High-resolution GWAS and diagnostic functional marker development for leaf shape in soybean

This study identified a major QTL governing leaf shape, pinpointed a highly associated SNP, and developed a dCAPSmarker, providing a useful molecular tool to facilitate marker-assisted breeding for leaf shape in soybean. Optimizing plant architecture to enhance canopy light distribution is a central objective in modern crop breeding. Leaf shape is a critical determinant of canopy structure and yield potential, yet the natural genetic variation underlying this trait in soybean remains underexploited for marker-assisted improvement. Here, we performed a genome-wide association study (GWAS) of leaf shape using a panel of 450 soybean accessions from northern China and identified a robust quantitative trait locus (qLS) for leaf shape on chromosome 20 that was consistently detected across multiple statistical models and two consecutive years. The lead SNP (SNP_35828042) resides within the second exon of GmJAG1 encoding a C2H2-type zinc finger transcription factor homologous to Arabidopsis JAGGED. This non-synonymous G/C variation results in an aspartic acid to histidine substitution (D9H) within the highly conserved EAR motif. Analysis of previously generated Cas9-edited GmJAG1 plants provided functional support for the role of GmJAG1 in regulating leaf shape. Population-level analysis revealed northward enrichment of the narrow-leaf-associated C allele, a pattern consistent with regional differentiation. We further developed a derived cleaved amplified polymorphic sequence (dCAPS) marker targeting the G/C polymorphism, which showed complete concordance with visual leaf-shape classification in the 41 tested accessions. This work provides population-scale validation of a GmJAG1-associated polymorphism, characterizes its geographical distribution, and delivers a practical molecular marker for screening soybean germplasm for leaf shape.