Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing

¹Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
²University of Chinese Academy of Sciences, Beijing 100049, China
³Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
⁴General Station of Animal Husbandry of Qinghai Province, Xining 810001, Qinghai, China
⁵Qinghai Conservation and Utilization Center of Livestock and Poultry Genetic Resources, Xining 810000, Qinghai, China
⁶Qinghai Sheep Breeding and Promotion Service Center, Gangcha 812300, Qinghai, China

Correspondence: Kai Zhao,Email: peiquanbang@163.com

Received: 12 November 2022 • Revised: 29 January 2023 • Accepted: 5 March 2023

Abstract

Objective
To elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits.
Methods
We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio.
Results
The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9 TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes.
Conclusion
This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

Keywords: Haplotypes; Hypoxic Adaptability; Indigenous Breeds; Selective Sweep; Production