Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle

Simple Summary Conformation traits have been a key breeding goal in dairy cattle for many years due to their relationship with animal productivity and other relevant characteristics. Therefore, the primary objectives of this study were to conduct genome-wide association studies (GWASs) for conformation traits and identify candidate genes and metabolic pathways associated with these traits in Brazilian Holstein cattle. Phenotypic, pedigree, and genomic (100 K SNP chip) data from 2339 Holstein animals raised across multiple Brazilian states were used for this study. Thirty-six significant SNPs were identified for five composite traits. These genomic markers overlap with candidate genes influencing biological processes such as myogenesis, adipogenesis, and angiogenesis. These findings contribute to unraveling the genetic background of conformation traits in Brazilian Holstein cattle.Abstract The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Holstein animals distributed across the states of Rio Grande do Sul, Paran & aacute;, S & atilde;o Paulo, and Minas Gerais were used. The genotypic data were obtained with a 100 K SNP marker panel. The single-step genome-wide association study (ssGWAS) method was employed in the analyses. Genes close to a significant SNP were identified in an interval of 100 kb up- and downstream using the Ensembl database available in the BioMart tool. The DAVID database was used to identify the main metabolic pathways and the STRING program was employed to create the gene regulatory network. In total, 36 significant SNPs were found on 15 chromosomes; 27 of these SNPs were linked to genes that may influence the traits studied. Fourteen genes most closely related to the studied traits were identified, as well as four genes that showed interactions in important metabolic pathways such as myogenesis, adipogenesis, and angiogenesis. Among the total genes, four were associated with myogenesis (TMOD2, TMOD3, CCND2, and CTBP2), three with angiogenesis (FGF23, FGF1, and SCG3), and four with adipogenesis and body size and development (C5H12orf4, CCND2, EMILIN1, and FGF6). These results contribute to a better understanding of the biological mechanisms underlying phenotypic variability in conformation traits in Brazilian Holstein cattle.