Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle

The purpose of this study was to identify genomic regions explaining a major proportion of the genetic variance in milk production and milk fat and protein content on a commercial herd of Holstein and Holstein x Jersey crossbred cattle bred in an extensive grazing system. We analyzed 305-day cumulative milk production records from 18876 cows at first lactation, of which 16907 and 16735 had milk fat and protein content records during the same period. After data quality control, genotypes from 998 animals on 40417 SNPs included in the Illumina Bovine SNP50 v2 BeadChip were available. Weighted single-step genome-wide association studies were conducted for milk yield (MY), fat content (FC) and protein content (PC). Windows of 10 adjacent single nucleotide polymorphisms explaining more than 0.31% of the genetic variance were considered relevant. Protein-coding genes located within those windows were retrieved, their functional relevance was assessed, the main functional categories and biological processes represented by them were identified, and an overrepresentation test was performed. Relevant windows for MY, FC and PC were 52, 57 and 56, and harbored 304, 293 and 269 protein-coding genes, respectively. The proteins encoded by those genes were mainly involved in cellular, metabolic and biological regulation processes. Cellular response to cytokine stimulus, GTPase activity and GTP binding, and heterotrimeric G-protein were the main overrepresented biological process, molecular functions, and protein class, respectively. Among the candidate genes found, some previously reported genes associated with milk traits, such as CDH2, DGAT1, GRINA, LIPA, PGR, RPGRIP1L, VPS28, MAF1, and FTO were identified. However, novel candidate genes related to transcriptional regulation and transporter activity were also found. These results contribute to a better understanding of the loci influencing milk traits in the main dairy cattle breeds in Argentina.