Faba bean populations already contain the inbreds needed for breeding

Faba bean populations already contain the inbreds needed for breeding | 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 Faba bean populations already contain the inbreds needed for breeding Henri Laugel, Wolfgang Link This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8211981/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 5 You are reading this latest preprint version Abstract Producing inbred lines in faba bean ( Vicia faba L.) breeding is, although crucial, a long, costly and laborious process due to the partial allogamy of the crop. However, in any genetically diverse and open pollinating faba bean population, this particular reproduction system leads to the so-called Identity Disequilibrium, resulting in a significant proportion of individuals being highly inbred. This study presents a cost-efficient approach to identify these highly inbred individuals from populations with a limited number of KASP markers. We found that 8.4% of individuals of the “Göttingen Winter Bean Population” were highly inbred. Using simulations, the most accurate inbreeding coefficient estimator from limited number of markers (ten to 100) was found to be the so-called estimator F L (which is based on a maximum likelihood approach). Our results allowed to explore the appropriate inbreeding coefficient value to be used as threshold to classify individuals as highly inbred, which optimizes the performance of our approach. Using 50 markers and taking 0.9 as inbreeding classification threshold, we identified 36 truly highly inbred individuals, along with six not-enough-inbred individuals (false positives) in our population. Using a low number of markers in a preliminary step to eliminate not-enough-inbred individuals, successfully permitted a significant and marked reduction of genotyping cost (up to 46%). Faba bean breeders can greatly benefit from the presented approach by identifying highly inbred individuals fast, at low cost and with limited labor, even though no DH technology is available. breeding method inbreeding coefficient partial allogamy likelihood estimator molecular markers single plant selection Full Text Supplementary Files SupplementaryMaterial1.docx SupplementaryMaterial2.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Major revisions 14 Jan, 2026 Reviewers agreed at journal 10 Dec, 2025 Reviewers invited by journal 10 Dec, 2025 Editor assigned by journal 26 Nov, 2025 First submitted to journal 26 Nov, 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. 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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-8211981","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":558314498,"identity":"6187f969-b3ec-4879-8f37-47e994bc8b66","order_by":0,"name":"Henri 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However, in any genetically diverse and open pollinating faba bean population, this particular reproduction system leads to the so-called Identity Disequilibrium, resulting in a significant proportion of individuals being highly inbred. This study presents a cost-efficient approach to identify these highly inbred individuals from populations with a limited number of KASP markers.\u003c/p\u003e\n\u003cp\u003eWe found that 8.4% of individuals of the “Göttingen Winter Bean Population” were highly inbred. Using simulations, the most accurate inbreeding coefficient estimator from limited number of markers (ten to 100) was found to be the so-called estimator F\u003csub\u003eL\u003c/sub\u003e (which is based on a maximum likelihood approach). Our results allowed to explore the appropriate inbreeding coefficient value to be used as threshold to classify individuals as highly inbred, which optimizes the performance of our approach. Using 50 markers and taking 0.9 as inbreeding classification threshold, we identified 36 truly highly inbred individuals, along with six not-enough-inbred individuals (false positives) in our population. Using a low number of markers in a preliminary step to eliminate not-enough-inbred individuals, successfully permitted a significant and marked reduction of genotyping cost (up to 46%).\u003c/p\u003e\n\u003cp\u003eFaba bean breeders can greatly benefit from the presented approach by identifying highly inbred individuals fast, at low cost and with limited labor, even though no DH technology is available.\u003c/p\u003e","manuscriptTitle":"Faba bean populations already contain the inbreds needed for breeding","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-15 10:29:08","doi":"10.21203/rs.3.rs-8211981/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major revisions","date":"2026-01-14T07:48:42+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2025-12-10T15:23:40+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-12-10T14:53:21+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-26T15:28:38+00:00","index":"","fulltext":""},{"type":"submitted","content":"Theoretical and Applied Genetics","date":"2025-11-26T05:46:37+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":"766a6180-d31d-454c-9d8b-0fbb89c591ce","owner":[],"postedDate":"December 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-04-29T18:16:27+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-15 10:29:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8211981","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8211981","identity":"rs-8211981","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}