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Agronomy
Volume 15
Issue 8
10.3390/agronomy15081916
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Identification of Key Waterlogging-Tolerance Genes in Cultivated and Wild Soybeans via Integrated QTL–Transcriptome Analysis

by
Yiran Sun
1,†,
Lin Chen
1,†,
Yuxin Jin
1,
Shukun Wang
1,
Shengnan Ma
2,
Lin Yu
2,
Chunshuang Tang
2,
Yuying Ye
1,
Mingxuan Li
1,
Wenhui Zhou
1,
Enshuang Chen
1,
Xinru Kong
1,
Jinbo Fu
1,
Jinhui Wang
1,
Qingshan Chen
1,* and
Mingliang Yang
1,*
1
National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
2
Crop Development Research Institute, Heilongjiang Academy of Land Reclamation Sciences, Harbin 150038, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2025, 15(8), 1916; https://doi.org/10.3390/agronomy15081916
Submission received: 12 July 2025 / Revised: 4 August 2025 / Accepted: 7 August 2025 / Published: 8 August 2025
(This article belongs to the Section Crop Breeding and Genetics)
Versions Notes

Abstract

Soybean (Glycine max), as an important crop for both oil and grains, is a major source of high-quality plant proteins for humans. Among various natural disasters affecting soybean production, waterlogging is one of the key factors leading to yield reduction. It can cause root rot and seedling death, and in severe cases, even total crop failure. Given the significant differences in responses to waterlogging stress among different soybean varieties, traditional single-trait indicators are insufficient to comprehensively evaluate flood tolerance. In this study, relative seedling length (RSL) was used as a comprehensive evaluation index for flood tolerance. Using a chromosome segment substitution line (CSSL) population derived from SN14 and ZYD00006, we successfully identified seven quantitative trait loci (QTLs) associated with seed waterlogging tolerance. By integrating RNA-Seq transcriptome sequencing and phenotypic data, the functions of candidate genes were systematically verified. Phenotypic analysis indicated that Suinong14 had significantly better flood tolerance than ZYD00006. Further research revealed that the Glyma.05G160800 gene showed a significantly up-regulated expression pattern in Suinong14; qPCR analysis revealed that this gene exhibits higher expression levels in submergence-tolerant varieties. Haplotype analysis demonstrated a significant correlation between different haplotypes and phenotypic traits. The QTLs identified in this study can provide a theoretical basis for future molecular-assisted breeding of flood-tolerant varieties. Additionally, the functional study of Glyma.05G161800 in regulating seed flood tolerance can offer new insights into the molecular mechanism of seed flood tolerance. These findings could accelerate the development of submergence-tolerant rice varieties, enhancing crop productivity and stability in flood-prone regions.
Keywords: cultivated soybean; wild soybean; flood tolerance; QTL; transcriptome analysis; candidate genes cultivated soybean; wild soybean; flood tolerance; QTL; transcriptome analysis; candidate genes

Share and Cite

MDPI and ACS Style

Sun, Y.; Chen, L.; Jin, Y.; Wang, S.; Ma, S.; Yu, L.; Tang, C.; Ye, Y.; Li, M.; Zhou, W.; et al. Identification of Key Waterlogging-Tolerance Genes in Cultivated and Wild Soybeans via Integrated QTL–Transcriptome Analysis. Agronomy 2025, 15, 1916. https://doi.org/10.3390/agronomy15081916

AMA Style

Sun Y, Chen L, Jin Y, Wang S, Ma S, Yu L, Tang C, Ye Y, Li M, Zhou W, et al. Identification of Key Waterlogging-Tolerance Genes in Cultivated and Wild Soybeans via Integrated QTL–Transcriptome Analysis. Agronomy. 2025; 15(8):1916. https://doi.org/10.3390/agronomy15081916

Chicago/Turabian Style

Sun, Yiran, Lin Chen, Yuxin Jin, Shukun Wang, Shengnan Ma, Lin Yu, Chunshuang Tang, Yuying Ye, Mingxuan Li, Wenhui Zhou, and et al. 2025. "Identification of Key Waterlogging-Tolerance Genes in Cultivated and Wild Soybeans via Integrated QTL–Transcriptome Analysis" Agronomy 15, no. 8: 1916. https://doi.org/10.3390/agronomy15081916

APA Style

Sun, Y., Chen, L., Jin, Y., Wang, S., Ma, S., Yu, L., Tang, C., Ye, Y., Li, M., Zhou, W., Chen, E., Kong, X., Fu, J., Wang, J., Chen, Q., & Yang, M. (2025). Identification of Key Waterlogging-Tolerance Genes in Cultivated and Wild Soybeans via Integrated QTL–Transcriptome Analysis. Agronomy, 15(8), 1916. https://doi.org/10.3390/agronomy15081916

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