Physiological and Transcriptomic Responses of Sunflower to Combined Saline–Alkali Stress

Physiological and Transcriptomic Responses of Sunflower to Combined Saline–Alkali Stress | 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 Physiological and Transcriptomic Responses of Sunflower to Combined Saline–Alkali Stress Jiangna Zheng, Xinlong Gao, Haina Zhang, Dan Li, Suen Liu, Mengzhe Li, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8994848/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 15 You are reading this latest preprint version Abstract Background Sunflower ( Helianthus annuus L.), an important oilseed crop, is often used as a pioneer species for improving saline–alkali soils. However, the molecular mechanisms underlying sunflower seedling responses to combined saline–alkali stress remain unclear. This study aimed to elucidate the molecular basis of saline–alkali tolerance at the seedling stage by comparing physiological and transcriptomic responses between tolerant and sensitive sunflower hybrids. The saline–alkali tolerant hybrid K-27 and the sensitive hybrid K-7 were used as experimental materials. Root samples were collected at 0, 3, 12, 24, 48, and 96 h after exposure to combined saline–alkali stress (0.5% NaCl + Na₂CO₃, adjusted to pH 9.0). Physiological parameters, including antioxidant enzyme activities, osmolyte contents, ion concentrations, membrane damage levels, and cell wall components, were measured, followed by transcriptome sequencing analysis. Results: Phenotypic analysis showed that the root length inhibition rate and fresh weight loss rate of K-27 were significantly lower than those of K-7, indicating stronger tolerance. Physiological analysis revealed that K-27 exhibited an inducible antioxidant enzyme response pattern.In addition, K-27 achieved osmotic adjustment through sustained proline accumulation (peaking at 12 h and remaining significantly higher than that of K-7 at 96 h) and exhibited higher basal levels of lignin and hemicellulose. Transcriptome analysis showed that the number of upregulated genes in K-27 was consistently higher than in K-7 at all time points, with 5,283 genes upregulated as early as 3 h after stress exposure. Venn analysis identified 44 core differentially expressed genes (cDEGs )shared between the two genotypes, which were mainly enriched in auxin biosynthesis regulation, phenylpropanoid biosynthesis, and glutathione metabolism. Among them, the benzoic acid carboxyl methyltransferase gene ( BAMT ) was continuously upregulated in K-27 but persistently downregulated in K-7. In addition, five other genes (encoding fatty aldehyde dehydrogenase, pectin methylesterase inhibitor, glutathione S-transferase, INPP5E, and HXXXD-type acyltransferase) exhibited significantly higher expression levels in K-27. Conclusion K-27 tolerates combined saline–alkali stress through coordinated multi-layered response mechanisms, including inducible antioxidant defense, maintenance of ion homeostasis, sustained osmotic adjustment, and activation of the phenylpropanoid metabolic pathway. Candidate genes such as BAMT may provide potential targets for molecular breeding of saline–alkali tolerant sunflower. Sunflower Combined saline–alkali stress Transcriptome Phenylpropanoid metabolism Benzoic acid carboxymethyltransferase (BAMT) Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile.docx Additional files Attached list 1 The summary of the SLAF tag and SNP marker on chromosomes Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 28 Apr, 2026 Reviews received at journal 28 Apr, 2026 Reviews received at journal 20 Apr, 2026 Reviewers agreed at journal 12 Apr, 2026 Reviewers agreed at journal 11 Apr, 2026 Reviewers agreed at journal 11 Apr, 2026 Reviewers agreed at journal 11 Apr, 2026 Reviewers agreed at journal 11 Apr, 2026 Reviews received at journal 22 Mar, 2026 Reviewers agreed at journal 16 Mar, 2026 Reviewers invited by journal 06 Mar, 2026 Editor invited by journal 04 Mar, 2026 Editor assigned by journal 03 Mar, 2026 Submission checks completed at journal 03 Mar, 2026 First submitted to journal 28 Feb, 2026 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. 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However, the molecular mechanisms underlying sunflower seedling responses to combined saline–alkali stress remain unclear. This study aimed to elucidate the molecular basis of saline–alkali tolerance at the seedling stage by comparing physiological and transcriptomic responses between tolerant and sensitive sunflower hybrids.\u003c/p\u003e\n\u003cp\u003eThe saline–alkali tolerant hybrid K-27 and the sensitive hybrid K-7 were used as experimental materials. Root samples were collected at 0, 3, 12, 24, 48, and 96 h after exposure to combined saline–alkali stress (0.5% NaCl + Na₂CO₃, adjusted to pH 9.0). Physiological parameters, including antioxidant enzyme activities, osmolyte contents, ion concentrations, membrane damage levels, and cell wall components, were measured, followed by transcriptome sequencing analysis.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePhenotypic analysis showed that the root length inhibition rate and fresh weight loss rate of K-27 were significantly lower than those of K-7, indicating stronger tolerance. Physiological analysis revealed that K-27 exhibited an inducible antioxidant enzyme response pattern.In addition, K-27 achieved osmotic adjustment through sustained proline accumulation (peaking at 12 h and remaining significantly higher than that of K-7 at 96 h) and exhibited higher basal levels of lignin and hemicellulose.\u003c/p\u003e\n\u003cp\u003eTranscriptome analysis showed that the number of upregulated genes in K-27 was consistently higher than in K-7 at all time points, with 5,283 genes upregulated as early as 3 h after stress exposure. Venn analysis identified 44 core differentially expressed genes (cDEGs )shared between the two genotypes, which were mainly enriched in auxin biosynthesis regulation, phenylpropanoid biosynthesis, and glutathione metabolism. Among them, the benzoic acid carboxyl methyltransferase gene (\u003cem\u003eBAMT\u003c/em\u003e) was continuously upregulated in K-27 but persistently downregulated in K-7. In addition, five other genes (encoding fatty aldehyde dehydrogenase, pectin methylesterase inhibitor, glutathione S-transferase, INPP5E, and HXXXD-type acyltransferase) exhibited significantly higher expression levels in K-27.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eK-27 tolerates combined saline–alkali stress through coordinated multi-layered response mechanisms, including inducible antioxidant defense, maintenance of ion homeostasis, sustained osmotic adjustment, and activation of the phenylpropanoid metabolic pathway. Candidate genes such as \u003cem\u003eBAMT\u003c/em\u003emay provide potential targets for molecular breeding of saline–alkali tolerant sunflower.\u003c/p\u003e","manuscriptTitle":"Physiological and Transcriptomic Responses of Sunflower to Combined Saline–Alkali Stress","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-11 19:20:43","doi":"10.21203/rs.3.rs-8994848/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-04-28T20:22:34+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-28T06:20:17+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-20T15:11:23+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"275339089510567460158405784559178497006","date":"2026-04-13T02:34:41+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"275667955302763775637254697178598973214","date":"2026-04-11T17:27:21+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"24779881609975377427460550241330013613","date":"2026-04-11T16:25:14+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"87931886210608153920482984096010852150","date":"2026-04-11T09:13:41+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"338346728985132333572950397505259129490","date":"2026-04-11T06:20:59+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-22T16:29:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"53592333300658541554196564891988556191","date":"2026-03-16T08:13:37+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-06T08:17:07+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-03-04T15:14:18+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-04T00:10:03+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-04T00:09:32+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2026-02-28T11:11:20+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"09568b0e-a86f-44ae-9290-3e2143865900","owner":[],"postedDate":"March 11th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-18T02:09:13+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-11 19:20:43","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8994848","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8994848","identity":"rs-8994848","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}