Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

SIMPLE SUMMARY: Body size is a significant economic trait for dairy cows due to its significant influence on the production, health, selection, and environmental adaptation of dairy cattle. However, measurements of body size are widely used to predict body weight. Managers of dairy farms also use them to assess the development and growth of the animals during the rearing process. Therefore, understanding the genetic basis of inter-individual variation of body size might accelerate future efforts aimed at dairy cattle improvement. Our genome-wide association study identified several genes and functional pathways associated with body size traits in Chinese Holstein cattle. Results of this study might serve as a foundation for genetic improvement programs for dairy cattle that are based on molecular genetics. ABSTRACT: Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10(−7)) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.