Male Fertility Evaluation with a Custom-Made 384-SNP Chip in Cattle

Infertility or subfertility is a common problem in humans and other mammals. Approximately 10-15% of human couples world-wide are affected by reduced rates of fertility, with 30-50% of cases being due to male factors. In the dairy industry, a variation of up to 25% of non-return rate is evident within a population of AI bulls that meet the normal commercially acceptable standards. In the beef industry, 18-30% of beef bulls used in natural service are reproductively deficient. Recent progress in genome-wide association studies (GWAS) with SNP markers makes it possible to design genetic diagnostic assays for bull fertility selection. Here we report the generation and validation of a custom-made bovine 384-SNP chip with the Illumina VeraCode GoldenGate technology. This chip contains 237 autosomal, 4 X-linked, and 143 Y-linked SNPs, from 192 autosomal, 4 X-linked and 17 Y-linked genes/families that have been confirmed to play a role in spermatogenesis, sperm function, and/or semen quality. The chip was validated among 520 Holstein AI bulls with detailed phenotypic records. The genotypic data were analyzed using the Illumina Genome Studio software and the association study was conducted with the ASReml package. Our preliminary results revealed that 123 SNPs have minor allele frequency (MAF)>0.05. Of these, 118 SNPs were found to be significantly associated with conception rate, sperm production EBV, sperm motility, and sperm morphology (p<0.05). Linkage disequilibrium and haplotype analysis are currently under way. The potential of using this chip for male fertility selection in cattle at an early age will be evaluated.