Genome-wide characterization of the CaCHI chitinases gene family in chickpea reveals CaCHI4's crucial role in salt stress tolerance in plants

Genome-wide characterization of the CaCHI chitinases gene family in chickpea reveals CaCHI4's crucial role in salt stress tolerance in plants | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genome-wide characterization of the CaCHI chitinases gene family in chickpea reveals CaCHI4's crucial role in salt stress tolerance in plants Yan Liang, Chaoni Liang, Fanzhen Fei, Minghui Yang, Jia Liu, Xiaoyun Zhou, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8202951/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background and aims Chickpea ( Cicer arietinum L.), an important legume crop, suffers substantial yield losses due to soil salinity. Plant chitinases (CHIs), classified as pathogenesis-related proteins primarily involved in biotic stress responses, have also been implicated in abiotic stress adaptation, including salt tolerance; however, their specific role in chickpea’s salinity response remains poorly understood. This study aimed to identify the chickpea chitinase ( CaCHI ) gene family and functionally characterize key members contributing to salt stress tolerance. Methods A genome-wide identification of CaCHI genes was performed, followed by phylogenetic and structural analyses. Expression profiling under salt stress and functional validation of CaCHI4 were conducted via heterologous overexpression in Arabidopsis thaliana and chickpea hairy roots. Physiological, biochemical, and transcriptomic assays were used to evaluate stress responses and elucidate underlying mechanisms. Results Twenty-five CaCHI genes were identified and grouped into five distinct classes. CaCHI4 , a GH19 Class I chitinase with conserved chitin-binding and catalytic domains, was markedly upregulated under salt stress. Overexpression of CaCHI4 enhanced salt tolerance, reduced reactive oxygen species accumulation, elevated antioxidant enzyme activities, and improved photosynthetic efficiency. Transgenic lines exhibited increased stomatal closure, improved water retention, higher chlorophyll fluorescence, and induction of stress-responsive genes. Transcriptome analysis revealed CaCHI4 -mediated regulation of signaling pathways including MAPK, hormone signaling, and flavonoid biosynthesis, along with antioxidant defense and cell wall remodeling. Conclusions CaCHI4 mediates a regulatory network enhancing salt stress tolerance in chickpea. These findings advance mechanistic understanding of chitinase function in abiotic stress and identify CaCHI4 as a promising candidate gene for breeding salt-tolerant chickpea varieties. Chickpea Salt stress Chitinases Gene family CaCHI4 Transcriptome Full Text Supplementary Files Supplementarydata11.17.docx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8202951","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":558110828,"identity":"72e26094-facb-4e7f-bfd2-69891994e390","order_by":0,"name":"Yan Liang","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Yan","middleName":"","lastName":"Liang","suffix":""},{"id":558110829,"identity":"e1c75462-712f-447b-8bb6-f05a06f051ce","order_by":1,"name":"Chaoni 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plants","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Chickpea, Salt stress, Chitinases, Gene family, CaCHI4, Transcriptome","lastPublishedDoi":"10.21203/rs.3.rs-8202951/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8202951/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eBackground and aims\u003c/em\u003e Chickpea (\u003cem\u003eCicer arietinum\u003c/em\u003e L.), an important legume crop, suffers substantial yield losses due to soil salinity. Plant chitinases (CHIs), classified as pathogenesis-related proteins primarily involved in biotic stress responses, have also been implicated in abiotic stress adaptation, including salt tolerance; however, their specific role in chickpea’s salinity response remains poorly understood. This study aimed to identify the chickpea chitinase (\u003cem\u003eCaCHI\u003c/em\u003e) gene family and functionally characterize key members contributing to salt stress tolerance.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eMethods \u003c/em\u003eA genome-wide identification of \u003cem\u003eCaCHI\u003c/em\u003e genes was performed, followed by phylogenetic and structural analyses. Expression profiling under salt stress and functional validation of \u003cem\u003eCaCHI4\u003c/em\u003e were conducted via heterologous overexpression in \u003cem\u003eArabidopsis thaliana\u003c/em\u003e and chickpea hairy roots. Physiological, biochemical, and transcriptomic assays were used to evaluate stress responses and elucidate underlying mechanisms.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eResults\u003c/em\u003eTwenty-five \u003cem\u003eCaCHI\u003c/em\u003e genes were identified and grouped into five distinct classes. \u003cem\u003eCaCHI4\u003c/em\u003e, a GH19 Class I chitinase with conserved chitin-binding and catalytic domains, was markedly upregulated under salt stress. Overexpression of \u003cem\u003eCaCHI4\u003c/em\u003e enhanced salt tolerance, reduced reactive oxygen species accumulation, elevated antioxidant enzyme activities, and improved photosynthetic efficiency. Transgenic lines exhibited increased stomatal closure, improved water retention, higher chlorophyll fluorescence, and induction of stress-responsive genes. Transcriptome analysis revealed \u003cem\u003eCaCHI4\u003c/em\u003e-mediated regulation of signaling pathways including MAPK, hormone signaling, and flavonoid biosynthesis, along with antioxidant defense and cell wall remodeling.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eConclusions\u003c/em\u003e \u003cem\u003eCaCHI4\u003c/em\u003e mediates a regulatory network enhancing salt stress tolerance in chickpea. These findings advance mechanistic understanding of chitinase function in abiotic stress and identify \u003cem\u003eCaCHI4\u003c/em\u003e as a promising candidate gene for breeding salt-tolerant chickpea varieties.\u003c/p\u003e","manuscriptTitle":"Genome-wide characterization of the CaCHI chitinases gene family in chickpea reveals CaCHI4's crucial role in salt stress tolerance in plants","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-15 08:37:59","doi":"10.21203/rs.3.rs-8202951/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"c6390023-63f1-45d8-8f66-afdce0f8d387","owner":[],"postedDate":"December 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-01-12T08:48:33+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-15 08:37:59","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8202951","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8202951","identity":"rs-8202951","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}