Novel role of VrPG1 in salt-tolerant germination of mungbean revealed by genome-wide association study

doi:10.1016/j.jia.2025.10.009

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Novel role of VrPG1 in salt-tolerant germination of mungbean revealed by genome-wide association study

Xi Zhang¹, Jinyang Liu ¹, Shicong Li¹, Jingbin Chen¹,Yun Lin¹, Yixiang Pu¹, Qiang Yan¹, Ranran Wu¹, Na Yuan¹, Prakit Somta ², Lixia Wang³, Xin Chen¹^#, Xingxing Yuan¹^#

¹Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China

²Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand

³Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Highlights
GWAS identified VrPG1 as a gene governing salt tolerance during mungbean germination.
Overexpression of VrPG1 in Arabidopsis significantly enhanced salt tolerance during seed germination, confirming its positive regulatory role.
A breeder-friendly kompetitive allele-specific PCR marker was developed for marker-assisted selection of salt tolerance in mungbean breeding programs.

Abstract
References

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摘要

土壤盐渍化严重损害了绿豆（Vigna radiata (L.) Wilczek）的出苗整齐度与产量。本研究利用374份绿豆自然群体和4,875,143个高质量SNP位点，并通过全基因组关联分析（GWAS），在多环境多模型下鉴定到与盐胁迫相对发芽性状显著关联的位点Chr01_26769549，并成功开发了 KASP分子标记。进一步单倍型和表达量分析共同证实多聚半乳糖醛酸酶基因VrPG1是调控种子萌发期耐盐性的关键候选基因。研究表明VrPG1存在两种单倍型（Hap1/Hap2），其中Hap1启动子区的突变增强了其转录活性。过表达VrPG1可通过促进拟南芥胚乳细胞壁的软化进而提高其盐胁迫下的发芽率。耐盐绿豆品种在萌发期表现出更高的多聚半乳糖醛酸酶活性及更早的薄壁细胞壁松弛现象，从而促进种子吸胀与胚根伸出。本研究揭示了VrPG1通过调控细胞壁重构增强绿豆萌发期耐盐性的新机制，为耐盐绿豆育种提供了新基因靶点和高效的分子标记辅助选择工具。

Abstract

Soil salinization severely impairs mungbean (Vigna radiata (L.) Wilczek) seedling uniformity and productivity. In this study, genome-wide association study (GWAS) was conducted using a natural population of 374 mungbean accessions and 4,875,143 SNPs. By evaluating the population under two independent environments and applying two statistical models, we identified a significant SNP (Chr01_26769549) associated with relative germination traits under salt stress. Based on this locus, a Kompetitive Allele-Specific PCR (KASP) marker was successfully developed for marker assisted selection. Integrated haplotype and expression analyses confirmed polygalacturonase gene VrPG1 as a key candidate gene regulating salt tolerance during seed germination. Two haplotypes of VrPG1 (Hap1/Hap2) were identified, with a mutation in the Hap1 promoter region enhancing its transcriptional activity. Overexpression of VrPG1 in Arabidopsis thaliana significantly increased germination rates under salt stress by promoting endosperm cell wall softening. Salt-tolerant mungbean varieties exhibit higher polygalacturonase activity and earlier loosening of thin-walled cell walls during the germination period, which promotes seed imbibition and radicle emergence. Collectively, these findings demonstrate that VrPG1 enhances salt tolerance during germination through cell wall remodeling. This study provides novel genetic targets and efficient marker-assisted selection tools for breeding salt-tolerant mungbean. This study provides novel genetic targets and efficient marker-assisted selection tools for breeding salt-tolerant mungbean varieties.

Keywords: mungbean salt tolerance germination GWAS polygalacturonase functional study

Online: 21 October 2025

Fund:

This research was supported by National Key R&D Program of China (2023YFD1202702), National Natural Science Foundation of China (3240151194), the China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08), the Jiangsu Seed Industry Revitalization Project, China (JBGS[2021]004), and the NSRF via the Program Management Unit for Human Resources and Institutional Development, Research, and Innovation, China (B16F640185).

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Xi Zhang, Jinyang Liu , Shicong Li, Jingbin Chen, Yun Lin, Yixiang Pu, Qiang Yan, Ranran Wu, Na Yuan, Prakit Somta, Lixia Wang, Xin Chen, Xingxing Yuan. 2025. Novel role of VrPG1 in salt-tolerant germination of mungbean revealed by genome-wide association study. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.10.009

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