QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep

SIMPLE SUMMARY: Ram semen traits including volume, gross motility, concentration, and percent post-thaw motility are routinely assessed prior to use in artificial breeding programs, as they have been shown to influence conception outcomes. Semen quality and associated traits are complex but heritable, and as such, identifying genes that underlie variability in these traits may help develop alternative means to improve conception outcomes and therefore reproductive efficiency in sheep. Therefore, the aim of this study was to identify genomic regions and associated genes that may significantly influence semen traits like volume, gross motility, concentration, and percent post-thaw motility in Merino sheep. Assessment of over 20 years’ worth of semen collection data identified 35 genomic regions to be significantly associated with Merino ram semen volume, gross motility, concentration, and percent post-thaw motility. A total of 290 candidate genes were identified within genomic regions found to be significantly associated with Merino ram semen traits. All Merino ram semen traits were also found to be lowly heritable, affirming results from previous studies. Validation of candidate genes identified in the current study could provide novel insights into molecular mechanisms contributing to variability in semen associated traits. ABSTRACT: Ram semen traits play a significant role in conception outcomes, which in turn may influence reproductive efficiency and the overall productivity and profitability of sheep enterprises. Since hundreds of ewes may be inseminated from a single ejaculate, it is important to evaluate semen quality prior to use in sheep breeding programs. Given that semen traits have been found to be heritable, genetic variation likely contributes to the variability observed in these traits. Identifying such genetic variants could provide novel insights into the molecular mechanisms underlying variability in semen traits. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with semen traits in Merino sheep. A genome-wide association study (GWAS) was undertaken using 4506 semen collection records from 246 Merino rams collected between January 2002 and May 2021. The R package RepeatABEL was used to perform a GWAS for semen volume, gross motility, concentration, and percent post-thaw motility. A total of 35 QTLs, located on 16 Ovis aries autosomes (OARs), were significantly associated with either of the four semen traits in this study. A total of 89, 95, 33, and 73 candidate genes were identified, via modified Bonferroni, within the QTLs significantly associated with volume, gross motility, concentration, and percent post-thaw motility, respectively. Among the candidate genes identified, SORD, SH2B1, and NT5E have been previously described to significantly influence spermatogenesis, spermatozoal motility, and high percent post-thaw motility, respectively. Several candidate genes identified could potentially influence ram semen traits based on existing evidence in the literature. As such, validation of these putative candidates may offer the potential to develop future strategies to improve sheep reproductive efficiency. Furthermore, Merino ram semen traits are lowly heritable (0.071–0.139), and thus may be improved by selective breeding.