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.