Genomic Evaluations
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Transcript of Genomic Evaluations
G. R. Wiggans
Animal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD
G.R. WiggansSpanish Visitors June 2010 (1)
Genomic Evaluations
G.R. WiggansSpanish Visitors June 2010 (2)
Structure of genomic evaluations All genotypes shared with Canada
Holstein, Jersey, Brown Swiss included
Participants
3 Breed Associations
7 major studs and 5 small ones
4 genotyping laboratories
Monthly evaluations
G.R. WiggansSpanish Visitors June 2010 (3)
Bull genomic evaluations
Designated studs have exclusive right to receive genomic evaluations of bulls until May 2013
G.R. WiggansSpanish Visitors June 2010 (4)
Genotyped Holstein by run
Run Date
Old* Young**
TotalMale Female Male Female
0904 7600 2711 9690 1943 21944
0906 7883 3049 11459 2974 25365
0908 8512 3728 12137 3670 28047
0910 8568 3965 13288 4797 30618
1001 8974 4348 14061 6031 33414
1002 9378 5086 15328 7620 37412
1004 9770 7415 16007 8630 41822
1005 9958 7940 16594 9772 44264
1006 9958 8122 17507 10713 46300
* Animals with traditional evaluation** Animals with no traditional evaluation
G.R. WiggansSpanish Visitors June 2010 (5)
How the system works
Studs and breeds nominate animals through web site
Hair, blood, semen, or extracted DNA sent to Labs
Genotypes sent to AIPL monthly
Evaluation updates provided to studs and breeds monthly
All evaluations updated at tri-annual traditional runs
G.R. WiggansSpanish Visitors June 2010 (6)
Conflict checking
Parent-progeny conflicts detected
Sex and breed checked
Conflicts reported to lab and requester for resolution
G.R. WiggansSpanish Visitors June 2010 (7)
Recent changes
Genotypes for some dams imputed from progeny
Traditional evaluations of genotyped cows adjusted to improve accuracy of genomic evaluations
G.R. WiggansSpanish Visitors June 2010 (8)
Imputation
Determine an animal’s genotype from genotypes of its parents and progeny
Genotype separated into sire and dam contributions. Identifies the allele on each member of a chromosome pair
G.R. WiggansSpanish Visitors June 2010 (10)
Imputation (cont.)
Inheritance of haplotypes tracked
Accuracy of imputation improves with number of progeny
Crossovers during meiosis contribute to uncertainty
G.R. WiggansSpanish Visitors June 2010 (11)
Cow Adjustment
Evaluations of elite cows biased upward
Cutoff studies showed little benefit from including cows as predictors
Reducing heritability would reduce the problem but industry is reluctant to do so
Adjustment of cow evaluations implemented
G.R. WiggansSpanish Visitors June 2010 (12)
Effect of Adjustment on Holstein
Bias Regression Gain REL
No Yes Diff No Yes Diff No Yes Diff
Milk (lb) -75.3
-27.9
47.4
.93 .90 -.03
29.5 32.5
3.0
Fat (lb) -5.7 -2.9 2.8 .98 .97 -.01
34.0 37.1
3.1
Protein (lb)
-0.2 0.8 1.0 .90 .97 .07 25.0 27.1
2.1
Fat (%) 0.0 0.0 0.0 .97 .99 .02 49.8 52.4
2.6
Protein (%)
0.0 0.0 0.0 .87 .88 .01 38.8 41.5
2.7
G.R. WiggansSpanish Visitors June 2010 (13)
Increased reliability of genomic predictions
Genomic evaluations of the top cows, top young bulls, and top heifers decreased
Among bulls, foreign bulls with a high proportion of genotyped daughters had largest changes
Cow Adjustment Summary
G.R. WiggansSpanish Visitors June 2010 (14)
Reliability for young HO Bulls
0
500
1000
1500
2000
2500
3000
3500
4000
52 5354 55 5657 58 5960 61626364 6566 67 6869 70 7172 73 7475 76 7778 79
Milk REL
Nu
mb
er
of
Bu
lls
N = 15,226
G.R. WiggansSpanish Visitors June 2010 (15)
Chip diversity
Low cost chip with 3072 (3K) SNP expected this summer
High density chip (860K) in development
Version 2 of BovineSNP50 announced with changes in SNP list
G.R. WiggansSpanish Visitors June 2010 (16)
Accommodating chip diversity Impute to higher density
Calculate effects for all high density SNP
Mechanism for accounting for loss in accuracy due to imputation error needed Percent missing genotypes
Only observed genotypes stored in database
Evaluations labeled as to source of genotype
G.R. WiggansSpanish Visitors June 2010 (17)
Illumina 3K chip
SNP chosen 3072, evenly spaced Some Y specific SNP 90 SNP for breed determination
Expect to impute genotypes for 43,382 SNP with high accuracy
Expect breeds to use 3K chip to replace microsatellites for parentage verification
Breeds allowed to genotype bulls for parentage only
G.R. WiggansSpanish Visitors June 2010 (18)
Proposed stud use of 3K chip Accuracy adequate for first stage
screening
Higher density genotyping reserved for bulls acquired. Confirm ID Second stage selection
Maximize accuracy of evaluation used for marketing
Genotype more candidates
G.R. WiggansSpanish Visitors June 2010 (19)
Current research
Prepare for Interbull validation of genomic evaluations
Improve accuracy of imputation Refine cow adjustment for use with 3K
chip Evaluate how to restore comparability
between evaluations of genotyped and non-genotyped cows
Investigate ways to increase accuracy by increasing predictor population