{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T14:46:28Z","timestamp":1773413188489,"version":"3.50.1"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:00:00Z","timestamp":1773100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Chickpea (\n                      <jats:italic>Cicer arietinum<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study analyzed transcriptomic responses to six stress conditions\u2014drought, heat, cold, salinity, Fusarium infection, and developmental stages\u2014using publicly available RNA-seq datasets. We identified differentially expressed genes (DEGs), enriched gene ontology (GO) terms, and protein\u2013protein interaction (PPI) networks. Critically, we developed ChickpeaOmicsR, the first comprehensive R package that automates the integration of transcriptomic, genomic, and proteomic data and 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Each stress triggered distinct molecular pathways. Drought and heat stress affected cell wall organization and defense responses, while cold stress influenced circadian rhythm genes. Fusarium stress involved pathways related to innate immunity and secondary metabolism. Developmental stages showed the highest transcriptome variability among the conditions tested.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>The development of ChickpeaOmicsR addresses critical gaps in chickpea research infrastructure. By providing an integrated and accessible tool that enables complex analyses for breeders without bioinformatics expertise, it accelerates the discovery of stress-resilient genes and the development of improved chickpea varieties.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fbinf.2026.1727493","type":"journal-article","created":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T09:01:56Z","timestamp":1773133316000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies"],"prefix":"10.3389","volume":"6","author":[{"given":"Alsamman M.","family":"Alsamman","sequence":"first","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA)","place":["Giza, Egypt"]},{"name":"Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC)","place":["Giza, Egypt"]}]},{"given":"Khaled H.","family":"Mousa","sequence":"additional","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA)","place":["Giza, Egypt"]}]},{"given":"Asmaa E.","family":"Abd El-Hak","sequence":"additional","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA)","place":["Giza, Egypt"]}]},{"given":"Doaa A.","family":"Korkar","sequence":"additional","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA)","place":["Giza, Egypt"]}]},{"given":"Anas M.","family":"Saedwi","sequence":"additional","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA)","place":["Giza, Egypt"]}]},{"given":"Sandy","family":"Khaled","sequence":"additional","affiliation":[{"name":"Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC)","place":["Giza, Egypt"]}]},{"given":"Al-Sayed","family":"Al-Soudy","sequence":"additional","affiliation":[{"name":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P)","place":["Ben Guerir, Morocco"]}]},{"given":"Achraf","family":"El Allali","sequence":"additional","affiliation":[{"name":"Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University","place":["Ben Guerir, Morocco"]}]},{"given":"Zakaria","family":"Kehel","sequence":"additional","affiliation":[{"name":"Genbank, International Center for Agricultural Research In the Dry Areas","place":["Rabat, Morocco"]}]},{"given":"Morad M.","family":"Mokhtar","sequence":"additional","affiliation":[{"name":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P)","place":["Ben Guerir, Morocco"]}]}],"member":"1965","published-online":{"date-parts":[[2026,3,10]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1292009","DOI":"10.3389\/fgene.2023.1292009","article-title":"Unveiling the genetic basis of fusarium wilt resistance in chickpea using gwas analysis and characterization of candidate genes","volume":"14","author":"Alsamman","year":"2024","journal-title":"Front. 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