Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis

Gu, Jin-Bao; Cheng, Yin-Jie; Li, Cong; Zhang, Bai-Hong; Zhang, Yu-Hang; Liang, Xiao-Yan; Li, Yang; Lin, Yan

doi:10.3390/ijms262311648

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Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis

by

Jin-Bao Gu

^1,2,†

,

Yin-Jie Cheng

^1,†

,

Cong Li

¹,

Bai-Hong Zhang

¹,

Yu-Hang Zhang

¹

,

Xiao-Yan Liang

¹,

Yang Li

^1,3,*,‡

and

Yan Lin

^1,2,*,‡

¹

Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou 510316, China

²

Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Zhanjiang 524300, China

³

State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

^‡

These authors also contributed equally to this work.

Int. J. Mol. Sci. 2025, 26(23), 11648; https://doi.org/10.3390/ijms262311648 (registering DOI)

Submission received: 20 October 2025 / Revised: 26 November 2025 / Accepted: 27 November 2025 / Published: 1 December 2025

(This article belongs to the Special Issue Latest Advances in Plant Abiotic Stress)

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Abstract

Soil salinity severely threatens soybean productivity worldwide. While transcriptional responses to salt stress are well-documented, the role of post-transcriptional regulation, particularly alternative splicing (AS), remains underexplored. This study combines physiological phenotyping, transcriptome-wide analysis, and molecular genetics to uncover the mechanisms behind the differences in salt tolerance between the salt-sensitive variety Huachun 6 (HC6) and the resistant variety Fiskeby III. Under salt stress, Fiskeby III exhibited superior survival rates and maintained ion homeostasis, as evidenced by a lower Na⁺/K⁺ ratio, compared with HC6. Transcriptomic and splicing analysis revealed extensive salt-induced alternative splicing reprogramming. Genes undergoing differential AS were enriched in pathways related to stress response, ion transport, and RNA splicing. Based on the overlap with both differentially expressed genes (DEG) and alternative splicing (DAS) genes under salt stress, a key splicing factor, GmSR34b, was identified as a central regulator of AS under salt stress. Under NaCl stress, the expression of GmSR34b in leaves peaked at 1 h and a salt stress-specific splicing variant was rapidly induced. A comparative analysis showed that the Fiskeby III cultivar prioritized maintenance of the full-length transcript during prolonged stress, whereas the HC6 cultivar accumulated higher levels of the splicing variant. This indicates differences in the regulation of alternative splicing between these two cultivars. Functional validation confirmed that overexpression of GmSR34b in soybean hairy roots inhibited salt tolerance. This study provides novel insights into the molecular mechanisms of salt tolerance in soybean, suggesting potential strategies for breeding resilient crops through the manipulation of splicing regulators.

Keywords: alternative splicing; transcriptome; salt stress; soybean; GmSR34b; splicing factor

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MDPI and ACS Style

Gu, J.-B.; Cheng, Y.-J.; Li, C.; Zhang, B.-H.; Zhang, Y.-H.; Liang, X.-Y.; Li, Y.; Lin, Y. Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis. Int. J. Mol. Sci. 2025, 26, 11648. https://doi.org/10.3390/ijms262311648

AMA Style

Gu J-B, Cheng Y-J, Li C, Zhang B-H, Zhang Y-H, Liang X-Y, Li Y, Lin Y. Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis. International Journal of Molecular Sciences. 2025; 26(23):11648. https://doi.org/10.3390/ijms262311648

Chicago/Turabian Style

Gu, Jin-Bao, Yin-Jie Cheng, Cong Li, Bai-Hong Zhang, Yu-Hang Zhang, Xiao-Yan Liang, Yang Li, and Yan Lin. 2025. "Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis" International Journal of Molecular Sciences 26, no. 23: 11648. https://doi.org/10.3390/ijms262311648

APA Style

Gu, J.-B., Cheng, Y.-J., Li, C., Zhang, B.-H., Zhang, Y.-H., Liang, X.-Y., Li, Y., & Lin, Y. (2025). Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis. International Journal of Molecular Sciences, 26(23), 11648. https://doi.org/10.3390/ijms262311648

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Identification of the Splicing Factor GmSR34b as a Negative Regulator of Salt Stress Response in Soybean Through Transcriptome and Alternative Splicing Analysis

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