Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with heat stress in non-heading Chinese cabbage

Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with heat stress in non-heading Chinese cabbage | 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 Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with heat stress in non-heading Chinese cabbage Wei Liu, Zhangyang Dai, Jingyi Jia, Xiaofeng Li, Hongfang Zhu, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5590134/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract Background Non-heading Chinese cabbage ( Brassica campestris (syn. Brassica rapa) ssp. chinensis ) (NHCC) is an important vegetable crop with economic benefits and is widely cultivated worldwide. Heat stress disrupts intracellular homeostasis, resulting in significant growth inhibition of buds and roots, severe retardation of growth and development, and even death. However, there are relatively few studies on the molecular response mechanism of NHCC to heat stress. Results In this study, RNA sequencing (RNA-seq) technology was employed to investigate the transcriptome data of the heat-tolerant variety "SHI" and the heat-sensitive variety "AJH" under high temperature. Differentially expressed genes (DEGs), including transcription factors (TFs), genes related to hormone synthesis, and genes related to protein processing in the endoplasmic reticulum, were identified in both varieties. The combination of multi-sample RNA-seq data and weighted gene co-expression network analysis (WGCNA) identified four key modules, namely the darkgreen module, the yellow module, the blue module, and the turquoise module, and core genes within them, including MYB-related , Hsp20 and DBB etc., were mined. Conclusion Our findings suggest that protein processing in the endoplasmic reticulum, photosynthesis, and plant hormone signaling are crucial for "SHI"'s response to heat stress and some candidate genes such as MYB-related , Hsp20 and DBB were identified. We validated our results with qRT-PCR, reinforcing the reliability of our data. These insights deepen our understanding of the physiological and molecular bases of NHCC heat tolerance and identify key genes for further molecular investigation. non-heading Chinese cabbage heat stress WGCNA analyses transcription factors gene expression Full Text Additional Declarations No competing interests reported. Supplementary Files TableS1.xlsx TableS2.xls TableS3.xlsx TableS4.xlsx SupplementaryTablesandFiguresList.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 16 May, 2025 Reviews received at journal 06 May, 2025 Reviews received at journal 06 May, 2025 Reviewers agreed at journal 30 Apr, 2025 Reviewers agreed at journal 29 Apr, 2025 Reviewers agreed at journal 26 Apr, 2025 Reviewers agreed at journal 23 Apr, 2025 Reviewers invited by journal 09 Apr, 2025 Submission checks completed at journal 07 Apr, 2025 First submitted to journal 07 Apr, 2025 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-5590134","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":440788272,"identity":"1b7b8a64-2373-4292-a015-73552d03a8a6","order_by":0,"name":"Wei Liu","email":"","orcid":"","institution":"Anhui Normal University","correspondingAuthor":false,"prefix":"","firstName":"Wei","middleName":"","lastName":"Liu","suffix":""},{"id":440788273,"identity":"d605a49e-d3fc-48f9-8bcb-a0af9d3322d1","order_by":1,"name":"Zhangyang Dai","email":"","orcid":"","institution":"Anhui Normal 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cabbage","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"non-heading Chinese cabbage, heat stress, WGCNA analyses, transcription factors, gene expression","lastPublishedDoi":"10.21203/rs.3.rs-5590134/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5590134/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eNon-heading Chinese cabbage (\u003cem\u003eBrassica campestris\u003c/em\u003e (syn. \u003cem\u003eBrassica\u003c/em\u003e rapa) ssp. \u003cem\u003echinensis\u003c/em\u003e) (NHCC) is an important vegetable crop with economic benefits and is widely cultivated worldwide. Heat stress disrupts intracellular homeostasis, resulting in significant growth inhibition of buds and roots, severe retardation of growth and development, and even death. However, there are relatively few studies on the molecular response mechanism of NHCC to heat stress.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eIn this study, RNA sequencing (RNA-seq) technology was employed to investigate the transcriptome data of the heat-tolerant variety \"SHI\" and the heat-sensitive variety \"AJH\" under high temperature. Differentially expressed genes (DEGs), including transcription factors (TFs), genes related to hormone synthesis, and genes related to protein processing in the endoplasmic reticulum, were identified in both varieties. The combination of multi-sample RNA-seq data and weighted gene co-expression network analysis (WGCNA) identified four key modules, namely the darkgreen module, the yellow module, the blue module, and the turquoise module, and core genes within them, including \u003cem\u003eMYB-related\u003c/em\u003e, \u003cem\u003eHsp20\u003c/em\u003e and \u003cem\u003eDBB\u003c/em\u003e etc., were mined.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eOur findings suggest that protein processing in the endoplasmic reticulum, photosynthesis, and plant hormone signaling are crucial for \"SHI\"'s response to heat stress and some candidate genes such as \u003cem\u003eMYB-related\u003c/em\u003e, \u003cem\u003eHsp20\u003c/em\u003e and \u003cem\u003eDBB\u003c/em\u003e were identified. We validated our results with qRT-PCR, reinforcing the reliability of our data. These insights deepen our understanding of the physiological and molecular bases of NHCC heat tolerance and identify key genes for further molecular investigation.\u003c/p\u003e","manuscriptTitle":"Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with heat stress in non-heading Chinese cabbage","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-11 16:23:32","doi":"10.21203/rs.3.rs-5590134/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-05-16T04:12:16+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-05-07T01:39:16+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-05-06T22:00:59+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"131199512584821860589655397135630383654","date":"2025-04-30T06:14:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"263880685708024550352678991414654259296","date":"2025-04-30T01:15:49+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"79725643776649269038902855739472829721","date":"2025-04-27T01:10:14+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"205943071146969731964362136343592340482","date":"2025-04-23T19:43:05+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-04-09T18:34:20+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-04-07T11:00:02+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2025-04-07T09:17:34+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"e0a577a9-74e6-46c8-ad96-e5451e119da8","owner":[],"postedDate":"April 11th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-07-24T05:08:26+00:00","versionOfRecord":[],"versionCreatedAt":"2025-04-11 16:23:32","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5590134","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5590134","identity":"rs-5590134","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}