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

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. ANAFI Workshop, Cremona, Italy, 7 February 2013 (22) Cole
Questions?