Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle

The objective of the present study was to evaluate the predictive ability of direct genomic values for economically important dairy traits when genotypes at some single nucleotide polymorphism (SNP) loci were imputed rather than measured directly. Genotypic data consisted of 42,552 SNP genotypes for each of 1,762 Jersey sires. Phenotypic data consisted of predicted transmitting abilities (PTA) for milk yield, protein percentage, and daughter pregnancy rate from May 2006 for 1,446 sires in the training set and from April 2009 for 316 sires in the testing set. The SNP effects were estimated using the Bayesian least absolute selection and shrinkage operator (LASSO) method with data of sires in the training set, and direct genomic values (DGV) for sires in the testing set were computed by multiplying these estimates by corresponding genotype dosages for sires in the testing set. The mean correlation across traits between DGV (before progeny testing) and PTA (after progeny testing) for sires in the testing set was 70.6% when all 42,552 SNP genotypes were used. When genotypes for 93.1, 96.6, 98.3, or 99.1% of loci were masked and subsequently imputed in the testing set, mean correlations across traits between DGV and PTA were 68.5, 64.8, 54.8, or 43.5%, respectively. When genotypes were also masked and imputed for a random 50% of sires in the training set, mean correlations across traits between DGV and PTA were 65.7, 63.2, 53.9, or 49.5%, respectively. Results of this study indicate that if a suitable reference population with high-density genotypes is available, a low-density chip comprising 3,000 equally spaced SNP may provide approximately 95% of the predictive ability observed with the BovineSNP50 Beadchip (Illumina Inc., San Diego, CA) in Jersey cattle. However, if fewer than 1,500 SNP are genotyped, the accuracy of DGV may be limited by errors in the imputed genotypes of selection candidates.