The objective of this study was to evaluate genomic predictions by the single-step genomic BLUP (ssGBLUP) considering heterogeneous variance of single nucleotide polymorphisms (SNP) in Japanese Holsteins. We used the record for 6 production traits (milk yield, fat yield, protein yield, fat percentage, protein percentage and somatic cell score) at the first three lactations, 3 type traits (feet & legs, mammary system and final score) at the first lactation and 1 reproduction trait (days open) at the first lactation. These data were truncated by the year of 2012 to validate the reliability of genomic enhanced breeding value (GEBV) with or without heterogeneous SNP variance. Genomic data included 4,849 bulls that were born before 2012. To estimate GEBV with heterogeneous SNP variance (wGEBV), the SNP variances were calculated with two methods; square of single SNP effect (M1) and mean of 20 adjacent SNP effects (M2). Validation reliability was assessed by the coefficient of determination (R2) from the linear regression of deregressed-EBV from the full data on GEBV and wGEBV for 580 to 658 validation bulls. The R2 for fat percentage from wGEBV with both M1 and M2 were 0.07 point higher than R2 for GEBV. For the other traits, R2 for wGEBV with M1 was similar to or slightly lower than one for GEBV and R2 with M2 had the similar to or slightly higher than one for M1, except for somatic cell score. Our results suggested that the traits influenced by major SNP should be evaluated with the heterogeneity of SNP variances and the ssGBLUP with an approach of SNP window can provide more reliable results. Keywords: heterogeneous SNP variance, Holstein, single-step genomic BLUP
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Biology & Species - Bovine (dairy) 1, , 391, 2018
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