Genome-Wide Association Analysis Reveals Genetic Loci and Candidate Genes Related to Soybean Leaf Shape

Soybean is the world’s foremost oilseed crop, and leaf morphology significantly influences yield potential by affecting light interception, canopy structure, and photosynthetic efficiency. In this study, leaf length, leaf width, maximum leaf width, leaf apex opening angle, and leaf area were measured in 216 soybean accessions, and genome-wide association studies (GWAS) were conducted using genomic resequencing data to identify genetic variants associated with leaf morphological traits. A total of 824 SNP loci were found to be significantly associated with leaf shape, and 130 candidate genes were identified in the genomic regions flanking these significant loci. KEGG enrichment analysis revealed that the above candidate genes were significantly enriched in arginine biosynthesis (ko00220), nitrogen metabolism (ko00910), carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/glycogenolysis (ko00010), starch and sucrose metabolism (ko00500), plant–pathogen interaction (ko04626), and amino acid biosynthesis (ko01230). By combining KEGG and GO enrichment analysis as well as expression level analysis, four candidate genes related to leaf shape (Glyma.10G141600, Glyma.13G062700, Glyma.16G041200 and Glyma.20G115500) were identified. Further, through candidate gene association analysis, it was found that the Glyma.10G141600 gene was divided into two major haplotypes. The leaf area of haplotype 1 was significantly smaller than that of haplotype 2. Subsequently, the cutting amplification polymorphism sequence (CAPS) molecular marker was developed. The marker Chr.10:37502955 can effectively distinguish the differences in leaf size through enzymatic digestion technology, and has excellent typing ability and application potential. The above results can provide a theoretical basis for molecular-assisted selection (MAS) of soybean leaf morphology.