SNPs Cumulating to Genetic Variation for Fertility in Crossbred (Bos taurus X Bos indicus) Bull Spermatozoa

Abstract Purpose : The objective of the present study is to identify important polymorphisms at single nucleotide in Holstein crossbred bull spermatozoa and to identify genetic variants significantly influence or associated to bull fertility. Methods: Spermatozoa from high- (HF) and low-fertile (LF) breeding bulls were subjected to high throughput Next-generation sequencing to identify important SNPs and novel variants associated with fertility. Results: A total of 77,036 genome wide SNPs were identified in the crossbred bull spermatozoa with a minimum read depth of 20, and among them, 10,269 were observed to be novel variants. A total of 42,290 and 34,748 variants were recorded in HF and LF bulls respectively, among which 6115 and 4673 were found to novel in respective group. Higher number of SNPs and Indels were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variation in HF bulls indicated their enrichment in various important pathways like oxidative phosphorylation and metabolic pathways. On the other hand, GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca 2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. Conclusions : 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, protection from oxidative stress and bull fertility. The identified SNPs could be used as a tool for identification and selection of bulls for high fertility upon validation in large number of bulls