu/tas/dairy_farm_services/e mbryo_transfer_service.html
  20. 20. ANAFI Workshop, Cremona, Italy, 7 February 2013 (20) Cole Conclusions  Genotyping can increase rates of genetic gain  Pedigree errors can be found and fixed  Accurate culling decisions save money  Better mate selection produces better offspring  Elite genetics can be marketed http://houston.cowparade.com/cow/large/917
  21. 21. ANAFI Workshop, Cremona, Italy, 7 February 2013 (21) Cole Acknowledgments Tom Lawlor Holstein Association USA Brattleboro, VT Albert De Vries Department of Animal Sciences University of Florida, Gainesville, FL Paul VanRaden, Dan Null, and Tabatha Cooper Animal Improvement Programs Laboratory, ARS, USDA Beltsville, MD
  22. 22. ANAFI Workshop, Cremona, Italy, 7 February 2013 (22) Cole Questions?
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