Whole genome sequencing of simmental cattle for SNP and CNV discovery

Ting Sun; Shengwei Pei; Yangkai Liu; Quratulain Hanif; Haiyue Xu; Ningbo Chen; Chuzhao Lei; Xiangpeng Yue

doi:10.1186/s12864-023-09248-x

Whole genome sequencing of simmental cattle for SNP and CNV discovery

BMC Genomics. 2023 Apr 5;24(1):179. doi: 10.1186/s12864-023-09248-x.

Authors

Ting Sun^#^{1

2

3}, Shengwei Pei^#¹, Yangkai Liu¹, Quratulain Hanif^{4

5}, Haiyue Xu¹, Ningbo Chen², Chuzhao Lei², Xiangpeng Yue⁶

Affiliations

¹ State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
² Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
³ College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
⁴ Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
⁵ Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
⁶ State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China. lexp@lzu.edu.cn.

^# Contributed equally.

Abstract

Backgroud: The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity.

Results: In 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 (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 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.

Conclusions: In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.

Keywords: CNV; SNP; Selection; Simmental cattle; Sperm motility.

MeSH terms

Animals
Cattle
DNA Copy Number Variations*
Male
Polymorphism, Single Nucleotide*
Quantitative Trait Loci
Sperm Motility
Whole Genome Sequencing

Abstract

MeSH terms

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