2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different.

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Presentation transcript:

2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different SNP Densities

National Association of Animal Breeders, April 2010 (2)Paul VanRaden 2010 New Haplotyping Program findhap.f90  Begin with population haplotyping Divide chromosomes into segments List haplotypes by genotype match Similar to FastPhase, IMPUTE (Kent)  End with pedigree haplotyping Detect crossover, fix noninheritance Impute nongenotyped ancestors

National Association of Animal Breeders, April 2010 (3)Paul VanRaden 2010 Haplotyping Tests – Real Data  Half of young animals assigned 3K Proven bulls, cows all had 50K Dams imputed using 50K and 3K  Half of ALL animals assigned 3K Could 3K CDDR genotypes help? 10,000 proven bulls yet to genotype Should cows with 3K be predictors?

National Association of Animal Breeders, April 2010 (4)Paul VanRaden 2010 Correlations of 3K and PA with 50K Half of YOUNG animals had 3K PTA, half 50K PTA TraitCorr(3K,50K) 2 Corr(PA,50K) 2 Gain NM$ % Milk % Fat % Prot % PL % SCS % DPR %

National Association of Animal Breeders, April 2010 (5)Paul VanRaden 2010 Using 3K as Reference Genotypes Half of ALL animal NM$ were from 3K, half 50K Using 3K as Reference Genotypes Half of ALL animal NM$ were from 3K, half 50K REL Gain as compared to all 50K Breed50K prog3K progImputed dams HO90%73%36% JE82%56%44% BS84%72%55%

National Association of Animal Breeders, April 2010 (6)Paul VanRaden 2010 Simulated 500K Genotypes  Linkage in base population Similar to actual linkage reported by: – Villa-Angulo et al, 2009 BMC Genetics 10:19 – De Roos et al, 2008 Genetics 179:1503 Underlying linkage corresponds to D’  Three subsets of mixed 50K and 500K: Only 1,586 (young) of 33,414 had 500K Also bulls > 99% REL, total 3,726 Also bulls > 90% REL, total 7,398

National Association of Animal Breeders, April 2010 (7)Paul VanRaden 2010 Results from 500K Simulation DensitySingleMixedSingle Chips50K50K and 500K500K MissingN = 01,5863,7267,39833,414 Before1%88%80%70%1% After.05%11%6%4%.05% REL

National Association of Animal Breeders, April 2010 (8)Paul VanRaden 2010 Polygenic Effect and DGV  Should direct genomic value (DGV) include the polygenic effect? CAN, FRA, and NLD include it USA DGV includes only SNP effects  Advantage: DGV would contain all genetic variance  Disadvantage: Polygenic effects of clones differ (treated as full sibs)