ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2026
High-resolution GWAS and diagnostic functional marker development for leaf shape in soybean.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
key messageThis 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.
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