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Evolutionary origin of genomic structural variations in domestic yaks

Author

Listed:
  • Xinfeng Liu

    (Lanzhou University
    Chinese Academy of Agricultural Sciences
    Qinghai Normal University)

  • Wenyu Liu

    (Lanzhou University)

  • Johannes A. Lenstra

    (Utrecht University)

  • Zeyu Zheng

    (Lanzhou University)

  • Xiaoyun Wu

    (Chinese Academy of Agricultural Sciences)

  • Jiao Yang

    (Lanzhou University)

  • Bowen Li

    (Lanzhou University)

  • Yongzhi Yang

    (Lanzhou University)

  • Qiang Qiu

    (Lanzhou University)

  • Hongyu Liu

    (Anhui Agricultural University)

  • Kexin Li

    (Lanzhou University)

  • Chunnian Liang

    (Chinese Academy of Agricultural Sciences)

  • Xian Guo

    (Chinese Academy of Agricultural Sciences)

  • Xiaoming Ma

    (Chinese Academy of Agricultural Sciences)

  • Richard J. Abbott

    (University of St Andrews)

  • Minghui Kang

    (Lanzhou University)

  • Ping Yan

    (Chinese Academy of Agricultural Sciences)

  • Jianquan Liu

    (Lanzhou University
    Qinghai Normal University)

Abstract

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.

Suggested Citation

  • Xinfeng Liu & Wenyu Liu & Johannes A. Lenstra & Zeyu Zheng & Xiaoyun Wu & Jiao Yang & Bowen Li & Yongzhi Yang & Qiang Qiu & Hongyu Liu & Kexin Li & Chunnian Liang & Xian Guo & Xiaoming Ma & Richard J., 2023. "Evolutionary origin of genomic structural variations in domestic yaks," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41220-x
    DOI: 10.1038/s41467-023-41220-x
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