Composite interval mapping for potato common scab in connected F1 populations

Composite interval mapping for potato common scab in connected F1 populations | 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 Composite interval mapping for potato common scab in connected F1 populations Fatima Latif Azam, Jeffrey B. Endelman, Dan Milbourne, Denis Griffin, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9173453/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 6 You are reading this latest preprint version Abstract Potato varieties with resistance to Common Scab (CS) are highly valued across different potato market segments, to avoid the economic losses up to 30-50% in severely affected fields. Phenotypic testing for CS resistance is challenging and often unreliable. Although many quantitative trait loci (QTL) mapping studies have been conducted, none have identified major-effect loci associated with scab resistance. In this study, we collected marker data with an amplicon sequencing method PotatoMASH to perform composite interval mapping in connected F1 populations to study the inheritance of scab resistance and to identify relevant-effect loci. We obtained heritability estimates between 0.47-0.74 for scab resistance across four environments. We identified multiple QTLs with additive and dominance effects, with each QTL explaining around 8.6% of the variance on average. The multi-QTL model retained 5 loci that collectively explained 31% of the variation. No QTL allele showed a statistically significant additive effect when both additive and dominance effects were fitted in the model. We observed that several QTL alleles inherited from the resistant parent Picasso had a positive effect in its resistant offspring Electra, despite exhibiting no detectable effect in Picasso. Genomic prediction (GP) showed no significant differences between the mean prediction accuracy for full-sibs compared to half-sibs, likely because the unshared parents were close relatives. Altogether, these findings demonstrate the complexity of scab resistance and suggest that marker-assisted selection alone is unlikely to be effective. However, GP has demonstrated potential to improve selection for this trait and should be considered in future breeding efforts. Common Scab Streptomyces spp. potato Solanum tuberosum quantitative trait loci composite interval mapping Full Text Additional Declarations Competing interest reported. The authors are not aware of any relevant interests that could affect the contents of this article. Jeff Endelman and Herman van Eck are members of the Editorial Board of the journal Theoretical and Applied Genetics. Supplementary Files FigureS1.png FigureS2.png FigureS3.1.png FigureS3.2.png FigureS7.pdf FigureS4.png FigureS6.png FigureS5.png FigureS10.png FigureS8.png FigureS9.png FigureS12.png FigureS11.png FileS2.csv FileS1.csv FileS6.csv FileS5.csv FileS3.csv FileS7.csv FileS4.csv FileS8diaQTLpedfile.csv FileS9.csv FileS10.csv FileS8diaQTLgenofile.csv FileS12.pdf FileS14.pdf FileS11.SupplementalTablesandFigures.docx FileS13.pdf Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 22 Apr, 2026 Reviewers agreed at journal 15 Apr, 2026 Reviewers invited by journal 13 Apr, 2026 Editor assigned by journal 01 Apr, 2026 Submission checks completed at journal 20 Mar, 2026 First submitted to journal 19 Mar, 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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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-9173453","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":623593241,"identity":"f559b666-5655-4972-8dcd-16340ce37e5e","order_by":0,"name":"Fatima Latif Azam","email":"","orcid":"","institution":"Teagasc","correspondingAuthor":false,"prefix":"","firstName":"Fatima","middleName":"Latif","lastName":"Azam","suffix":""},{"id":623593242,"identity":"34853346-e52e-4de9-b485-df281eed4909","order_by":1,"name":"Jeffrey B. 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The authors are not aware of any relevant interests that could affect the contents of this article. Jeff Endelman and Herman van Eck are members of the Editorial Board of the journal Theoretical and Applied Genetics.","formattedTitle":"Composite interval mapping for potato common scab in connected F1 populations","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"theoretical-and-applied-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"taag","sideBox":"Learn more about [Theoretical and Applied Genetics](https://www.springer.com/journal/122)","snPcode":"122","submissionUrl":"https://submission.nature.com/new-submission/122/3","title":"Theoretical and Applied Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Common Scab, Streptomyces spp., potato, Solanum tuberosum, quantitative trait loci, composite interval mapping","lastPublishedDoi":"10.21203/rs.3.rs-9173453/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9173453/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Potato varieties with resistance to Common Scab (CS) are highly valued across different potato market segments, to avoid the economic losses up to 30-50% in severely affected fields. Phenotypic testing for CS resistance is challenging and often unreliable. Although many quantitative trait loci (QTL) mapping studies have been conducted, none have identified major-effect loci associated with scab resistance. In this study, we collected marker data with an amplicon sequencing method PotatoMASH to perform composite interval mapping in connected F1 populations to study the inheritance of scab resistance and to identify relevant-effect loci. We obtained heritability estimates between 0.47-0.74 for scab resistance across four environments. We identified multiple QTLs with additive and dominance effects, with each QTL explaining around 8.6% of the variance on average. The multi-QTL model retained 5 loci that collectively explained 31% of the variation. No QTL allele showed a statistically significant additive effect when both additive and dominance effects were fitted in the model. We observed that several QTL alleles inherited from the resistant parent Picasso had a positive effect in its resistant offspring Electra, despite exhibiting no detectable effect in Picasso. Genomic prediction (GP) showed no significant differences between the mean prediction accuracy for full-sibs compared to half-sibs, likely because the unshared parents were close relatives. Altogether, these findings demonstrate the complexity of scab resistance and suggest that marker-assisted selection alone is unlikely to be effective. However, GP has demonstrated potential to improve selection for this trait and should be considered in future breeding efforts.","manuscriptTitle":"Composite interval mapping for potato common scab in connected F1 populations","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-04-20 22:24:45","doi":"10.21203/rs.3.rs-9173453/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2026-04-22T21:57:08+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"177502414317552595568709597741037081390","date":"2026-04-15T11:27:31+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-04-13T08:57:40+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-04-01T14:02:18+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-21T02:24:56+00:00","index":"","fulltext":""},{"type":"submitted","content":"Theoretical and Applied Genetics","date":"2026-03-20T00:15:25+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"theoretical-and-applied-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"taag","sideBox":"Learn more about [Theoretical and Applied Genetics](https://www.springer.com/journal/122)","snPcode":"122","submissionUrl":"https://submission.nature.com/new-submission/122/3","title":"Theoretical and Applied Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"467b24a4-9bf6-49b5-9396-2217535b76b8","owner":[],"postedDate":"April 20th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-04-20T22:24:45+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-20 22:24:45","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9173453","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9173453","identity":"rs-9173453","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}