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Genome-wide selective sweep analysis of the high-altitude adaptability of yaks by using the copy number variant

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Abstract

The domestic yak (Bos grunniens) from the Qinghai–Tibet Plateau is an important animal model in high-altitude adaptation studies. Here, we performed the genome-wide selective sweep analysis to identify the candidate copy number variation (CNV) for the high-altitude adaptation of yaks. A total of 531 autosomal CNVs were determined from 29 yak genome-wide resequencing data (15 high- and 14 low-altitude distributions) by using a CNV caller with a CNV identification interval > 5 kb, CNV silhouette score > 0.7, and minimum allele frequency > 0.05. Most high-frequency CNVs were located at the exonic (44.63%) and intergenic (46.52%) regions. In accordance with the results of the selective sweep analysis, 7 candidate CNVs were identified from the interaction of the top 20 CNVs with highest divergence from the FST and VST between the low (LA) and high (HA) altitudes. Five genes (i.e., GRIK4, IFNLR1, LOC102275985, GRHL3, and LOC102275713) were also annotated from the seven candidate CNVs and their upstream and downstream ranges at 300 kb. GRIK4, IFNLR1, and LOC102275985 were enriched in five known signal pathways, namely, glutamatergic synapse, JAK–STAT signaling pathway, cytokine–cytokine receptor interaction, neuroactive ligand–receptor interaction, and olfactory transduction. These pathways are involved in the environmental adaptability and various physiological functions of animals, especially the physiological regulation under a hypoxic environment. The results of this study advanced the understanding of CNV as an important genomic structure variant type that contributes to HA adaptation and helped further explain the molecular mechanisms underlying the altitude adaptability of yaks.

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Acknowledgements

This work was supported by Open Project Program of State Key Laboratory of Barley and Yak Gemplasm Resources and Genetics Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa Tibet 850002, China.

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  1. E. Guang-Xin, Bai-Gao Yang, and Yan-Bin Zhu contributed equally to this work.

Authors and Affiliations

  1. College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715, China

    E. Guang-Xin, Bai-Gao Yang, Xing-Hai Duang & Wang-Dui Basang

  2. State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, 850002, China

    Yan-Bin Zhu

  3. Sichuan Academy of Grassland Sciences, Chengdu, 611731, Sichuan, China

    Xiao-Lin Luo & Tian-Wu An

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  1. E. Guang-Xin
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Guang-Xin, E., Yang, BG., Zhu, YB. et al. Genome-wide selective sweep analysis of the high-altitude adaptability of yaks by using the copy number variant. 3 Biotech 10, 259 (2020). https://doi.org/10.1007/s13205-020-02254-w

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