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.

Improvement in nitrogen fixation capacity could be part of the domestication process in soybean

“…The RI population obtained by crossing the cultivated Glycine max (C08) with the wild-type Glycine soja (W05) was adopted from a previous study (Qi et al, 2014). In our previous research (Qi et al, 2014), a core panel of 96 RI lines was re-sequenced at~1 × depth to generate high-quality single-nucleotide polymorphism (SNP) information.…”

“…The non-nodulating soybean nod139 (Carroll et al, 1986) was used as the negative control for BNF. Ninety-six RI lines from a biparental population were adopted for QTL analyses (Qi et al, 2014). Seeds were disinfected with chlorine gas for 16 h and then germinated in plastic trays with moistened sterile vermiculite for 3 days until the radicles reached a length of 3-5 cm.…”

“…In our previous research (Qi et al, 2014), a core panel of 96 RI lines was re-sequenced at~1 × depth to generate high-quality single-nucleotide polymorphism (SNP) information. An array of high-quality SNPs was grouped into bin marker.…”

“…Hence, we and other groups have characterized and compared the genomic variations of wild and cultivated soybeans by next-generation sequencing, contributing to our knowledge of the diversity and population structure of soybeans (Lam et al, 2010;Li et al, 2014;Zhou et al, 2015). To identify QTLs controlling important traits of soybean, we also constructed a recombinant inbred (RI) population from one wild and one cultivated soybean accession, and used this RI population to clone a salt tolerance causal gene from a salt tolerance major QTL (Qi et al, 2014). In this work, we made further use of this RI population to identify novel QTLs for total nodule fresh weight and ureides contents.…”

Comparative analyses of transcriptome and proteome in response to cotton bollworm between a resistant wild soybean and a susceptible soybean cultivar

“…Thus, identifying native resistant genes and elucidating the molecular mechanism of resistance to defoliating insects are of great significance for the improvement of soybean. As the ancestors of cultivated soybean, wild soybean (Glycine soja) retained more genetic diversity and carried more useful stress-resistant genes, which might be lost during domestication in cultivated soybean Li et al 2014;Qi et al 2014;Winter et al 2007). Therefore, mining genes with resistance to stresses from the wild soybean sources becomes the concern of soybean researchers.…”