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

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Presentation on theme: "2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different."— Presentation transcript:

1 2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA Paul.VanRaden@ars.usda.gov 2009 Mixing Different SNP Densities Mixing Different SNP Densities

2 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

3 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?

4 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$.899.51879% Milk.920.52383% Fat.920.51683% Prot.920.55582% PL.933.49887% SCS.912.41785% DPR.937.53986%

5 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%

6 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

7 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% REL82.681.582.583.184.0

8 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)

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