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Agronomy
Volume 15
Issue 12
10.3390/agronomy15122752
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

GWAS Combined with RNA-Seq for Candidate Gene Identification of Soybean Cyst Nematode Disease and Functional Characterization of GmRF2-like Gene

by
Shuo Qu
,
Miaoli Zhang
,
Shihao Hu
,
Gengchen Song
,
Haiyan Li
,
Weili Teng
,
Yongguang Li
,
Xue Zhao
* and
Yingpeng Han
*
Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(12), 2752; https://doi.org/10.3390/agronomy15122752 (registering DOI)
Submission received: 25 October 2025 / Revised: 23 November 2025 / Accepted: 27 November 2025 / Published: 28 November 2025
(This article belongs to the Special Issue Evaluation of Germplasm Resources, Molecular Breeding, and Utilization in Soybean)
Versions Notes

Abstract

Soybean (Glycine max) is a globally important grain and oil crop, but its yield and quality are severely limited by soybean cyst nematode (SCN, Heterodera glycines Ichinohe), a devastating soil-borne pathogen. Here, we evaluated SCN race 3 resistance in 306 soybean germplasms and combined a genome-wide association study (GWAS) with transcriptome analysis to identify key resistance-related genes. GWAS using 30× resequencing data (632,540 SNPs) revealed 77 significant quantitative trait loci (QTLs) associated with SCN resistance, while transcriptome comparison between the extreme resistant accession Dongnong L10 and susceptible Heinong 37 identified 4185 upregulated and 3195 downregulated genes. Integrating these results, we characterized the GmRF2-like gene as a candidate resistance gene. Subcellular localization showed GmRF2-like encodes a nuclear-localized protein. Functional validation via soybean hairy root transformation demonstrated that overexpression of GmRF2-like significantly inhibits SCN race 3 infection. Collectively, our findings confirm that GmRF2-like plays a positive role in soybean resistance to SCN race 3, providing critical insights for dissecting the molecular mechanism of SCN resistance and facilitating the development of resistant soybean varieties.
Keywords: soybean; soybean cyst nematode; compressed mixed linear model; gene cloning; gene function soybean; soybean cyst nematode; compressed mixed linear model; gene cloning; gene function

Share and Cite

MDPI and ACS Style

Qu, S.; Zhang, M.; Hu, S.; Song, G.; Li, H.; Teng, W.; Li, Y.; Zhao, X.; Han, Y. GWAS Combined with RNA-Seq for Candidate Gene Identification of Soybean Cyst Nematode Disease and Functional Characterization of GmRF2-like Gene. Agronomy 2025, 15, 2752. https://doi.org/10.3390/agronomy15122752

AMA Style

Qu S, Zhang M, Hu S, Song G, Li H, Teng W, Li Y, Zhao X, Han Y. GWAS Combined with RNA-Seq for Candidate Gene Identification of Soybean Cyst Nematode Disease and Functional Characterization of GmRF2-like Gene. Agronomy. 2025; 15(12):2752. https://doi.org/10.3390/agronomy15122752

Chicago/Turabian Style

Qu, Shuo, Miaoli Zhang, Shihao Hu, Gengchen Song, Haiyan Li, Weili Teng, Yongguang Li, Xue Zhao, and Yingpeng Han. 2025. "GWAS Combined with RNA-Seq for Candidate Gene Identification of Soybean Cyst Nematode Disease and Functional Characterization of GmRF2-like Gene" Agronomy 15, no. 12: 2752. https://doi.org/10.3390/agronomy15122752

APA Style

Qu, S., Zhang, M., Hu, S., Song, G., Li, H., Teng, W., Li, Y., Zhao, X., & Han, Y. (2025). GWAS Combined with RNA-Seq for Candidate Gene Identification of Soybean Cyst Nematode Disease and Functional Characterization of GmRF2-like Gene. Agronomy, 15(12), 2752. https://doi.org/10.3390/agronomy15122752

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