GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle

SIMPLE SUMMARY: Understanding the genetic architecture underlying milk production traits in cattle is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we performed a genome-wide association study for milk production and quality traits in Holstein cattle. In the total of ten significant single-nucleotide polymorphisms (SNPs) associated with milk fat and protein, six are located in previously reported quantitative traits locus (QTL) regions. The study not only identified the effect of DGAT1 gene on milk fat and protein but also found several novel candidate genes. In addition, some pleiotropic SNPs and QTLs were identified that associated with more than two traits, these results could provide some basis for molecular breeding in dairy cattle. ABSTRACT: High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10(−7)), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.