Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus x Bos indicus) bull spermatozoa

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

Automated summary

In this study, high-throughput next-generation sequencing was used to identify important SNPs and novel variants associated with fertility in high-fertile (HF) and low-fertile (LF) breeding bulls. The results showed a higher number of SNPs in HF bulls compared to LF bulls. GO analysis revealed the involvement of genes with significant variations in oxidative phosphorylation and metabolic pathways in HF bulls, while genes related to Ca2++ ion binding, ribosomal structure, translation, and ribosomal small subunit assembly were found to have significant variations in LF bulls. Several candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A were identified, which are associated with sperm functionality, survival, oxidative stress, and bull fertility.