Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses

SIMPLE SUMMARY: The performance of genome-wide association studies with high-density single-nucleotide polymorphism panels and next-generation sequencing is a robust approach to the identification of genetic variants that can elucidate variation in complex diseases and economically important traits in farm animals. We identified many markers associated with crucial traits, such as muscle development in Simmental beef cattle. This information can be used to pinpoint candidate genes affecting traits of interest. Our results contribute to the clarification of molecular mechanisms underlying processes associated with hind-leg meat yield and carcass depth in beef cattle. ABSTRACT: Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Beadchip (~670 k SNPs) and next-generation sequencing (~12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.