Genome-Wide Association Study of Heifer Pregnancy in Red Angus Cattle

Reproductive performance in cattle herds is one of the most critical factors influencing the economic viability of beef enterprises. Heifers that become pregnant as yearlings will have more calves over their lifetime and allow for greater recovery of heifer development costs. However, genetic improvement of the trait heifer pregnancy (HPG) under traditional genetic approaches is difficult due to low heritability and accuracy of selection. An approach to address this dilemma is to identify QTL that could be used to improve HPG. The objective of this study was to identify QTL associated with HPG in Red Angus cattle. A genome wide association study (GWAS) was performed using deregressed HPG EBV, estimated using a single trait animal model and three generation pedigree formed from animals in the data used for national cattle evaluation performed during December 2014 for Red Angus Association of America. Initially, animals were genotyped using various illumina SNP chip-platforms ranging in density from 32,186 to 140,114 SNP. Genotypes data were then imputed with FImpute so each animal (n = 9,380) possessed 74,659 SNP genotypes. Individual animals that contained a reported breed percent >50 percent Red Angus with a deregressed EBV reliability greater than 0.05 were merged with the genotype file and marker quality control was performed yielding 567 animals. 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), or those SNP in extreme LD (r² > 0.99). These criteria left 64,010 SNP available for GWAS. Genomic windows of approximately 1 Mb (25.12 ± 8.31 SNP) in size were determined to significantly influence HPG if the size of their effect explained greater than 0.75% of the genetic variance in the trait. Bayes B in the software GenSel was used in GWAS. Two marker windows were associated with HPG. One QTL was located on bovine chromosome 28 and accounted for nearly 2% of the genetic variance, while the second on chromosome 11 accounted for 1.6% of the variance. These QTL results differ from other reports and suggest that QTL for HPG are not in concordance with GWAS results involving breeds such as Brangus and Simmental. Discovery of these QTL are encouraging for genetic improvement programs in Red Angus cattle. Continued genotyping and increased reporting across family lines within the Red Angus breed would serve to enhance these results.