A novel natural variation in the promoter of GmCHX1 regulates the conditional gene expression to improve salt tolerance in soybean.

Identification and characterization of soybean germplasm and gene(s)/allele(s) for salt tolerance is an effective way to develop improved varieties for saline soils. Previous studies identified GmCHX1 (Glyma03g32900) as a major salt tolerance gene in soybean, and two main functional variations were found in the promoter region (148/150-bp insertion) and the third exon with a retrotransposon insertion (3.78-kb). In the current study, we identified four salt-tolerant soybean lines, including PI 483460B (G. soja), carrying the previously identified salt-sensitive variations at GmCHX1, suggesting new gene(s) or new functional allele(s) of GmCHX1 in these soybean lines. Subsequently, we conducted quantitative trait loci (QTL) mapping in a recombinant-inbred line population (Williams 82 (salt-sensitive) × PI 483460B) to identify the new salt tolerance loci/alleles. A new locus of qSalt_Gm18 was mapped on chromosome (Chr.) 18 associated with leaf scorch score (LSS). Another major QTL qSalt_Gm03 was identified to be associated with chlorophyll content ratio (CCR) and LSS in the same chromosomal region of GmCHX1 on Chr. 03. Novel variations in a STRE (stress response element) cis-element in the promoter region of GmCHX1 was identified to regulate a salt-inducible gene expression in these four newly identified salt-tolerant lines including PI 483460B. This new allele of GmCHX1 with salt-inducible expression pattern provides an energy cost efficient (conditional gene expression) strategy to protect soybean yield in the saline soils without yield penalty under nonstress conditions. Our results suggest that there might be few other major salt tolerance loci as GmCHX1 in soybean germplasm and further improvement of salt tolerance in soybean may rely on gene pyramiding and gene-editing techniques.