Whole genome sequencing of simmental cattle for SNP and CNV discovery

BackgroudThe single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity.ResultsIn this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25x) short-read next generation sequencing and single-molecule long reads sequencing data. A total of similar to 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility.ConclusionsIn conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.

Automated summary

In this study, high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls were analyzed for genetic variations (SNPs and CNVs) using high-coverage short-read next generation sequencing and single-molecule long reads sequencing data. The study identified a large number of SNPs and CNVs in Simmental bulls, as well as positive selected genes (PSGs) and CNVRs overlapping with quantitative trait loci (QTLs) related to immunity, muscle development, and reproduction. Moreover, the study discovered two new variants in LEPR, potentially related to artificial breeding for improving economic traits, and identified genes and pathways related to male fertility. Notably, a CNV on SPAG16 was found to be completely deleted in all PSM bulls and half of HSM bulls, suggesting a crucial role in bull fertility.