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Journal of Integrative Agriculture  2026, Vol. 25 Issue (6): 2341-2352    DOI: 10.1016/j.jia.2024.09.005
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Genome-wide association study of appearance quality traits and development of KASP makers in vegetable soybean

Shuo Yang1*, Qianru Jia2, 4*, Qiong Wang2, 4, Junyan Wang2, 4, Jiahao Li3, Shengyan Hu2, 4, Wei Zhang2, 4, Hongmei Zhang2, 4, Ya Guo3, Xin Chen4, Yuelin Zhu1#, Huatao Chen2, 4#

1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China

2 Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing 210014, China

3 The School of IoT (Internet of Things), Jiangnan University, Wuxi 214122, China

4 Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China

 Highlights 
Genome-wide association study (GWAS) analysis of 264 soybean accessions identified 525 SNPs significantly associated with pod appearance traits (length, width, and color) across multiple environments.
Five candidate genes were pinpointed as potentially regulating these key pod quality traits.
Functional KASP markers were developed for three major SNPs, providing practical tools for molecular breeding of vegetable soybean with improved visual appeal.
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摘要  

菜用大豆(Glycine maxL.Merr.),通常称为毛豆,是一种在豆荚结荚期(R6)收获的豆类蔬菜,在中国农业中具有重要地位。菜用大豆的外观品质对消费者的偏好和市场适销性至关重要,这些品质性状包括豆荚的长度、宽度和颜色等因素。本研究在南京、淮安和南通三地种植了264种菜用大豆,并使用PlantPhenoM(一种豆荚表型鉴定和分析系统)对豆荚性状进行了评估。结果显示,菜用大豆外观品质性状的变异范围为8.64%30.00%。通过表型数据和全基因组关联研究(GWAS),我们鉴定出了525个与不同地区外观质量性状显著相关的SNP位点。此外,还筛选出了与目标性状相关的候选基因Glyma.04G004700Glyma.15G051600Glyma.18G25700Glyma.18G225900Glyma.18G272300,并成功开发了KASP标记。本研究为培育优良的菜用大豆品种提供了宝贵的见解,并为菜用大豆外观品质性状候选基因及分子标记相关研究奠定了基础。



Abstract  

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.

Keywords:  appearance quality        genome-wide association study        KASP marker       vegetable soybean  
Received: 27 April 2024   Accepted: 04 July 2024 Online: 12 September 2024  
Fund: 

This study was supported by the Zhongshan Biological Breeding Laboratory, China (ZSBBL-KY2023-03), the Jiangsu Agricultural Science and Technology Innovation Fund, China (CX(22)5002) and a project funded by the China Postdoctoral Science Foundation (2023M731401).

About author:  #Correspondence Yuelin Zhu, E-mail: ylzhu@njau.edu.cn; Huatao Chen, E-mail: cht@jaas.ac.cn * These authors contributed equally to this study.

Cite this article: 

Shuo Yang, Qianru Jia, Qiong Wang, Junyan Wang, Jiahao Li, Shengyan Hu, Wei Zhang, Hongmei Zhang, Ya Guo, Xin Chen, Yuelin Zhu, Huatao Chen. 2026. Genome-wide association study of appearance quality traits and development of KASP makers in vegetable soybean. Journal of Integrative Agriculture, 25(6): 2341-2352.

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