Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

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dc.creatorXiaoting Xia
dc.creatorFengwei Zhang
dc.creatorShuang Li
dc.creatorXiaoyu Luo
dc.creatorLixin Peng
dc.creatorZheng Dong
dc.creatorPausch, H.
dc.creatorLeonard, A.S.
dc.creatorCrysnanto, D.
dc.creatorShikang Wang
dc.creatorBin Tong
dc.creatorLenstra, J.A.
dc.creatorHan Jianlin
dc.creatorFuyong Li
dc.creatorTieshan Xu
dc.creatorLihong Gu
dc.creatorLiangliang Jin
dc.creatorRuihua Dang
dc.creatorYongzhen Huang
dc.creatorXianyong Lan
dc.creatorGang Ren
dc.creatorYu Wang
dc.creatorYuanpeng Gao
dc.creatorZhijie Ma
dc.creatorHaijian Cheng
dc.creatorYun Ma
dc.creatorHong Chen
dc.creatorWeijun Pang
dc.creatorChuzhao Lei
dc.creatorNingbo Chen
dc.date2023-09-18
dc.date2023-09-27T12:14:56Z
dc.date2023-09-27T12:14:56Z
dc.date.accessioned2026-06-27T17:11:51Z
dc.descriptionBackground Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. Results In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a “north–south” gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. Conclusions Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.
dc.identifierhttps://hdl.handle.net/10568/132029
dc.identifier.urihttp://hdl.handle.net/123456789/145103
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceXiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Pausch, H., Leonard, A.S., Crysnanto, D., Shikang Wang, Bin Tong, Lenstra, J.A., Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu, Liangliang Jin, Ruihua Dang, Yongzhen Huang, Xianyong Lan, Gang Ren, Yu Wang, Yuanpeng Gao, Zhijie Ma, Haijian Cheng, Yun Ma, Hong Chen, Weijun Pang, Chuzhao Lei and Ningbo Chen. 2023. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Genome Biology 24:211.c
dc.subjectcattle
dc.subjectgenetics
dc.subjectanimal breeding
dc.subjectgenomes
dc.titleStructural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
dc.typeJournal Article

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Instituto Internacional de Investigaciones Pecuarias (ILRI)