Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies

Alsamman M. Alsamman^1*Khaled H. Mousa¹Asmaa E. Abd El-Hak¹Doaa A. Korkar A. Korkar¹Anas M. Saedwi¹Sandy Khaled²Al-Sayed Al-Soudy³Achraf El Allali⁴Zakaria Kehel⁵Morad M. Mokhtar^3*

• ¹International Center for Agriculture Research in the Dry Areas (ICARDA) Egypt, Giza, Egypt
• ²Agricultural Genetic Engineering Research Institute, Giza, Egypt
• ³Chemical Biochemical Sciences-Green Process Engineering, College of Chemical Sciences and Engineering, Mohammed VI Polytechnic University, Benguerir, 43150, Morocco, Benguerir, Morocco
• ⁴Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Lot 660, Ben Guerir, 43150, Morocco, Ben Guerir, Morocco
• ⁵International Center for Agricultural Research in the Dry Areas Morocco, Rabat, Morocco

Chickpea (Cicer arietinum L.) is a key legume crop and a major source of dietary protein in developing countries, yet its productivity is constrained by multiple biotic and abiotic stresses. Advances in RNA-seq and whole-genome sequencing enable detailed exploration of stress-responsive gene expression, but existing resources lack integrated, user-friendly tools for multi-omics analysis in chickpea. This study analyzes transcriptomic responses to six stress conditions—drought, heat, cold, salinity, Fusarium infection, and developmental stages—using publicly available RNA-seq datasets. We identified differentially expressed genes (DEGs), enriched gene ontology (GO) terms, and protein–protein interaction (PPI) networks. Critically, we developed ChickpeaOmicsR, the first comprehensive R package that automates integration of transcriptomic, genomic, and proteomic data; standardizes fragmented chickpea gene nomenclature; enables breeders without bioinformatics expertise to perform complex analyses (e.g., DEG identification, PPI visualization, GWAS integration) in minutes; and provides pre-validated datasets and analytical workflows unavailable in existing tools. Each stress triggered distinct molecular pathways: drought and heat affected cell wall organization and defense responses, while cold influenced circadian rhythm genes. Fusarium stress involved innate immunity and secondary metabolism. Developmental stages showed the highest transcriptome variability. ChickpeaOmicsR addresses critical gaps in chickpea research infrastructure, accelerating the development of stress-resilient varieties.