Genome-wide association study for sperm concentration in Holstein-Friesian bulls

The aim of the study was to screen the entire bull genome to identify markers and candidate genes underlying sperm concentration. The analysed data set originates from a population of 877 Polish Holstein-Friesian bulls. Based on sperm concentration value, two extreme groups of bulls were created: Low (L, n = 126) and High (H, n = 140). Each bull was genotyped using the Illumina BovineSNP50 BeadChip. Genome-wide association analysis was performed with the use of GoldenHelix SVS7 software. An additive model with a Cohran-Armitage test, Correlation/Trend adjusted by a Bonferroni test, was used to estimate the effect of SNP marker for sperm concentration. Thirteen markers reached genome-wide significance. The most significant SNPs were located on chromosome 3 (rs109154964 and rs108965556), 14 (rs41621145) and 18 (rs41615539), in the close vicinity of protein arginine methyltransferase 6 (PRMT6), Sel1 repeat containing 1 (SELRC1), triple QxxK/R motif containing (TRIQK) and zinc finger homeobox 3 (ZFHX3) genes, respectively. For three other candidate genes located close to significant markers (within a distance of ca 1 Mb), namely histone deacetylase 9 (HDAC9), an inhibitor of DNA binding 2 (ID2) and glutathione S-transferase theta 1 (GSTT1), their potential role in the production of male germ cells was confirmed in earlier studies. Six additional candidate genes (Vav3, GSTM1, CDK5, NOS3, PDP1 and GAL3ST1) were suspected of being significantly associated with sperm concentration or semen biochemistry. Our results indicate the genetic complexity of sperm concentration but also open the possibility for finding causal polymorphism useful in marker-assisted selection.