John B. ColeAnimal Improvement Programs LaboratoryAgricultural Research Service, USDABeltsville, MD 20705-2350, USA
The use and economic value of genomic testing for calves on dairy farms
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?
ANAFI Workshop, Cremona, Italy, 7 February 2013 (3) Cole
Many animals have been genotyped
Evaluation Date (YYMM)
Gen
otyp
es
1004 1008 1012 1104 1108 1112 1204 1208 12120
50000
100000
150000
200000
250000Bulls Cows
335,929 genotyped animals
ANAFI Workshop, Cremona, Italy, 7 February 2013 (4) Cole
Why are good decisions important?
1 2 3 4 5 6 7 8 9 10 11 120
0.51
1.52
2.53
2010 2011 2012
M:FP = price of 1 kg of milk / price of 1 kg of a 16% protein ration
Month
Milk
:Fee
d Pr
ice
Rati
o
July 2012 Grain CostsSoybeans: $15.60/bu (€0.46/kg)Corn: $ 7.36/bu (€0.23/kg)
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 )
ANAFI Workshop, Cremona, Italy, 7 February 2013 (6) Cole
Can I afford genomic testing?
Number of SNP 9K 50K 800KU.S. Price €32 €92 €184International Price €41 €100€192
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
ANAFI Workshop, Cremona, Italy, 7 February 2013 (8) Cole
Odds of finding a missing relative……if the missing relative has been genotyped:
92%
Animal
MissingMissing
98%
100%
If a missing parent is genotyped, we will find it!
ANAFI Workshop, Cremona, Italy, 7 February 2013 (9) Cole
0%
10%
20%
30%
40%
50%
60%
0-2months
3-15months
16-23months
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
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?
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!
Gen
etic
Mer
it fo
r NM
$46 US Holsteins – unknown parents
ANAFI Workshop, Cremona, Italy, 7 February 2013 (12) Cole
Change in Genetic Merit for NM$ after genotyping
-600
-400
-200
0
200
400
600
Gen
etic
Mer
it fo
r NM
$46 US Holsteins – genotyped
ANAFI Workshop, Cremona, Italy, 7 February 2013 (13) Cole
If we cull the lowest 10Average of the remaining ones is
+$99.2 higher
-600
-400
-200
0
200
400
600
Gen
etic
Mer
it fo
r NM
$The poorest animals can be culled
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
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
ANAFI Workshop, Cremona, Italy, 7 February 2013 (16) Cole
What bulls were available?Bu
lls u
sed
in
herd
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
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
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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!
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Identify your elite animals
When you genotype yourcows you will know whichanimals to contract as bulldams
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/embryo_transfer_service.html
ANAFI Workshop, Cremona, Italy, 7 February 2013 (20) Cole
Conclusions
Genotyping can increaserates of genetic gain
Pedigree errors can befound 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
ANAFI Workshop, Cremona, Italy, 7 February 2013 (21) Cole
Acknowledgments
Tom LawlorHolstein Association USABrattleboro, VT
Albert De VriesDepartment of Animal SciencesUniversity of Florida, Gainesville, FL
Paul VanRaden, Dan Null, and Tabatha CooperAnimal Improvement Programs Laboratory, ARS, USDA Beltsville, MD
ANAFI Workshop, Cremona, Italy, 7 February 2013 (22) Cole
Questions?
