Genome-Wide Association Study for Milk Fatty Acids in First Lactation Holstein Cows

Detecting genes associated with milk fat composition could provide better biological understanding of bovine milk fat production and new possibilities to change the milk fat composition by genetic selection. In this study, we conducted a genome-wide association study (GWAS) for five groups of milk fatty acids (saturated, unsaturated, short, medium, and long chain) in a sample of 377 Holstein cattle using estimated breeding values via SNP1101 software. A single SNP regression model including a polygenic term fitting the SNP based genomic relationship matrix was used. Genotypes from the Illumina BovineSNP50 Bead chip were imputed to the Illumina high dense panel (777k). The GWAS identified a total of 75 genome-wide significant SNPs (FDR < 0.01) associated with the five milk fatty acid groups. The chromosome regions associated with milk fatty acid groups were located on BTA14 and 20. However, most of significant SNPs were detected on BTA14, around the DGAT1 gene, which is known to be a major gene for milk fat production. The GWAS was also repeated by fitting a single SNP located in the DGAT1 gene as a covariate in the model to adjust for the effect of this major gene and its potential carry over effects. The new analyses resulted in no significant associations with fatty acid groups (>10% FDR). However, several distinct peaks in the log-likelihood profile were observed across the genome indicating that an increase in sample size in future studies might lead to significant associations in addition to the one observed with the DGAT1 gene.