G.R. Wiggans* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *[email protected]G.R. Wiggans ADSA 2010 (1) Improved reliability approximation for genomic evaluations in the United States Abstr . 617
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G.R. Wiggans* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *[email protected].
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G.R. Wiggans* and P.M. VanRadenAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD
*Traditional evaluation**No traditional evaluation
G.R. WiggansADSA 2010 (11)
G matrix
Computing time increases by (number of SNP)*(number of genotyped animals)2
Options for calculating genomic relationships Get faster computer Run program in parallel Compute relationships before evaluations Calculate only for new animals; store old ones Calculate based only on SNP from 3K chip Use Eigenvalues & Eigenvectors to reduce
processing
If G used to calculate EBV greater precision needed
G.R. WiggansADSA 2010 (12)
Genotype quality and reliability
Problems – greater with imputation
Missing genotypes Genotype incorrect
Remedies
Discount for missing SNP genotypes Consider if parents were genotyped Discount uniformly for 3K chip
G.R. WiggansADSA 2010 (13)
Implementation of 3K chip
Chip expected to ship this week
2,882 usable SNP, plus 14 on Y Chromosome
Unofficial evaluations expected Sept. 7
Large initial use expected
New genotyping laboratories
G.R. WiggansADSA 2010 (14)
Conclusions
Improved REL approximation implemented April 2010
REL reduced for animals less related to predictor population MN control-line bulls Foreign bulls
Approximation relies on G matrix
Modification planned to account for loss in accuracy from imputation