Genetic variances of SNP loci for milk yield in dairy cattle

Regression coefficients and genetic variances for 40,890 single nucleotide polymorphisms (SNPs) for milk yield were calculated using mixed model equations, with deregressed proof (DRP) as the dependent variable. Bulls were genotyped using the Illumina BovineSNP50 v2 BeadChip and SNPs were edited according the minor allele frequency (MAF) and high incidence of missing genotype. Evaluation was conducted in two rounds. In the preliminary round, the direct genetic values (DGVs) of all genotyped bulls (2,904) were computed and the absolute difference between the DGV and the input DRP of each bull was investigated. Bulls with an absolute difference greater than the mean absolute difference plus two standard deviations were eliminated from the data set prior to the final analysis (2,766 bulls remaining). SNP regression coefficients from the final analysis had a mean absolute value of 0.506 kg and a standard deviation of 0.409 kg. The SNP with the highest regression coefficient and genetic variance was ARSBFGLNGS4939 on chromosome 14. This SNP is located within the gene DGAT1 (diacylglycerol O-acyltransferase 1). Other SNPs with high regression coefficients and genetic variance are localised in proximity to DGAT1. The mean genetic variance of an individual SNP was 0.170, with a standard deviation of 0.384 and a mean heterozygosity of 0.372. The sum of genetic variances of all SNPs was only 6,968.8, probably because of the existence of genetic covariances between loci. The largest sum of genetic variances was on chromosome 14 (498.4, 7.15 % of the total). After the final analysis, the correlation between the DGV and the input DRP was 0.951 for all bulls. The variance of the predicted DGV was 98.11 % of the variance of the input estimated breeding value (EBV) and 63.65 % of the variance of the DRP.