Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing

Xinpeng Qi, Man-Wah Li, Min Xie, Xin Liu, Meng Ni, Guihua Shao, Chi Song, Aldrin Kay-Yuen Yim, Ye Tao, Fuk-Ling Wong, Sachiko Isobe, Chi-Fai Wong, Kwong-Sen Wong, Chunyan Xu, Chunqing Li, Ying Wang, Rui Guan, Fengming Sun, Guangyi Fan, Zhixia Xiao, Feng Zhou, Tsui-Hung Phang, Xuan Liu, Suk-Wah Tong, Ting-Fung Chan, Siu-Ming Yiu, Satoshi Tabata, Jian Wang, Xun Xu () and Hon-Ming Lam ()
Additional contact information
Xinpeng Qi: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Man-Wah Li: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Min Xie: BGI-Shenzhen
Xin Liu: BGI-Shenzhen
Meng Ni: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Guihua Shao: Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences
Chi Song: BGI-Shenzhen
Aldrin Kay-Yuen Yim: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Ye Tao: BGI-Shenzhen
Fuk-Ling Wong: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Sachiko Isobe: Kazusa DNA Research Institute
Chi-Fai Wong: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Kwong-Sen Wong: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Chunyan Xu: BGI-Shenzhen
Chunqing Li: BGI-Shenzhen
Ying Wang: BGI-Shenzhen
Rui Guan: BGI-Shenzhen
Fengming Sun: BGI-Shenzhen
Guangyi Fan: BGI-Shenzhen
Zhixia Xiao: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Feng Zhou: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Tsui-Hung Phang: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Xuan Liu: The University of Hong Kong
Suk-Wah Tong: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Ting-Fung Chan: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Siu-Ming Yiu: The University of Hong Kong
Satoshi Tabata: Kazusa DNA Research Institute
Jian Wang: BGI-Shenzhen
Xun Xu: BGI-Shenzhen
Hon-Ming Lam: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong

Nature Communications, 2014, vol. 5, issue 1, 1-11

Abstract: Abstract Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

Date: 2014
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DOI: 10.1038/ncomms5340

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