Genetic variation in bulls divergent for fertility

Abstract

Bovine fertility remains a critical issue underpinning the sustainability of the agricultural sector. Since the realisation of an unfavourable relationship between fertility and production traits in cattle, methods to select for improved fertility have been the subject of intense research. Research has focused primarily on fertility in the cow, with little attention on the role of the bull. Despite the use of artificial insemination to breed high-quality livestock, fertility rates can fall as low as 25% in sub-fertile bulls. Genetic variants have previously been shown to regulate fertility; however, these variants require further elucidation in cattle. Targeted sequencing and whole-exome sequencing approaches were employed to catalogue genetic variation in ?-defensin genes and also genetic variants in all other annotated bovine genes, to identify exome-wide variants associated with bull fertility. In addition, validation of associated sequence variants in an independent population of bulls was performed. A haplotype containing 94 SNPs covering ~138kb was found to be significantly associated with fertility (P = 0.002). This haplotype spans 8 ?-defensin genes including the bovine orthologue of DEFB126 which has been shown to play a role in male fertility in other species. In humans, DEFB126 SNPs have been shown to reduce the ability of sperm to penetrate cervical mucus. Predicted O-linked glycosylation sites were also identified in DEFB126 protein sequence. Reduced glycosylation in DEFB126 has previously been shown to be correlated with poor sperm penetration and men with altered glycosylation were sub-fertile. Interestingly, a recent study by our group showed expression of BBD126 on the caudal sperm surface with staining concentrated on the sperm cell tails, where glycosylation is predicted to occur. Also, significant differences in the ability of high-fertility bulls with the haplotype to cluster and bind to bovine oviductal epithelial cells compared to high-fertility bulls without the haplotype was shown. SNPs most associated with bull fertility (n=58) were subsequently selected from both datasets for genotyping in an independent population of AI bulls (n=123). The SNP most associated with the fertility phenotype in the validation analysis was located in the FOXJ3 gene (P = 0.0016), with a SNP frequency differential between low and high-fertility bulls of more than 20% (low-fertility v high-fertility: 69% v 48%). This represents the first analysis of genetic variation in the expanded suite of ?-defensin genes in cattle. Given the known association of ?-defensin genes with somatic cell count, an important indicator of economic importance for mastitis, the identified variants were added to a SNP chip. In total, 863 SNPs discovered by this dual sequencing approach have been added to version 3 of the International Dairy and Beef SNP chip to validate their association in large numbers of cattle and across multiple phenotypes of economic interest. FOXJ3 and a ?-defensin haplotype have been shown to be significantly associated with fertility in bulls. DEFB126 has been shown in humans to have a polymorphism resulting in decreased ability to penetrate cervical mucus and two variants in BBD126 are located in the ?-defensin haplotype. In conclusion, this research supports a role for FOXJ3 and a ?-defensin haplotype encompassing BBD126, in regulating male fertility in cattle.