Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties to raise the output. However, complex correlation patterns among quantitative traits with genetic interactions bring a challenge for vegetable soybean breeding. Here, a genome-wide association study (GWAS) was applied for six yield-related traits with 188 vegetable soybean accessions. A total of 81 SNPs were identified for pod length, plant height, pods number, pod thickness, pod width, and seed weight per plant by Blink model. Among these significant SNPs, 79 were novel SNPs, while 2 overlapped with previously reported SNPs. A total of 220 genes were found in 100 kb upstream and downstream regions of significant SNPs, of which 17 genes were functional proteins. Among these function proteins, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed as significant haplotype variations, which encode MYB-related transcription factor, auxin-responsive family protein, F-box protein and CYP450, respectively. In addition, the relative expression with four candidate genes in the V030 and V071 (Among them, the plant height, pod number and fresh pod weight of V030 were lower than V071 strains) vegetable soybean were significantly different and these genes could be involved in plant growth and development via various pathways. Therefore, we proposed four genes from vegetable soybean germplasm that could be the key candidate genes for pod yield and plant height and these studies will accelerate the process of high-yield vegetable soybean breeding.