188 Identification of quantitative trait loci and associated candidate genes for pregnancy success in Brangus heifers

In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female who produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production. Here, genome-wide association studies (GWAS) were performed on pregnancy outcome traits from a population of Brangus heifers (average percent Brahman = 37.5%) on a ranch in South Florida. Heifers were genotyped with the Bovine GGP F250 array (Neogen) that contains ∼250,000 SNPs, which are primarily within protein coding regions. Heifers were bred in a fall/winter breeding season involving a single round of timed artificial insemination followed by natural mating for three months. Two phenotypes were analysed: pregnancy outcome to first-service artificial insemination (PAI; n = 1484) and pregnancy status at the end of the breeding season (PEBS; n = 1728). Heritabilities were estimated using AIREMLF90 from the BLUPF90 software package. The GWAS were conducted with genomic best linear unbiased prediction (GBLUP) procedures using a 500 kb sliding window. Bodyweight and Brahman percent were used as fixed effects. Quality control parameters were set with a minor allele frequency < 5% and call rate < 90%. Manhattan plots were produced using R software. The heritability for PAI was estimated as 0.153, with a standard error of 0.052. One large quantitative trait locus (QTL) that explained more than 1.7% of the genetic variation for PAI was found on BTA7, in a region containing FGF1, SPRY4, and ARHGAP26. FGF1 has been previously associated with the maternal reproductive tract and is a potential regulator of embryonic development. Other QTLs explaining between 0.5–1% of the genetic variation were found on BTA1, 5, 12, 15, 16, 18, 19, and 22. The heritability of PEBS was estimated at 0.130, with a standard error of 0.044. Three large QTLs that each explained more than 1.8% of genetic variation were identified on BTA 5, 7, and 9. The QTL on BTA7 was synonymous with the QTL for PAI. The QTL on BTA5 was linked to a large number of genes, including TAC3, STAT6, NEMP1, and PTGES3, all of which have been identified in the literature for reproductive functions or association with pregnancy outcomes. The region of BTA9 contained only one gene, OGFRL1, with unknown reproductive function. In summary, QTL and candidate SNPs associated with reproductive function of beef heifers were identified, including a large QTL associated with FGF1. Confirmation of these associations with larger populations could lead to the development of genomic estimates of reproductive function in beef cattle. Moreover, additional research is warranted to study the function of candidate genes associated with QTL.