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

Abstract 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 (H 2 O 2 ) 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.