Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

Feng Cheng; Rifei Sun; Xilin Hou; Hongkun Zheng; Fenglan Zhang; Yangyong Zhang; Bo Liu; Jianli Liang; Mu Zhuang; Yunxia Liu; Dongyuan Liu; Xiaobo Wang; Pingxia Li; Yumei Liu; Ke Lin; Johan Bucher; Ningwen Zhang; Yan Wang; Hui Wang; Jie Deng; Yongcui Liao; Keyun Wei; Xueming Zhang; Lixia Fu; Yunyan Hu; Jisheng Liu; Chengcheng Cai; Shujiang Zhang; Shifan Zhang; Fei Li; Hui Zhang; Jifang Zhang; Ning Guo; Zhiyuan Liu; Jin Liu; Chao Sun; Yuan Ma; Haijiao Zhang; Yang Cui; Micheal R. Freeling; Theo Borm; Guusje Bonnema; Jian Wu; Xiaowu Wang

doi:10.1038/ng.3634

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

Feng Cheng, Rifei Sun, Xilin Hou, Hongkun Zheng, Fenglan Zhang, Yangyong Zhang, Bo Liu, Jianli Liang, Mu Zhuang, Yunxia Liu, Dongyuan Liu, Xiaobo Wang, Pingxia Li, Yumei Liu, Ke Lin, Johan Bucher, Ningwen Zhang, Yan Wang, Hui Wang, Jie DengYongcui Liao, Keyun Wei, Xueming Zhang, Lixia Fu, Yunyan Hu, Jisheng Liu, Chengcheng Cai, Shujiang Zhang, Shifan Zhang, Fei Li, Hui Zhang, Jifang Zhang, Ning Guo, Zhiyuan Liu, Jin Liu, Chao Sun, Yuan Ma, Haijiao Zhang, Yang Cui, Micheal R. Freeling, Theo Borm, Guusje Bonnema, Jian Wu, Xiaowu Wang^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

280 Citations (Scopus)

Abstract

Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

Original language	English
Pages (from-to)	1218-1224
Journal	Nature Genetics
Volume	48
Issue number	10
DOIs	https://doi.org/10.1038/ng.3634
Publication status	Published - 2016

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10.1038/ng.3634

NUE-CROPS: Improving nutrient efficiency in major European food, feed and biofuel crops to reduce the negative environmental impact of crop production
1/05/09 → 30/04/14
Project: EU research project

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Cheng, F., Sun, R., Hou, X., Zheng, H., Zhang, F., Zhang, Y., Liu, B., Liang, J., Zhuang, M., Liu, Y., Liu, D., Wang, X., Li, P., Liu, Y., Lin, K., Bucher, J., Zhang, N., Wang, Y., Wang, H., ... Wang, X. (2016). Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nature Genetics, 48(10), 1218-1224. https://doi.org/10.1038/ng.3634

@article{5c3f2591943245978c740b4c43ee4930,

title = "Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea",

abstract = "Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.",

author = "Feng Cheng and Rifei Sun and Xilin Hou and Hongkun Zheng and Fenglan Zhang and Yangyong Zhang and Bo Liu and Jianli Liang and Mu Zhuang and Yunxia Liu and Dongyuan Liu and Xiaobo Wang and Pingxia Li and Yumei Liu and Ke Lin and Johan Bucher and Ningwen Zhang and Yan Wang and Hui Wang and Jie Deng and Yongcui Liao and Keyun Wei and Xueming Zhang and Lixia Fu and Yunyan Hu and Jisheng Liu and Chengcheng Cai and Shujiang Zhang and Shifan Zhang and Fei Li and Hui Zhang and Jifang Zhang and Ning Guo and Zhiyuan Liu and Jin Liu and Chao Sun and Yuan Ma and Haijiao Zhang and Yang Cui and Freeling, {Micheal R.} and Theo Borm and Guusje Bonnema and Jian Wu and Xiaowu Wang",

year = "2016",

doi = "10.1038/ng.3634",

language = "English",

volume = "48",

pages = "1218--1224",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature",

number = "10",

}

Cheng, F, Sun, R, Hou, X, Zheng, H, Zhang, F, Zhang, Y, Liu, B, Liang, J, Zhuang, M, Liu, Y, Liu, D, Wang, X, Li, P, Liu, Y, Lin, K, Bucher, J, Zhang, N, Wang, Y, Wang, H, Deng, J, Liao, Y, Wei, K, Zhang, X, Fu, L, Hu, Y, Liu, J, Cai, C, Zhang, S, Zhang, S, Li, F, Zhang, H, Zhang, J, Guo, N, Liu, Z, Liu, J, Sun, C, Ma, Y, Zhang, H, Cui, Y, Freeling, MR, Borm, T, Bonnema, G, Wu, J & Wang, X 2016, 'Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea', Nature Genetics, vol. 48, no. 10, pp. 1218-1224. https://doi.org/10.1038/ng.3634

TY - JOUR

T1 - Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

AU - Cheng, Feng

AU - Sun, Rifei

AU - Hou, Xilin

AU - Zheng, Hongkun

AU - Zhang, Fenglan

AU - Zhang, Yangyong

AU - Liu, Bo

AU - Liang, Jianli

AU - Zhuang, Mu

AU - Liu, Yunxia

AU - Liu, Dongyuan

AU - Wang, Xiaobo

AU - Li, Pingxia

AU - Liu, Yumei

AU - Lin, Ke

AU - Bucher, Johan

AU - Zhang, Ningwen

AU - Wang, Yan

AU - Wang, Hui

AU - Deng, Jie

AU - Liao, Yongcui

AU - Wei, Keyun

AU - Zhang, Xueming

AU - Fu, Lixia

AU - Hu, Yunyan

AU - Liu, Jisheng

AU - Cai, Chengcheng

AU - Zhang, Shujiang

AU - Zhang, Shifan

AU - Li, Fei

AU - Zhang, Hui

AU - Zhang, Jifang

AU - Guo, Ning

AU - Liu, Zhiyuan

AU - Liu, Jin

AU - Sun, Chao

AU - Ma, Yuan

AU - Zhang, Haijiao

AU - Cui, Yang

AU - Freeling, Micheal R.

AU - Borm, Theo

AU - Bonnema, Guusje

AU - Wu, Jian

AU - Wang, Xiaowu

PY - 2016

Y1 - 2016

N2 - Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

AB - Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

U2 - 10.1038/ng.3634

DO - 10.1038/ng.3634

M3 - Article

AN - SCOPUS:84982129468

SN - 1061-4036

VL - 48

SP - 1218

EP - 1224

JO - Nature Genetics

JF - Nature Genetics

IS - 10

ER -

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

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NUE-CROPS: Improving nutrient efficiency in major European food, feed and biofuel crops to reduce the negative environmental impact of crop production

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