ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Abiotic Stress
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1621869
Genome-wide association study and transcriptome analysis reveal candidate genes related to drought stress in the germination stage of soybean
Provisionally accepted
- 1School of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, China
- 2Key Laboratory of Biology and Genetics Improvement of Soybean, Nanjing Agricultural University, Nanjing, China
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Drought is the major abiotic stress threatening soybean production globally. However, the genetic basis of soybean drought resistance at the germination stage remains largely unknown. In this study, the drought-tolerance phenotypes of a diverse panel of 207 soybean accessions were examined. Leveraging 95,043 high-density single nucleotide polymorphism (SNP) markers, a total of 58 quantitative trait loci (QTLs) were detected using the restricted two stage multi-locus genome-wide association study (RTM-GWAS) method and 10 of these QTLs were considered as large-contribution QTLs that have larger phenotype variation. Furthermore, RNA-sequencing was performed on the roots of two soybean accessions with contrasting drought tolerance. A total of 1183, 1354, and 1581 differentially expressed genes (DEGs) between two soybean accessions after 0, 12, and 24 h of drought treatment were separately obtained, and 4012 and 4586 genes responsive to drought stress were identified at 12, and 24 h, respectively. By utilizing these DEGs, a weighted gene co-expression network analysis (WGCNA) was constructed, and 13 distinct modules were obtained, among which 4 modules were considered as key modules. Subsequently, 40 hub genes were identified in these four modules. In addition, by combining RTM-GWAS and transcriptome analysis, 22 candidate genes underlying large-contribution QTLs were identified. Based on the functional annotations, Glyma.12G141700, Glyma.15G040000, Glyma.05G049300, Glyma.14G105900, and Glyma.15G041100 were regarded as most possible candidate genes which regulate soybean drought tolerance at the germination stage. The QTLs, key modules, and hub genes discovered in this study will provide a new understanding of the genetic basis of soybean drought resistance at the germination stage, and lay a theoretical foundation for the improvement and innovation of high-quality soybean germplasm.
Keywords: Soybean, drought tolerance, Germination stage, RTM-GWAS, RNA-Seq
Received: 02 May 2025; Accepted: 09 Jul 2025.
Copyright: © 2025 Kong, Xu, Wu, Zhou, Wang, Zhao, Wang and Song. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Chune Wang, School of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, China
Yingpei Song, School of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, China
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