Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

Liming Zhao; Lvfeng Yuan; Fadi Li; Xiaoxue Zhang; Huibin Tian; Zongwu Ma; Deyin Zhang; Yukun Zhang; Yuan Zhao; Kai Huang; Xiaolong Li; Jiangbo Cheng; Dan Xu; Xiaobin Yang; Kunchao Han; Xiuxiu Weng; Weimin Wang

doi:10.1016/j.jgg.2024.03.015

Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

J Genet Genomics. 2024 Apr 4:S1673-8527(24)00068-7. doi: 10.1016/j.jgg.2024.03.015. Online ahead of print.

Authors

Liming Zhao¹, Lvfeng Yuan², Fadi Li¹, Xiaoxue Zhang³, Huibin Tian¹, Zongwu Ma³, Deyin Zhang¹, Yukun Zhang¹, Yuan Zhao¹, Kai Huang¹, Xiaolong Li¹, Jiangbo Cheng¹, Dan Xu¹, Xiaobin Yang¹, Kunchao Han¹, Xiuxiu Weng¹, Weimin Wang⁴

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, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China.
² Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China.
³ College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
⁴ 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, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China. Electronic address: wangweimin@lzu.edu.cn.

PMID: 38582298
DOI: 10.1016/j.jgg.2024.03.015

Abstract

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genome selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveal those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

Keywords: GPR35; Hu sheep; NAV1; selection signature; single nucleotide polymorphism; whole-genome resequencing.