Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing

  • Dehong Tian (Key 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) ;
  • Buying Han (Key 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) ;
  • Xue Li (Key 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) ;
  • Dehui Liu (Key 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) ;
  • Baicheng Zhou (General Station of Animal Husbandry of Qinghai Province) ;
  • Chunchuan Zhao (Qinghai Conservation and Utilization Center of Livestock and Poultry Genetic Resources) ;
  • Nan Zhang (Qinghai Conservation and Utilization Center of Livestock and Poultry Genetic Resources) ;
  • Lei Wang (Qinghai Sheep Breeding and Promotion Service Center) ;
  • Quanbang Pei (Qinghai Sheep Breeding and Promotion Service Center) ;
  • Kai Zhao (Key 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)
  • Received : 2022.11.12
  • Accepted : 2023.03.05
  • Published : 2023.07.01
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Abstract

Objective: This study aimed 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

Acknowledgement

Dr Zhao supported by K.C. Wong Education Foundation. Dr Tian and Zhao were supported by the 1,000 Talent program of Qinghai Province. We thank the editor and anonymous reviewers for their constructive comments. We greatly appreciate our collaborators for their assistance in sample collection.

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