Evolutionary origin of genomic structural variations in domestic yaks

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. Abbott, Minghui Kang (), Ping Yan () and Jianquan Liu ()
Additional contact information
Xinfeng Liu: Lanzhou 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

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-41220-x

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