Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping

Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping | 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 Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping Matuszkiewicz Mateusz, Grądzielewska Agnieszka, Święcicka Magdalena, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3837331/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 9 You are reading this latest preprint version Abstract Background: Leaf rust (LR) is among the most destructive fungal diseases of rye ( Secale cereale L.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. Results : A genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye. A mapping population, G38A, was constructed by crossing two inbred lines: 723 (susceptible to LR) and JKI-NIL-Pr3 (a donor of the LR resistance gene Pr3 ). For genotyping, SNP-DArT and silico-DArT markers were used. Resistance phenotyping was conducted by visual assessment of the infection severity in detached leaf segments inoculated with two isolates of Puccinia recondita f. sp. secalis , namely, 60/17/2.1 (isolate S) in the main experiment and 86/n/2.1_5x (isolate N) in the validation experiment, at 10 and 17 days post-infection (dpi), respectively. In total, 42773 SNP-DArT and 105866 silico-DArT markers were included in the main analysis including isolate S, of which 129 and 140 SNP-DArTs and 767 and 776 silico-DArTs were significantly associated ( p ≤ 0.001; −log 10 ( p ) ≥ 3.0) with the immune response to LR at 10 and 17 dpi, respectively. Most significant markers were mapped to chromosome 1R. The number of common markers from both systems and at both time points occupying common chromosomal positions was 37, of which 21 were positioned in genes, comprising 18 markers located in exons and three in introns. This gene pool included genes encoding proteins with a known function in response to LR (e.g., a NBS-LRR disease resistance protein-like protein and carboxyl-terminal peptidase). Conclusion: This study has expanded and supplemented existing knowledge of the genetic basis of rye resistance to LR by (1) detecting two QTLs associated with the LR immune response of rye, of which one located on the long arm of chromosome 1R is newly detected, (2) assigning hundreds of markers significantly associated with the immune response to LR to genes in the ‘Lo7’ genome, and (3) predicting the potential translational effects of polymorphisms of SNP-DArT markers located within protein-coding genes. Secale cereale Genome-Wide Association Study (GWAS) immune response plant fungal pathogens DArTseq markers silicoDArT markers Full Text Additional Declarations No competing interests reported. Supplementary Files FigureS1.docx FigureS2.docx FigureS3.docx FigureS4.docx FigureS5.docx TableS1.xlsx TableS2.csv TableS3.csv TableS4.csv TableS5.csv TableS6.csv TableS7.csv TableS8.csv TableS9.csv TableS10.csv TableS11.csv TableS12.xlsx TableS13.xlsx TableS14.xlsx TableS15.xlsx TableS16.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 23 Feb, 2024 Reviews received at journal 22 Feb, 2024 Reviewers agreed at journal 11 Feb, 2024 Reviews received at journal 05 Feb, 2024 Reviewers agreed at journal 29 Jan, 2024 Reviewers invited by journal 16 Jan, 2024 Editor assigned by journal 08 Jan, 2024 Submission checks completed at journal 08 Jan, 2024 First submitted to journal 05 Jan, 2024 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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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-3837331","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":265926059,"identity":"10a7a40b-9a9e-48d1-b49d-a6b5ebcd61ec","order_by":0,"name":"Matuszkiewicz Mateusz","email":"","orcid":"","institution":"Warsaw University of Life Sciences","correspondingAuthor":false,"prefix":"","firstName":"Matuszkiewicz","middleName":"","lastName":"Mateusz","suffix":""},{"id":265926060,"identity":"3e83ba2c-da2d-413d-aa6f-df7c53795fd5","order_by":1,"name":"Grądzielewska Agnieszka","email":"","orcid":"","institution":"Educo BSH 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mapping","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":"Secale cereale, Genome-Wide Association Study (GWAS), immune response, plant fungal pathogens, DArTseq markers, silicoDArT markers","lastPublishedDoi":"10.21203/rs.3.rs-3837331/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3837331/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eLeaf rust (LR) is among the most destructive fungal diseases of rye (\u003cem\u003eSecale cereale \u003c/em\u003eL.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e:\u003c/p\u003e\n\u003cp\u003eA genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye. A mapping population, G38A, was constructed by crossing two inbred lines: 723 (susceptible to LR) and JKI-NIL-Pr3 (a donor of the LR resistance gene \u003cem\u003ePr3\u003c/em\u003e). For genotyping, SNP-DArT and silico-DArT markers were used. Resistance phenotyping was conducted by visual assessment of the infection severity in detached leaf segments inoculated with two isolates of \u003cem\u003ePuccinia recondita\u003c/em\u003e f. sp. \u003cem\u003esecalis\u003c/em\u003e, namely, 60/17/2.1 (isolate S) in the main experiment and 86/n/2.1_5x (isolate N) in the validation experiment, at 10 and 17 days post-infection (dpi), respectively.\u003c/p\u003e\n\u003cp\u003eIn total, 42773 SNP-DArT and 105866 silico-DArT markers were included in the main analysis including isolate S, of which 129 and 140 SNP-DArTs and 767 and 776 silico-DArTs were significantly associated (\u003cem\u003ep \u003c/em\u003e≤ 0.001; −log\u003csub\u003e10\u003c/sub\u003e(\u003cem\u003ep\u003c/em\u003e) ≥ 3.0) with the immune response to LR at 10 and 17 dpi, respectively. Most significant markers were mapped to chromosome 1R. The number of common markers from both systems and at both time points occupying common chromosomal positions was 37, of which 21 were positioned in genes, comprising 18 markers located in exons and three in introns. This gene pool included genes encoding proteins with a known function in response to LR (e.g., a NBS-LRR disease resistance protein-like protein and carboxyl-terminal peptidase).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study has expanded and supplemented existing knowledge of the genetic basis of rye resistance to LR by (1) detecting two QTLs associated with the LR immune response of rye, of which one located on the long arm of chromosome 1R is newly detected, (2) assigning hundreds of markers significantly associated with the immune response to LR to genes in the ‘Lo7’ genome, and (3) predicting the potential translational effects of polymorphisms of SNP-DArT markers located within protein-coding genes.\u003c/p\u003e","manuscriptTitle":"Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-10 07:47:19","doi":"10.21203/rs.3.rs-3837331/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-02-23T06:43:38+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-02-22T15:37:50+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"51c23341-9eaf-4f06-b609-646742a2d6df","date":"2024-02-12T03:23:19+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-02-05T13:36:03+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"ce1a744a-333e-42a2-9f8a-4e7210e63df2","date":"2024-01-29T06:43:12+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-01-17T01:20:45+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-01-08T16:10:46+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-01-08T16:09:44+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2024-01-05T13:01:05+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":"e9e186e2-b311-4d92-b173-b0f90e8c7c0d","owner":[],"postedDate":"January 10th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2024-03-29T07:12:19+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-10 07:47:19","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3837331","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3837331","identity":"rs-3837331","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}