title: Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.
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.
authors.affiliation: 1] School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong [2].
authors.forename: Xinpeng
authors.initials: X
authors.lastname: Qi
authors.affiliation: 1] School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong [2].
authors.forename: Man-Wah
authors.initials: MW
authors.lastname: Li
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, PR China [2].
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Meng
authors.initials: M
authors.lastname: Ni
authors.affiliation: Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
authors.forename: Guihua
authors.initials: G
authors.lastname: Shao
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Chi
authors.initials: C
authors.lastname: Song
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Aldrin
authors.initials: A
authors.lastname: Kay-Yuen Yim
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Tao
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Fuk-Ling
authors.initials: FL
authors.lastname: Wong
authors.affiliation: Kazusa DNA Research Institute, Chiba 292-0818, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Isobe
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Chi-Fai
authors.initials: CF
authors.lastname: Wong
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Kwong-Sen
authors.initials: KS
authors.lastname: Wong
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Chunqing
authors.initials: C
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Rui
authors.initials: R
authors.lastname: Guan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Fengming
authors.initials: F
authors.lastname: Sun
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Zhixia
authors.initials: Z
authors.lastname: Xiao
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhou
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Tsui-Hung
authors.initials: TH
authors.lastname: Phang
authors.affiliation: Department of Computer Science, The University of Hong Kong, Pokfulam HKSAR, Hong Kong.
authors.forename: Xuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Suk-Wah
authors.initials: SW
authors.lastname: Tong
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: Department of Computer Science, The University of Hong Kong, Pokfulam HKSAR, Hong Kong.
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.affiliation: Kazusa DNA Research Institute, Chiba 292-0818, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, PR China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin HKSAR, Hong Kong.
authors.forename: Hon-Ming
authors.initials: HM
authors.lastname: Lam
mesh_terms: D002874:Chromosome Mapping; D018745:Genome, Plant; D005838:Genotype; D016623:Ion Pumps / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics*; D040641:Quantitative Trait Loci; D055049:Salt Tolerance; D012965:Sodium Chloride / Q000378:metabolism; D013025:Glycine max / Q000235:genetics* / Q000502:physiology
chemical_list: D016623:Ion Pumps; D010940:Plant Proteins; D012965:Sodium Chloride