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

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.

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

High external phosphate (Pi) increases sodium ion uptake and reduces salt tolerance of 'Pi-tolerant' soybean.

Previous studies on the interaction between environmental inorganic phosphate (Pi) and salinity stress using soybean cultivars sensitive to high external Pi had two limitations: (1) the phenotype was dominated by overaccumulation of phosphorus (P); and (2) no detailed analysis was performed for sodium ion uptake. In this study, we focused on the effects of high external Pi on the sodium ion uptake in 'Pi-tolerant' soybean cultivars. The P accumulation in Pi-tolerant soybean Union was much lower [9.0 mg g(-)(1) dry weight (DW); contrasting to 38-76 mg g(-)(1) DW in the 'Pi-sensitive' soybean cultivars]. At in planta level, high level of external Pi significantly (P < 0.001) increased net sodium ion uptake and aggravated salinity stress symptoms. The effects of high external Pi diminished when de-rooted plants were used, suggesting that root is the primary organ interacting with Pi in the growth medium. Two-cell models, including soybean suspension cells and the tobacco Bright Yellow-2 cell line, were also employed to study the effects of high external Pi at the cellular level. Consistent to in planta results, high external Pi uplifted cellular sodium ion uptake and reduced cell viability under salinity stress. Gene expression analyses further showed that HPi (2 mM Pi supplements; excessive level of Pi) could reduce the fold of induction of GmSOS1 and GmCNGC under salinity stress, suggesting that they may be possible molecular targets involved in the interaction between high external Pi and Na(+) uptake.

Salt tolerance in soybean.

Soybean is an important cash crop and its productivity is significantly hampered by salt stress. High salt imposes negative impacts on growth, nodulation, agronomy traits, seed quality and quantity, and thus reduces the yield of soybean. To cope with salt stress, soybean has developed several tolerance mechanisms, including: (i) maintenance of ion homeostasis; (ii) adjustment in response to osmotic stress; (iii) restoration of osmotic balance; and (iv) other metabolic and structural adaptations. The regulatory network for abiotic stress responses in higher plants has been studied extensively in model plants such as Arabidopsis thaliana. Some homologous components involved in salt stress responses have been identified in soybean. In this review, we tried to integrate the relevant works on soybean and proposes a working model to describe its salt stress responses at the molecular level.

Ectopic expression of GmPAP3 alleviates oxidative damage caused by salinity and osmotic stresses.

The primary biochemical reaction of purple acid phosphatases (PAP) is to catalyze the hydrolysis of phosphate esters and anhydrides. However, the soybean GmPAP3 gene expression is induced by NaCl, osmotic, and oxidative treatments, indicating a possible role of PAP in abiotic stress responses. Confocal and electron microscopic studies demonstrated that GmPAP3 protein is mainly localized in mitochondria, a primary site for reactive oxygen species (ROS) production. When subjected to NaCl and polyethylene glycol (PEG) treatments, ectopic expression of GmPAP3 in transgenic tobacco BY-2 cells mimicked the protective effects exhibited by the antioxidant ascorbic acid: increase in the percentage of cells with active mitochondria; reduction in the percentage of dead cells; and reduced accumulation of ROS. In addition, when GmPAP3 transgenic Arabidopsis thaliana seedlings were subjected to NaCl, PEG, and paraquat (PQ) treatments, the percentage of root elongation was significantly higher than the wild type. Furthermore, PQ-induced lipid peroxidation in these transgenic seedlings was also reduced. In summary, the mitochondrial localized GmPAP3 may play a role in stress tolerance by enhancing ROS scavenging.

Tonoplast-located GmCLC1 and GmNHX1 from soybean enhance NaCl tolerance in transgenic bright yellow (BY)-2 cells.

Genes encoding ion transporters that regulate ion homeostasis in soybean have not been carefully investigated. Using degenerate primers, we cloned a putative chloride channel gene (GmCLC1) and a putative Na+/H+ antiporter gene (GmNHX1) from soybean. Confocal microscopic studies using yellow fluorescent fusion proteins revealed that GmCLC1 and GmNHX1 were both localized on tonoplast. The expressions of GmCLC1 and GmNHX1 were both induced by NaCl or dehydration stress imposed by polyethylene glycol (PEG). Using mitochondrial integrity and cell death as the damage indicators, a clear alleviation under NaCl stress (but not PEG stress) was observed in both GmCLC1 and GmNHX1 transgenic cells. Using fluorescent dye staining and quenching, respectively, a higher concentration of chloride ion (Cl-) or sodium ion (Na+) was observed in isolated vacuoles in the cells of GmCLC1 and of GmNHX1 transgenic lines. Our result suggested that these vacuolar-located ion transporters function to sequester ions from cytoplasm into vacuole to reduce its toxic effects.

GmPAP3, a novel purple acid phosphatase-like gene in soybean induced by NaCl stress but not phosphorus deficiency.

Purple acid phosphatases (PAPs) are commonly found in plants, but the physiological functions of different classes of PAPs are not thoroughly understood. In the present study, we identified a novel gene, GmPAP3, from salt-stressed soybean using suppression subtractive hybridization (SSH) techniques. Protein sequence alignment studies and phylogenetic analysis strongly suggested that GmPAP3 belongs to the group of plant PAPs and PAP-like proteins that are distinct from those of fungi and animals. In addition, the invariable consensus metal binding residues of PAPs were all conserved in GmPAP3. Surprisingly, analysis of protein sorting signals showed that a putative mitochondrion targeting transit peptide is present on GmPAP3. Northern blot analysis revealed that NaCl stress causes a general induction of GmPAP3 expression in both roots and leaves of various cultivated (Glycine max) and wild (Glycine soja) soybean varieties. Further test using two genetically unrelated cultivated soybean varieties showed that the expression pattern of GmPAP3 is distinct from other PAP genes in soybeans. NaCl stress and oxidative stress but not phosphorus (P) starvation induces the expression of GmPAP3. These results suggest that the physiological role of GmPAP3 might be related to the adaptation of soybean to NaCl stress, possibly through its involvement in reactive oxygen species (ROS) forming and/or scavenging or stress-responding signal transduction pathways.