Genome-Wide Association Study for Stayability in Red Angus Cattle

Beef female stayability (STAY), as defined by the Red Angus Association of America (RAAA), is the ability of a female to produce five consecutive calves by six years of age given she produced as a heifer. Stayability has been described as an economically relevant trait, and the magnitude of the value placed on STAY in various commercially available general purpose economic selection indices indicates its value to producers is greater than any other trait included in those indices. Given the importance of STAY to the profitability of commercial beef operations, the objective of this study was to identify QTL associated with STAY in Red Angus cattle. A genome wide association study (GWAS) was performed using deregressed STAY EBV, calculated using a single trait animal model and three generation pedigree formed using data for the national cattle evaluation in December 2014 for the RAAA. Initially, animals were genotyped using various Illumina SNP chip-platforms ranging in density from 32,186 to 140,114 SNP. Genotypes were then imputed with FImpute so each animal possessed 74,659 SNP genotypes. Individual animals whose breed percent was >50 percent Red Angus with a deregressed EBV reliability >0.05 were merged with the genotype file and marker quality control was performed. Criteria for sifting genotypes consisted of removing those markers where the average call rate was < 0.85, minor allele frequency < 0.01, those not in Hardy-Weinberg equilibrium (P < 0.0001), and those SNP in extreme LD (r² > 0.99). These criteria resulted in 2,664 animals with 62,807 SNP available for GWAS. Genomic windows of approximately 1Mb (25.12 ± 8.31 SNP) in size were determined to significantly influence stayability if the size of their effect explained greater than 0.75% of the genetic variance in the trait. Association studies were performed using Bayes B methodology in the software package GenSel. Twelve marker windows were identified as QTL associated with STAY. These windows were located on BTA 2, 5, 6, 9, 12, 15 and 16. On two chromosomes, 9 and 15, multiple windows were identified (3 and 4, respectively). Although these are the first set of markers reported to be associated with STAY in Bos taurus beef cattle, similar chromosomes were identified in GWAS involving Nellore-Angus crossbred cows (BTA4, 5, 15, 19) for STAY, as well as for calving interval (BTA 5) and productive lifespan (BTA 15) in dairy cattle.