全基因组重测序揭示中国牛的遗传结构与选择

Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing.

作者信息

Mei Chugang, Wang Hongcheng, Liao Qijun, Wang Lizhong, Cheng Gong, Wang Hongbao, Zhao Chunping, Zhao Shancen, Song Jiuzhou, Guang Xuanmin, Liu George E, Li Anning, Wu Xueli, Wang Chongzhi, Fang Xiaodong, Zhao Xin, Smith Stephen B, Yang Wucai, Tian Wanqiang, Gui Linsheng, Zhang Yingying, Hill Rodney A, Jiang Zhongliang, Xin Yaping, Jia Cunling, Sun Xiuzhu, Wang Shuhui, Yang Huanming, Wang Jian, Zhu Wenjuan, Zan Linsen

机构信息

College of Animal Science and Technology, Northwest A&F University, Yangling, China.

BGI Genomics, BGI-Shenzhen, Shenzhen, China.

出版信息

Mol Biol Evol. 2018 Mar 1;35(3):688-699. doi: 10.1093/molbev/msx322.

DOI:10.1093/molbev/msx322

PMID:29294071

Abstract

The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus. Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color (ERCC2, MC1R, ZBTB17, and MAP2K1), dairy traits (NCAPG, MAPK7, FST, ITFG1, SETMAR, PAG1, CSN3, and RPL37A), and meat production/quality traits (such as BBS2, R3HDM1, IGFBP2, IGFBP5, MYH9, MYH4, and MC5R). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.

摘要

中国的牛遗传资源丰富多样，但其价值和潜力尚未被发掘。为了确定中国牛的遗传多样性和群体结构，我们分析了来自六个具有表型和地理代表性的中国牛品种的46头牛的全基因组，以及18头红安格斯牛基因组、11头日本黑牛基因组，还有先前研究中可获取的普通牛和瘤牛基因组。我们的结果表明，中国牛起源于普通牛和瘤牛的杂交。此外，我们发现中国牛的遗传变异水平取决于瘤牛血统的比例。我们还发现了许多与特定品种特征驯化相关的潜在选择性清除区域，这些区域包括与毛色（ERCC2、MC1R、ZBTB17和MAP2K1）、产奶性状（NCAPG、MAPK7、FST、ITFG1、SETMAR、PAG1、CSN3和RPL37A）以及肉产量/品质性状（如BBS2、R3HDM1、IGFBP2、IGFBP5、MYH9、MYH4和MC5R）相关的基因。这些发现极大地扩展了牛的遗传变异目录，并揭示了中国牛进化历史和驯化性状的新见解。