A Coding SNP in GmPM30 Enhances Soybean Salinity Tolerance and Yield through the GmLEA1-GmPM30-GmLEC1 Module.

Salt stress limits soybean quality and yield. Despite the genetic validation of many salinity tolerance genes, the roles and regulatory mechanisms of their natural variations in population-level salt tolerance remain unclear. This study identifies seed maturation protein PM30 (GmPM30), a late embryogenesis abundant (LEA) gene, as enhancing soybean salt tolerance. A significant T/C nonsynonymous polymorphism in the coding region of GmPM30 confers haplotype HapT with greater salt tolerance than HapC via stronger GmLEA1-GmPM30-GmLEC1 (Lectin) interactions, reducing ion leakage, malondialdehyde (MDA) content, and hydrogen peroxide (H₂O₂) accumulation under salt stress. RNA-seq demonstrates that GmPM30-HapT activates more extensive and robust stress response pathways than HapC. Evolutionary analyses reveal artificial selection of the GmLEA1-GmPM30-GmLEC1 module during soybean domestication and breeding, with GmPM30 being geographically adapted to high-latitude regions with greater saline-alkaline stress. Pyramiding lines with elite alleles (GmLEA1-Hap3-GmPM30-HapT-GmLEC1-Hap3) boosts grain yield on saline soil. An efficient marker developed for GmPM30-HapT enables marker-assisted selection (MAS) breeding, and haplotype hybrids with successful GmPM30-HapT integration exhibit improved yield-related traits in saline farmlands. This study establishes a novel workflow linking evolutionary genomics, molecular mechanisms, and breeding applications through the GmLEA1-GmPM30-GmLEC1 module, providing a replicable blueprint for rapid crop improvement by using natural selection strategies.