An integrated transcriptomic and proteomics analysis reveals the impact of drought stress on Pisum sativum.

Drought stress is a major limitation to global crop productivity, yet the molecular basis of drought responses in Pisum sativum (pea) a nutritionally important legume remains poorly understood. We hypothesized that drought induces coordinated transcriptional and proteomic reprogramming in pea chloroplasts and leaves, thereby activating photoprotective, antioxidant, and stress-responsive pathways. To investigate this, we applied integrated transcriptomic (Solexa-Illumina sequencing) and proteomic (iTRAQ) analyses, focusing on chloroplast-targeted transcripts and proteins. Our findings revealed significant upregulation of chloroplast- and stress-related genes and proteins, including dehydrins, PSBS, heat shock proteins, LEA proteins, ROS scavengers, and aquaporins. Induction of ABA-responsive and heat shock transcription factors suggested the activation of photoprotective and photo acclimation mechanisms. Integration of transcriptomic and proteomic datasets demonstrated concordant regulation of key pathways: upregulation of PSBS, DHN, and PIP transcripts corresponded with increased protein abundance, supporting their dual roles in photoprotection and osmotic adjustment. Similarly, ROS and calcium-associated transcripts were accompanied by elevated levels of antioxidant enzymes and signaling proteins, highlighting coordinated chloroplast-nucleus communication. Proteomic enrichment of photosynthetic light-harvesting complexes, molecular chaperones, and vacuole proton pumps further underscored chloroplasts as central hubs of drought response. Together, these results reveal multi-layered molecular networks enabling drought tolerance in pea, providing a valuable resource for improving legume resilience.