Genomic Regions Associated with Udder Conformation Traits in the Mexican Holstein Cattle

Genome Wide Association Study (GWAS) is a method which allows the detection of genes or quantitative traits loci related to economically important traits. The aim of this study was to identify the significant SNP markers associated to udder traits (Udder deep (UD), texture (TX), median suspensory (MS), fore attachment (FA), fore teat placement (FTP), fore teat length (FTL), rear teat placement (FTP), rear attachment height (RAH), rear attachment width (RAW) and dairy form (DF)), in Mexican Holstein cattle, and search if these markers were previously referenced in the UMD_3.1 database. The phenotypes used were genetic breeding values. After the quality control analysis, a total of 1,535 individuals and 31,030 SNP (from a set of 42,224 imputed markers) were included. GWAS, were performed with a mixed model and regression analysis (GRAMMAR), accounting for the genomic kinship matrix, using the GenABEL package of R. SNP markers with a p<0.0001 were assumed significant. For all traits, a total of 10 SNP were statistically significant (indicating chromosome and position for each SNP), one for FA (11: 21535801), three for MS (19: 23701216, 29: 43498073, 29: 43429511), two for RTP (2: 50069820, 16: 3762358), two for UD (12: 22885975, 29: 2324336) and two for TX (2: 12138830, 24:26189197). Eight significant SNP were located in genomic regions previously referenced to conformation traits in dairy cattle. The SNPs 11:21535801 and SNP 16:3762358 have not been referenced in dairy cattle but have been associated to body and carcass weight respectively in in Angus cattle.