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Volume 26
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10.3390/ijms26178385
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions

by
Xiulin Liu
1,
Sobhi F. Lamlom
1,2,
Xueyang Wang
1,
Chunlei Zhang
1,
Fengyi Zhang
1,
Kezhen Zhao
1,
Rongqiang Yuan
1,
Bixian Zhang
3,* and
Honglei Ren
1,*
1
Soybean Research Institute of Heilongjiang Academy of Agriculture Sciences, Harbin 150086, China
2
Plant Production Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt
3
Institute of Biotechnology of Heilongjiang Academy of Agricultural Sciences, Harbin 150023, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(17), 8385; https://doi.org/10.3390/ijms26178385 (registering DOI)
Submission received: 26 May 2025 / Revised: 31 July 2025 / Accepted: 2 August 2025 / Published: 28 August 2025
(This article belongs to the Special Issue Recent Advances in Soybean Molecular Breeding)
Review Reports Versions Notes

Abstract

Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, bHLH (8.08%), bZIP (7.18%), and WRKY (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices.
Keywords: soybean; phosphorus deficiency; transcriptome sequencing; differentially expressed genes (DEGs); phosphorus use efficiency soybean; phosphorus deficiency; transcriptome sequencing; differentially expressed genes (DEGs); phosphorus use efficiency

Share and Cite

MDPI and ACS Style

Liu, X.; Lamlom, S.F.; Wang, X.; Zhang, C.; Zhang, F.; Zhao, K.; Yuan, R.; Zhang, B.; Ren, H. Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions. Int. J. Mol. Sci. 2025, 26, 8385. https://doi.org/10.3390/ijms26178385

AMA Style

Liu X, Lamlom SF, Wang X, Zhang C, Zhang F, Zhao K, Yuan R, Zhang B, Ren H. Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions. International Journal of Molecular Sciences. 2025; 26(17):8385. https://doi.org/10.3390/ijms26178385

Chicago/Turabian Style

Liu, Xiulin, Sobhi F. Lamlom, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Kezhen Zhao, Rongqiang Yuan, Bixian Zhang, and Honglei Ren. 2025. "Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions" International Journal of Molecular Sciences 26, no. 17: 8385. https://doi.org/10.3390/ijms26178385

APA Style

Liu, X., Lamlom, S. F., Wang, X., Zhang, C., Zhang, F., Zhao, K., Yuan, R., Zhang, B., & Ren, H. (2025). Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions. International Journal of Molecular Sciences, 26(17), 8385. https://doi.org/10.3390/ijms26178385

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