Title : Genome-wide identification and functional validation of drought stress regulatory genes in chickpea
Abstract:
Drought stress is a major abiotic constraint limiting chickpea (Cicer arietinum L.) productivity, particularly under rainfed and semi-arid agro-ecological conditions. The drought response in chickpea is governed by complex and coordinated regulatory networks involving protein-coding genes, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs), which collectively modulate stress perception, signaling, and adaptive responses. In the present study, an integrated genome-wide multi-omics approach was employed to dissect drought-responsive regulatory networks and identify promising gene–miRNA pairs for genome editing–based improvement of drought resilience in chickpea.Comprehensive phenotyping under controlled drought stress conditions was conducted to assess key physiological and morphological traits, enabling accurate discrimination of drought-responsive phenotypes.
Transcriptome (mRNA), lncRNA, and small RNA sequencing datasets generated from drought-stressed and well-watered chickpea plants were analyzed to identify differentially expressed mRNAs, lncRNAs, and miRNAs. Functional annotation and pathway enrichment analyses revealed that drought-responsive genes were predominantly associated with abscisic acid signaling, reactive oxygen species homeostasis, osmotic regulation, transcriptional control, and root development. Integration of expression profiles with miRNA target prediction and lncRNA–miRNA–mRNA interaction analyses facilitated the construction of regulatory networks governing drought stress responses.Based on combined phenotypic performance, expression dynamics, and regulatory interactions, key drought-associated gene–miRNA regulatory modules were prioritized as promising targets for genome editing. These candidates represent potential negative regulators of drought tolerance, whose precise modification using CRISPR/Cas-based genome editing is expected to enhance drought resilience without compromising agronomic performance. Overall, this study provides a robust multi-omics framework linking drought phenotyping with regulatory network analysis and genome editing, offering a scalable strategy for developing climate-resilient chickpea cultivars.
