Genomics and Fertility in Stallions

Stallion fertility is of high economic importance for the horse industry. The discovery of molecular mechanisms affecting fertility will be facilitated by the horse genome assembly, the development of genome-wide transcript and single-nucleotide polymorphism (SNP) arrays, and next-generation sequencing of whole mammalian genomes for analyzing complex fertility traits. Candidate genes can be identified via their involvement in key processes of horse reproduction or other species and their fertility-influencing mutations in genes described for species other than horses. We prioritized candidate genes that have been shown to play a major role in stallion reproduction and for which a relevant role in male reproduction in man or mice has been revealed, and located these genes on the horse genome assembly EquCab2.0. First, we sequenced candidate genes for stallion reproduction, including CRISP3, SPATA1, INHBA, ACE, SP17, FSHB, and PRLR, and screened these genes for polymorphisms associated with pregnancy rate per estrus in stallions. Genome-wide association studies using the equine Illumina 50K beadchip were performed to discover highly associated SNPs for stallion fertility. Among the candidate genes identified, we could find associations for candidate genes not yet analyzed. Molecular genetic studies of candidate genes from known pathways are encouraging, and with the novel tools available for genome-wide association studies and whole-genome sequencing, our knowledge on genetics of stallion fertility will be advanced.