Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing

Chugang Mei, Hongcheng Wang, Qijun Liao, Lizhong Wang, Gong Cheng, Hongbao Wang, Chunping Zhao, Shancen Zhao, Jiuzhou Song, Xuanmin Guang, George E. Liu, Anning Li, Xueli Wu, Chongzhi Wang, Xiaodong Fang, Xin Zhao, Stephen B. Smith, Wucai Yang, Wanqiang Tian, Linsheng Gui & 11 others Yingying Zhang, Rodney A. Hill, Zhongliang Jiang, Yaping Xin, Cunling Jia, Xiuzhu Sun, Shuhui Wang, Huanming Yang, Jian Wang, Wenjuan Zhu, Linsen Zan

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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.
Original languageEnglish
Pages (from-to)688-699
Number of pages12
JournalMolecular Biology and Evolution
Volume35
Issue number3
Early online dateDec 2017
DOIs
Publication statusPublished - Mar 2018

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cattle
genome
Genome
domestication
Red Angus
genetic resource
genetic variation
Wagyu
taurine
meat production
cattle breeds
meat
zebu
genetic resources
population structure
Taurine
dairies
hybridization
Meat
China

Cite this

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. / Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing. In: Molecular Biology and Evolution. 2018 ; Vol. 35, No. 3. pp. 688-699.
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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.",
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author = "Chugang Mei and Hongcheng Wang and Qijun Liao and Lizhong Wang and Gong Cheng and Hongbao Wang and Chunping Zhao and Shancen Zhao and Jiuzhou Song and Xuanmin Guang and Liu, {George E.} and Anning Li and Xueli Wu and Chongzhi Wang and Xiaodong Fang and Xin Zhao and Smith, {Stephen B.} and Wucai Yang and Wanqiang Tian and Linsheng Gui and Yingying Zhang and Hill, {Rodney A.} and Zhongliang Jiang and Yaping Xin and Cunling Jia and Xiuzhu Sun and Shuhui Wang and Huanming Yang and Jian Wang and Wenjuan Zhu and Linsen Zan",
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Mei, C, Wang, H, Liao, Q, Wang, L, Cheng, G, Wang, H, Zhao, C, Zhao, S, Song, J, Guang, X, Liu, GE, Li, A, Wu, X, Wang, C, Fang, X, Zhao, X, Smith, SB, Yang, W, Tian, W, Gui, L, Zhang, Y, Hill, RA, Jiang, Z, Xin, Y, Jia, C, Sun, X, Wang, S, Yang, H, Wang, J, Zhu, W & Zan, L 2018, 'Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing', Molecular Biology and Evolution, vol. 35, no. 3, pp. 688-699. https://doi.org/10.1093/molbev/msx322

Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing. / 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.

In: Molecular Biology and Evolution, Vol. 35, No. 3, 03.2018, p. 688-699.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing

AU - Mei, Chugang

AU - Wang, Hongcheng

AU - Liao, Qijun

AU - Wang, Lizhong

AU - Cheng, Gong

AU - Wang, Hongbao

AU - Zhao, Chunping

AU - Zhao, Shancen

AU - Song, Jiuzhou

AU - Guang, Xuanmin

AU - Liu, George E.

AU - Li, Anning

AU - Wu, Xueli

AU - Wang, Chongzhi

AU - Fang, Xiaodong

AU - Zhao, Xin

AU - Smith, Stephen B.

AU - Yang, Wucai

AU - Tian, Wanqiang

AU - Gui, Linsheng

AU - Zhang, Yingying

AU - Hill, Rodney A.

AU - Jiang, Zhongliang

AU - Xin, Yaping

AU - Jia, Cunling

AU - Sun, Xiuzhu

AU - Wang, Shuhui

AU - Yang, Huanming

AU - Wang, Jian

AU - Zhu, Wenjuan

AU - Zan, Linsen

PY - 2018/3

Y1 - 2018/3

N2 - 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.

AB - 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.

KW - Admixture

KW - Chinese cattle

KW - Indicine components

KW - Selection

KW - Whole genome sequencing

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U2 - 10.1093/molbev/msx322

DO - 10.1093/molbev/msx322

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JO - Molecular Biology and Evolution

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SN - 0737-4038

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