accuracy of direct genomic values in holstein bulls and cows using subsets of snp markers的准确性直接在荷斯坦公牛和母牛使用基因值的子集snp标记.pdfVIP

Moser et al. Genetics Selection Evolution 2010, 42:37 Ge n e t i c s /content/42/1/37 Se l e c t i o n Evolution RESEARCH Open Access Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers Gerhard Moser1,2*, Mehar S Khatkar1,2, Ben J Hayes1,3, Herman W Raadsma1,2 Abstract Background: At the current price, the use of high-density single nucleotide polymorphisms (SNP) genotyping assays in genomic selection of dairy cattle is limited to applications involving elite sires and dams. The objective of this study was to evaluate the use of low-density assays to predict direct genomic value (DGV) on five milk production traits, an overall conformation trait, a survival index, and two profit index traits (APR, ASI). Methods: Dense SNP genotypes were available for 42,576 SNP for 2,114 Holstein bulls and 510 cows. A subset of 1,847 bulls born between 1955 and 2004 was used as a training set to fit models with various sets of pre-selected SNP. A group of 297 bulls born between 2001 and 2004 and all cows born between 1992 and 2004 were used to evaluate the accuracy of DGV prediction. Ridge regression (RR) and partial least squares regression (PLSR) were used to derive prediction equations and to rank SNP based on the absolute value of the regression coefficients. Four alternative strategies were applied to select subset of SNP, namely: subsets of the highest ranked SNP for each individual trait, or a single subset of evenly spaced SNP, where SNP were selected based on thei