Unveiling the Wheat NTP Gene Family: Insights from Genome-Wide Identification and TaNTP6 Haplotype Analysis

Unveiling the Wheat NTP Gene Family: Insights from Genome-Wide Identification and TaNTP6 Haplotype Analysis | 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 Unveiling the Wheat NTP Gene Family: Insights from Genome-Wide Identification and TaNTP6 Haplotype Analysis Xiaoqing Hu, Dan Wang, Panyu Du, Mengxiang Liu, Nan Lin, Fuju Tai, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7526017/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 19 Nov, 2025 Read the published version in BMC Plant Biology → Version 1 posted 10 You are reading this latest preprint version Abstract Background Nucleotidyl transferase proteins (NTPs) regulate RNA homeostasis by mediating templated-independent nucleotide additions to RNA termini, thereby being implicated in crucial roles during plant growth, development, and stress responses. However, investigations of the NTP gene family have been limited to Arabidopsis , rice, maize, and soybean, with NTP genes in wheat remaining uncharacterized. Results In this study, we identified 34 TaNTP genes in wheat and classified them into three phylogenetic groups (G1–G3). All 20 segmental duplication events occurred specifically in G3. Motif and domain analyses showed distinct features: G3 TaNTPs contain unique motifs, while G1 members possess an extra PAP_assoc domain absent in G2 and G3. Protein interaction networks further supported group divergence, with G1 and G3 proteins forming separate modules (Module Ⅰ and Ⅱ), and G2 distributed across both, suggesting functional specialization or dual roles. Expression profiling revealed that most TaNTPs are lowly expressed in leaves but upregulated under heat-drought stress. Many are also responsive to salt, ABA, and SA, supporting roles in stress adaptation. Notably, TaNTP6A/B/D show high expression levels in grains. Significant associations were observed between specific TaNTP6A/B/D haplotypes and thousand-kernel weight (TKW), implying a crucial regulatory role in grain development. Through haplotype analysis, we identified superior haplotypes associated with increased grain yield: TaNTP6A-Hap1 , TaNTP6B-Hap2 , and TaNTP6D-Hap5 / 6 . Additionally, subcellular localization analysis revealed that TaNTP4A and TaNTP1A, the orthologs of AtHESO1 and AtURT1, are detectable in both the nucleus and cytoplasm, but exhibit predominant nuclear localization. Conclusions These results provide pivotal insights into the NTP family in wheat. Importantly, the identification of superior TaNTP6A/B/D haplotypes offers valuable genetic resources for facilitating high-yield wheat breeding programs. Nucleotidyl transferase Expression analysis Haplotypes Wheat Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryFigures.docx SupplementaryTables.xlsx Cite Share Download PDF Status: Published Journal Publication published 19 Nov, 2025 Read the published version in BMC Plant Biology → Version 1 posted Editorial decision: Revision requested 03 Oct, 2025 Reviews received at journal 02 Oct, 2025 Reviews received at journal 28 Sep, 2025 Reviewers agreed at journal 17 Sep, 2025 Reviewers agreed at journal 17 Sep, 2025 Reviewers invited by journal 14 Sep, 2025 Editor invited by journal 10 Sep, 2025 Editor assigned by journal 09 Sep, 2025 Submission checks completed at journal 09 Sep, 2025 First submitted to journal 03 Sep, 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. 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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-7526017","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":516421117,"identity":"cd02a988-27fa-45f2-807d-bdf5cd8fb8c8","order_by":0,"name":"Xiaoqing Hu","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Xiaoqing","middleName":"","lastName":"Hu","suffix":""},{"id":516421121,"identity":"65e19ba4-26a7-4af1-8c12-9465c6b31954","order_by":1,"name":"Dan Wang","email":"","orcid":"","institution":"Puyang Academy of Agricultural and Forestry 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Analysis","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"Nucleotidyl transferase, Expression analysis, Haplotypes, Wheat","lastPublishedDoi":"10.21203/rs.3.rs-7526017/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7526017/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eNucleotidyl transferase proteins (NTPs) regulate RNA homeostasis by mediating templated-independent nucleotide additions to RNA termini, thereby being implicated in crucial roles during plant growth, development, and stress responses. However, investigations of the \u003cem\u003eNTP\u003c/em\u003e gene family have been limited to \u003cem\u003eArabidopsis\u003c/em\u003e, rice, maize, and soybean, with \u003cem\u003eNTP\u003c/em\u003e genes in wheat remaining uncharacterized.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eIn this study, we identified 34 TaNTP genes in wheat and classified them into three phylogenetic groups (G1\u0026ndash;G3). All 20 segmental duplication events occurred specifically in G3. Motif and domain analyses showed distinct features: G3 TaNTPs contain unique motifs, while G1 members possess an extra PAP_assoc domain absent in G2 and G3. Protein interaction networks further supported group divergence, with G1 and G3 proteins forming separate modules (Module Ⅰ and Ⅱ), and G2 distributed across both, suggesting functional specialization or dual roles. Expression profiling revealed that most TaNTPs are lowly expressed in leaves but upregulated under heat-drought stress. Many are also responsive to salt, ABA, and SA, supporting roles in stress adaptation. Notably, \u003cem\u003eTaNTP6A/B/D\u003c/em\u003e show high expression levels in grains. Significant associations were observed between specific \u003cem\u003eTaNTP6A/B/D\u003c/em\u003e haplotypes and thousand-kernel weight (TKW), implying a crucial regulatory role in grain development. Through haplotype analysis, we identified superior haplotypes associated with increased grain yield: \u003cem\u003eTaNTP6A-Hap1\u003c/em\u003e, \u003cem\u003eTaNTP6B-Hap2\u003c/em\u003e, and \u003cem\u003eTaNTP6D-Hap5\u003c/em\u003e/\u003cem\u003e6\u003c/em\u003e. Additionally, subcellular localization analysis revealed that TaNTP4A and TaNTP1A, the orthologs of AtHESO1 and AtURT1, are detectable in both the nucleus and cytoplasm, but exhibit predominant nuclear localization.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eThese results provide pivotal insights into the NTP family in wheat. Importantly, the identification of superior \u003cem\u003eTaNTP6A/B/D\u003c/em\u003e haplotypes offers valuable genetic resources for facilitating high-yield wheat breeding programs.\u003c/p\u003e","manuscriptTitle":"Unveiling the Wheat NTP Gene Family: Insights from Genome-Wide Identification and TaNTP6 Haplotype Analysis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-22 14:40:56","doi":"10.21203/rs.3.rs-7526017/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-03T05:24:12+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-02T08:21:43+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-28T09:52:29+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"272492677516124839253747016383864238850","date":"2025-09-17T09:32:47+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"147128126232712303425214317478805753748","date":"2025-09-17T09:20:40+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-14T11:52:32+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-09-10T05:27:40+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-09T13:11:40+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-09-09T13:11:27+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2025-09-03T10:27:01+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":"31537cb0-8c41-4a6d-97bc-30f19dcd7654","owner":[],"postedDate":"September 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-24T16:08:21+00:00","versionOfRecord":{"articleIdentity":"rs-7526017","link":"https://doi.org/10.1186/s12870-025-07640-1","journal":{"identity":"bmc-plant-biology","isVorOnly":false,"title":"BMC Plant Biology"},"publishedOn":"2025-11-19 15:57:51","publishedOnDateReadable":"November 19th, 2025"},"versionCreatedAt":"2025-09-22 14:40:56","video":"","vorDoi":"10.1186/s12870-025-07640-1","vorDoiUrl":"https://doi.org/10.1186/s12870-025-07640-1","workflowStages":[]},"version":"v1","identity":"rs-7526017","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7526017","identity":"rs-7526017","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}