J. B. Cole * and P. M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350

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Presentation transcript:

J. B. Cole * and P. M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Use of Haplotypes to Predict Selection Limits and Mendelian Sampling

ADSA, July 2010 (2) Cole and VanRaden Introduction Mendelian sampling is the difference between an individual's PTA and its PA Sustained genetic gain under selection depends on Mendelian sampling variance (Woolliams et al., 1999) Increased reliabilities from genomic selection due to better estimates of Mendelian sampling (Hayes et al., 2009)

ADSA, July 2010 (3) Cole and VanRaden Introduction (cont’d) You do not benefit substantially from genomic selection until you have a large enough pool of genotyped animals to provide good estimates of marker effects Good marker effects are essential for reliable prediction of Mendelian sampling

ADSA, July 2010 (4) Cole and VanRaden Objectives Describe the predicted Mendelian sampling (MS) variation in Brown Swiss, Holstein, and Jersey cattle Calculate selection limits based on haplotypes present in the genotyped population Examine adjustments to breeding values for changes in heterozygosity

ADSA, July 2010 (5) Cole and VanRaden Materials 43,382 SNP from the Illumina BovineSNP50 SNP solutions from the June, 2010 evaluation Three breeds 1,455 Brown Swiss males and females 40,351 Holstein males and females 4,064 Jersey males and females Three traits Daughter pregnancy rate (DPR) Milk yield (Milk) Lifetime net merit (NM$)

ADSA, July 2010 (6) Cole and VanRaden Methods Haplotypes imputed with findhap.f90 (VanRaden et al., 2010) Calculations and simulations performed with SAS 9.2 Plots produced with R and ggplot (Wickham, 2009) Operating system is 64-bit RedHat Enterprise Linux 5

ADSA, July 2010 (7) Cole and VanRaden Predicted Mendelian sampling Lower bound assumes all SNP on a chromosome are unlinked Upper bound assumes all SNP on a chromosome are perfectly linked “I have discovered a truly marvelous proof…this slide is too narrow to contain it” Also could be calculated from linkage disequilibrium blocks

ADSA, July 2010 (8) Cole and VanRaden Distribution of Mendelian sampling variance

ADSA, July 2010 (9) Cole and VanRaden Predicted Mendelian sampling variance TraitBreedLowerExpectedUpper DPRBS HO JE MilkBS35,335215,168507,076 HO228,011261,3641,069,741 JE150,076205,440601,979 NM$BS2,53919,60240,458 HO16,60119,60287,449 JE3,97819,60244,552

ADSA, July 2010 (10) Cole and VanRaden Why are Holsteins so different? There are many more HO haplotypes represented There are multiple QTL affecting NM$ in HO

ADSA, July 2010 (11) Cole and VanRaden Sampling variance over time — DPR BSHO JE

ADSA, July 2010 (12) Cole and VanRaden Sampling variance over time — Milk BSHO JE

ADSA, July 2010 (13) Cole and VanRaden Sampling variance over time — NM$ BSHO JE

ADSA, July 2010 (14) Cole and VanRaden Correlations with inbreeding LowerUpper TraitBreedGenomicPedigreeGenomicPedigree DPRBS HO JE MilkBS HO JE NM$BS HO JE

ADSA, July 2010 (15) Cole and VanRaden Selection limits Lower bound found by summing the best chromosomes Upper bound found by summing the best alleles at each locus NM$ was adjusted to account for changes in heterozygosity

ADSA, July 2010 (16) Cole and VanRaden Calculated selection limits TraitBreedLowerUpperLargest DGV DPRBS20538 HO JE19535 MilkBS14,19334,0234,544 HO24,88377,9237,996 JE16,13340,2495,620 NM$BS3,8579,1401,102 HO7,51523,5882,528 JE4,67811,5171,556

ADSA, July 2010 (17) Cole and VanRaden Adjusting for heterozygosity Chromosomal EBV for NM$ were adjusted by adding or subtracting 6% of an additive genetic standard deviation ($11.88) per 1% change in heterozygosity (Smith et al., 1998) Only 4 chromosomes (BTA 6, 10, 14, and 16) differed between the adjusted and unadjusted groups

ADSA, July 2010 (18) Cole and VanRaden What’s the best cow we can make? A “Supercow” constructed from the best haplotypes in the Holstein population would have an EBV(NM$) of $7515

ADSA, July 2010 (19) Cole and VanRaden Conclusions Selection limits and sampling variances differ among breeds Sampling variance has decreased slightly over time The top animals in each breed are well below predicted selection limits Adjustment for heterozygosity had little effect on breeding values for NM$

ADSA, July 2010 (20) Cole and VanRaden Questions?