1. Increased reliability of genetic evaluations for dairy cattle in the United States from use of genomic information
Abstr.

2. Genomic evaluation system
Became official for Holstein and Jersey in January 2009 and in August 2009 for Brown Swiss
466 bulls marketed based on genomic evaluation only (out of 8,131 genotyped young bulls)
Holstein predictor population included 10,430 bulls and 9,372 cows for August

3. Characteristics of system
Full sharing of genotypes with Canada
542 Brown Swiss genotypes from exchange with Switzerland
Interbull evaluations used for foreign predictor bulls, converted evaluations for cows
10% polygenetic effect
10 countries contribute > 100 genotypes

4. Genotyped Holsteins Date Young animals** All animals Bulls* Cows*
Heifers 
04-09
7,600 
2,711  
   9,690    
  1,943
21,944
01-10
8,974 
4,348  
14,061   
  6,031
33,414
02-10
9,378 
5,086  
15,328   
  7,620
37,412
04-10
9,770 
7,415  
16,007   
  8,630
41,822
05-10
9,958 
7,940  
16,594   
  9,772
44,264
06-10
8,122  
17,507   
10,713
46,300
07-10
9,963 
8,186  
18,187   
11,309
47,645
08-10
10,430
9,372
18,652
11,021
49,475
  *Traditional evaluation
**No traditional evaluation

5. Adjustment of Cow Evaluations
Traditional cow evaluations inflated compared to bull evaluations
US industry wanted cow’s own performance to influence genomic evaluations. Most countries use only bull evaluations for SNP effect estimation
Information from genotyped cows did not increasing reliability of yield traits
Cow contributions adjusted to be comparable to those from bulls
Beltsville Agricultural Research Center
Centennial •

6. Validation Populations
Predictor population - Animals with August 2006 evaluations
No Females
No adjustment of cows
Cow evaluations adjusted
Predicted population – Bulls with no evaluation in August 2006 but did have an evaluation in June 2010
Beltsville Agricultural Research Center
Centennial •

7. Adjustment Method
Mean and variance of deregressed values reduced to be comparable with bull evaluations of similar accuracy

8. Adjustment Parameters
Breed
Milk
Fat
Protein SD
Mean (kg)
Holstein
0.84
-356
0.72
-12.5
0.77
-10.4
Jersey
-292
0.67
-14.2
-11.0
Deregressed Mendelian Sampling (MS) =
(PTA-PA) / f(REL)
Adj. MS = .84*MS - 356
Adj. PTA = f(REL)*(Adj. MS+ PAn) + (1- f(REL)*PAn)
f(REL) = weight in PTA from own records and progeny
Beltsville Agricultural Research Center
Centennial •

9. Effects on Regression (ß)
Deregressed value = α + ß·PTA
Trait
No Females
Unadjusted
Adjusted
Milk
0.91
0.87
Fat
0.95
0.96
Protein
0.89
0.83
0.88
% Fat
0.99
1.00
1.02
% Protein
0.90
Beltsville Agricultural Research Center
Centennial •

10. Beltsville Agricultural Research Center
Effects on Bias
Bias = actual - predicted
Trait
No Females
Unadjusted
Adjusted
Milk
-127.5
-117.0
-8.7
Fat
-6.9
-5.8
-1.9
Protein
-2.5
-1.8
1.3
% Fat
-0.005
-0.002
% Protein
0.007
0.008
Beltsville Agricultural Research Center
Centennial •

11. Effects on Genomic Reliability
Trait
No Females
Unadjusted
Adjusted
Milk
66.5
64.6
67.5
Fat
72.4
69.8
73.1
Protein
63.0
60.6
63.7
% Fat
85.3
85.8
% Protein
76.0
76.4
78.0
Beltsville Agricultural Research Center
Centennial •

12. Genotyped Populations
animalsa
Predictor populationb
Predicted populationc
Bulls Cows Total
Breed
Holstein
46,300
5,822
2,461
8,283
2,654
Jersey
4,478
1,623
390
2,013
394
Brown Swiss
1,584
994
111
1,105
132
a As of June 2010.
b Bulls and cows with official evaluations for yield traits as of August 2006.
c Bulls with a June 2010 domestic traditional evaluation.

13. Holstein prediction accuracy
Traita
Biasb b
REL (%)
REL gain (%)
Milk (kg)
−4.0
0.91
67.5
29.4
Fat (kg)
−0.9
0.96
73.1
35.0
Protein (kg)
0.6
0.88
63.7
25.6
Fat (%)
0.0
1.02
85.7
47.6
Protein (%)
0.90
77.9
39.8
PL (months)
−1.5
1.04
64.2
33.2
SCS
60.4
26.5
DPR (%)
−0.2
1.08
46.8
17.0
Sire CE
1.0
0.79
40.9
13.8
Daughter CE
−1.0
0.93
44.3
18.1
Sire SB
2.1
0.87
29.8
7.2
Daughter SB
0.3
0.89
29.3
2.7
a CE = calving ease and SB = stillbirth.
b 2010 deregressed value – 2006 genomic evaluation.

14. Jersey and Swiss Gains Breed Trait (Avg) REL (%) REL gain (%) Jersey
Yield
55.8
16.3
Health
53.2
20.7
Brown Swiss
56.2
18.2
31.8
4.7

15. Selective Genotyping
Superiority of test population which biases estimated regressions and reliability
Trait
PTA diff
SD of PTA
PTA diff / SD
Milk (kg)
16.9
304.0
0.06
Fat (kg)
1.4
11.2
0.12
Protein (kg)
0.9
8.0
0.11
PL (months)
0.5
2.3
0.21
SCS
−0.04
0.2
−0.11
DPR (%)
0.13
0.10

16. Adding predictor animals
Collaboration
Willing to collaborate at various levels
Sharing genotypes
Discussions with DEU (BS) & DNK (JE)

17. Conclusions Number of predictor animals determines accuracy
Increase in reliability over parent average 25% points across traits for Holstein
Investigating increasing predictor population through exchange and collaboration

19. New Chips 3K chip HD Chip 2,882 SNP for imputation
14 Y-Chromosome SNP for sex determination
Impute 43,382 and use like SNP50 genotype
More labs
HD Chip
777,962 SNP on chip
~600K useful for Dairy
>1,000 HD genotypes needed for imputation
Cost/Benefit being considered