Genome-wide association study of appearance quality traits and development of KASP makers in vegetable soybean

Vegetable soybean ((Glycine max (L.) Merr.), commonly referred to as edamame, holds significant agricultural importance in China as a legume vegetable harvested at the pod-filling stage (R6). The visual appeal of vegetable soybeans is crucial for consumer preference and marketability, and it depends on factors such as pod length, pod width, and pod color. This study cultivated 264 vegetable soybeans in Nanjing, Huai’an, and Nantong, Jiangsu Province, China to assess pod traits using PlantPhenoM, a system for pod phenotypic identification and analysis. The results revealed a variability range of 8.64 to 30.00% in appearance quality traits among the vegetable soybeans. Leveraging phenotypic data and employing a genome-wide association study (GWAS) identified 525 SNPs significantly linked to the appearance quality traits in different regions. In addition, five candidate genes (Glyma.04G004700, Glyma.15G051600, Glyma.18G225700, Glyma.18G225900, and Glyma.18G272300) associated with target traits were identified, and KASP markers for S04_372771 (pod length), S18_51477324 (pod width), and S18_55553200 (pod color) were developed. This study offers valuable insights for breeding superior vegetable soybean varieties and lays the groundwork for exploring candidate genes and molecular markers related to appearance and quality traits in vegetable soybeans.