Genome-wide association study for semen quality traits in German Warmblood stallions

•A genome-wide association study for semen quality traits showed genome-wide significant loci.•Among the associated regions we identified ten regions harboring fertility related candidate genes.•For an associated region on chromosome 20 the CRISP gene cluster is in close proximity.•The present association study is an important step for molecular characterization of genes related with semen quality.

We performed a genome-wide association study for semen quality traits in 139 German Warmblood stallions. Stallions were genotyped using the Illumina equine SNP50 Beadchip. Traits analysed were de-regressed estimated breeding values (EBVs) for gel-free volume, sperm concentration, total number of sperm, progressive motility and the total number of progressively motile sperm. The GWAS revealed 29 SNPs on 12 different chromosomes as genome-wide significantly associated with semen quality traits. For ten genomic regions we could retrieve candidate genes influencing stallion fertility. Among the candidate genes, we could find the genes encoding cysteine-rich secretory proteins (CRISP1, CRISP2 and CRISP3). This was the first GWAS in horses performed for semen quality traits.