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A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication

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Abstract

The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome (oMSY), using nanopore sequencing and Hi-C technologies. The oMSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages (HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31822052) and the National Thousand Youth Talents Plan, Natural Science Foundation of China (31802027), and Natural Science Basic Research Plan in Shaanxi Province of China (2019JQ-002). We thank the High-Performance Computing platform of Northwest A&F University for providing computing resources. We also thank members of the NextGen project for sharing their data.

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  1. Contributed equally to this work

Authors and Affiliations

  1. Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China

    Ran Li, Peng Yang, Ming Li, Wenwen Fang, Hojjat Asadollahpour Nanaei, Duo Du, Yudong Cai, Xuelei Dai, Qimeng Yang, Chunna Cao & Yu Jiang

  2. State Key Laboratory of 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, 730020, China

    Xiangpeng Yue

  3. State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China

    Shangquan Gan

  4. Faculty of Animal Science and Technology, Yunan Agricultural University, Kunming, 650201, China

    Weidong Deng

  5. Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China

    Sangang He, Wenrong Li & Mingjun Liu

  6. State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Runlin Ma

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Corresponding author

Correspondence to Yu Jiang.

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Compliance and ethics

The author(s) declare that they have no conflict of interest. Blood samples were taken by conforming with the Helsinki Declaration of 1975 (as revised in 2008) concerning Animal Rights.

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Li, R., Yang, P., Li, M. et al. A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication. Sci. China Life Sci. 64, 1116–1130 (2021). https://doi.org/10.1007/s11427-020-1807-0

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  • DOI: https://doi.org/10.1007/s11427-020-1807-0

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