Unveiling crosstalk between abiotic and biotic stress responses in soybean (Glycine max) using integrative RNA-Seq meta-analysis.

Soybean (Glycine max) is a critical world crop, highly valued for its high protein and oil content. However, its yield is increasingly threatened by varied abiotic and biotic stresses. Biotic and abiotic stresses often show antagonistic or synergistic cross-talk, whereby one stress may induce cross-tolerance or cross-susceptibility to another stress. Therefore, investigating the molecular interactions for the identification of key hub genes is essential for development of multistress resilient soybean crop. The current research conducts an extensive meta-analysis of available RNA-Seq data to identify conserved transcriptional responses to major stress conditions. 903 and 1,136 meta-differentially expressed genes (meta-DEGS) were found under abiotic (drought, heat, cold, salt) and biotic (aphids, mites, rust, viruses) stresses, respectively, with 28 genes regulated across both types of stresses. Central to the stress response was co-upregulation of protein kinases and NAC transcription factors, regulation of redox buffers and programmed cell death. Abiotic stresses initiate a proteostasis-centred response, involving elevated protein folding, degradation, and ribosome biogenesis, and repression of energy-expensive pathways like photosynthesis. Contrarily, biotic stress triggers immune responses through upregulation of defence and signalling genes, while suppressing circadian function and growth. Furthermore, network analysis, promoter motif discovery and miRNA profiling revealed key hub genes, such as Bystin, BING4, Nucleolar Protein 6, DOF transcription factors, miR171, and miR172. Briefly, in this research we identified putative converging genes of soybean where abiotic and biotic stresses signalling cross-talk. Candidate miRNAs, DOF and NAC transcription factors, HSP chaperones, and ERAD- and ribosome-related genes as for stress resilience in soybean were identified. This systems-level understanding provides promising targets for functional validation and afterwards developing climate-resilient and pathogen-tolerant soybean cultivars through targeted genetic and breeding strategies.