Novel role of VrPG1 in salt-tolerant germination of mungbean revealed by genome-wide association study

GWAS identified VrPG1 as a gene governing salt tolerance during mungbean germination. Overexpression of VrPG1 in Arabidopsis significantly enhanced salt tolerance during seed germination, confirming its positive regulatory role. A breeder-friendly kompetitive allele-specific PCR marker was developed for marker-assisted selection of salt tolerance in mungbean breeding programs. Soil salinization severely impairs mungbean ( Vigna radiata (L.) Wilczek) seedling uniformity and productivity. In this study, genome-wide association study (GWAS) was conducted using a natural population of 374 mungbean accessions and 4,875,143 SNPs. By evaluating the population under two independent environments and applying two statistical models, we identified a significant SNP (Chr01_26769549) associated with relative germination traits under salt stress. Based on this locus, a Kompetitive Allele-Specific PCR (KASP) marker was successfully developed for marker assisted selection. Integrated haplotype and expression analyses confirmed polygalacturonase gene VrPG1 as a key candidate gene regulating salt tolerance during seed germination. Two haplotypes of VrPG1 (Hap1/Hap2) were identified, with a mutation in the Hap1 promoter region enhancing its transcriptional activity. Overexpression of VrPG1 in Arabidopsis thaliana significantly increased germination rates under salt stress by promoting endosperm cell wall softening. Salt-tolerant mungbean varieties exhibit higher polygalacturonase activity and earlier loosening of thin-walled cell walls during the germination period, which promotes seed imbibition and radicle emergence. Collectively, these findings demonstrate that VrPG1 enhances salt tolerance during germination through cell wall remodeling. This study provides novel genetic targets and efficient marker-assisted selection tools for breeding salt-tolerant mungbean. This study provides novel genetic targets and efficient marker-assisted selection tools for breeding salt-tolerant mungbean varieties.