Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study
Abstract
1. Introduction
2. Results
2.1. Reference Guided Assembly of Transcripts and Re-Annotation of Mapped Genes
2.2. Analysis of Transcript Abundance Across Four Developmental Stages of Soybean Flowers
2.3. Overview of Differential Gene Expression (DEGs) Across Four Developmental Stadiums of Soybean Flowers
2.4. Analysis of Characteristically Expressed Gene Families in Cluster 4
2.5. Pairwise Analysis of DEGs: Stadium 2 vs. Stadium 0
2.6. Gene Ontology Analysis of DEGs of the Four Investigated Sample Pairs
2.7. Gene Set Enrichment Analysis (GSEA) Across the Four Investigated Sample Pairs, Focusing on Phytohormone-Related Genes
2.8. Expression Involved in Plant Hormone Signal Transduction Across the Four Investigated Floral Stadiums
2.9. Expression Analysis of MADS-Box Genes During Floral Development Across the Four Investigated Stadiums
3. Discussion
3.1. Reference-Guided Transcriptome Assembly and Stadium-Specific Differential Gene Expression Analysis During Soybean Floral Development
3.2. Functional Characterization of Cluster-4 Reveals Hormonal and Transcriptional Control of Early Floral Morphogenesis in Soybean
3.3. Transition from Auxin-Dominated Processes to Stress-Associated Pathways in Soybean Flower Development at Stadium 2
3.4. Coordinated Auxin, ABA, and Epigenetic Reprogramming Define Distinct Phases of Soybean Floral Maturation
3.5. Stadium-Specific Expression of MADS-Box Transcription Factors and Novel Candidate Gene GmNMH7 Reveals Complex Regulatory Networks in Soybean Flower Development
3.6. Proposed Model and Breeding Implications
3.7. Limitations and Future Directions
4. Materials and Methods
4.1. Plant Materials and RNA-Sequencing
4.2. Reference-Guided Assembly and Re-Annotation of Mapped Genes
4.3. Analysis of Differentially Expressed Genes (DEGs)
4.4. Gene Set Enrichment Analysis (GSEA)
4.5. KEGG Pathway Analysis
4.6. Digital Gene Expression Analysis (RPM)
4.7. Gene Expression Analysis by RT-qPCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Virág, E.; Hegedűs, G.; Nagy, Á.; Pallos, J.P.; Kutasy, B. Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study. Int. J. Mol. Sci. 2025, 26, 6455. https://doi.org/10.3390/ijms26136455
Virág E, Hegedűs G, Nagy Á, Pallos JP, Kutasy B. Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study. International Journal of Molecular Sciences. 2025; 26(13):6455. https://doi.org/10.3390/ijms26136455
Chicago/Turabian StyleVirág, Eszter, Géza Hegedűs, Ágnes Nagy, József Péter Pallos, and Barbara Kutasy. 2025. "Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study" International Journal of Molecular Sciences 26, no. 13: 6455. https://doi.org/10.3390/ijms26136455
APA StyleVirág, E., Hegedűs, G., Nagy, Á., Pallos, J. P., & Kutasy, B. (2025). Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study. International Journal of Molecular Sciences, 26(13), 6455. https://doi.org/10.3390/ijms26136455