Realised genetic gain and predictive ability across breeding cycles for cooking time in common bean based on multivariate genomic selection

Realised genetic gain and predictive ability across breeding cycles for cooking time in common bean based on multivariate genomic selection | 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 Realised genetic gain and predictive ability across breeding cycles for cooking time in common bean based on multivariate genomic selection Renu Saradadevi, Winnyfred Amongi, Clare Mukankusi, Allan Male, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8256298/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 13 You are reading this latest preprint version Abstract Common beans ( Phaseolus vulgaris L.) are a major source of protein and energy in sub-Saharan Africa, but their long cooking time (CKT) imposes social, economic, environmental and health burdens. This study aimed to accelerate genetic gain for shorter CKT while maintaining or improving other seed traits such as seed iron (Fe) and zinc (Zn) content, water absorption capacity (WAC) and 100-seed weight (SW100) across rapid cycles of early-generation genomic selection. Two related founder populations were selected from the African bean panel and intercrossed in 2020 (population A) and 2021 (population B), followed by rapid two-year cycles of augmented S 0 -derived family selection. Best linear unbiased predictions (BLUPs) of breeding values were obtained from pedigree, genomic and single-step (combined pedigree and genomic) multivariate linear mixed model analysis across two cycles. Shorter CKT was correlated with higher WAC but lower Fe and Zn. Realised genetic gain from cycle 1 to cycle 2 was high for CKT (average -8.0 min y -1 ) and WAC (average +7.7% y -1 ), but was accompanied by small decreases in Fe, Zn and SW100. Genomic and single-step models resulted in high accuracy of BLUPs and moderate predictive ability across breeding cycles. The predicted genomic BLUPs for CKT in cycle 2B S 0 seedlings were strongly correlated by rank with their realised genomic BLUPs in S 0 -derived self bulks one year later, especially in a leave-one-trait-out approach in single-step multivariate genomic analysis. Indirect selection in S 0 progeny plants based on correlated and easy-to-measure traits may increase the rate of genetic gain in all traits. Phaseolus vulgaris self-pollinating crop pedigree selection genomic selection single-step genomic selection cooking time biofortification optimal contributions selection desired gains index S0-derived family selection Full Text Additional Declarations No competing interests reported. Supplementary Files 20251202OnlineResourcessubmit.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 17 Mar, 2026 Reviews received at journal 26 Feb, 2026 Reviews received at journal 19 Feb, 2026 Reviewers agreed at journal 10 Feb, 2026 Reviewers agreed at journal 08 Feb, 2026 Reviewers agreed at journal 04 Feb, 2026 Reviews received at journal 04 Feb, 2026 Reviewers agreed at journal 15 Jan, 2026 Reviewers agreed at journal 19 Dec, 2025 Reviewers invited by journal 15 Dec, 2025 Editor assigned by journal 08 Dec, 2025 Submission checks completed at journal 03 Dec, 2025 First submitted to journal 02 Dec, 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. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-8256298","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":561855059,"identity":"c9405412-601d-435e-8776-ac7a7d1019cd","order_by":0,"name":"Renu Saradadevi","email":"","orcid":"","institution":"The University of Western Australia, The UWA Institute of Agriculture","correspondingAuthor":false,"prefix":"","firstName":"Renu","middleName":"","lastName":"Saradadevi","suffix":""},{"id":561855060,"identity":"b54d3af8-f717-483a-b24e-d111f3d35b6a","order_by":1,"name":"Winnyfred Amongi","email":"","orcid":"","institution":"Alliance of 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selection","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":"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":"Phaseolus vulgaris, self-pollinating crop, pedigree selection, genomic selection, single-step genomic selection, cooking time, biofortification, optimal contributions selection, desired gains index, S0-derived family selection","lastPublishedDoi":"10.21203/rs.3.rs-8256298/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8256298/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eCommon beans (\u003cem\u003ePhaseolus vulgaris\u003c/em\u003e L.) are a major source of protein and energy in sub-Saharan Africa, but their long cooking time (CKT) imposes social, economic, environmental and health burdens. This study aimed to accelerate genetic gain for shorter CKT while maintaining or improving other seed traits such as seed iron (Fe) and zinc (Zn) content, water absorption capacity (WAC) and 100-seed weight (SW100) across rapid cycles of early-generation genomic selection. Two related founder populations were selected from the African bean panel and intercrossed in 2020 (population A) and 2021 (population B), followed by rapid two-year cycles of augmented S\u003csub\u003e0\u003c/sub\u003e-derived family selection. Best linear unbiased predictions (BLUPs) of breeding values were obtained from pedigree, genomic and single-step (combined pedigree and genomic) multivariate linear mixed model analysis across two cycles. Shorter CKT was correlated with higher WAC but lower Fe and Zn. Realised genetic gain from cycle 1 to cycle 2 was high for CKT (average -8.0 min y\u003csup\u003e-1\u003c/sup\u003e) and WAC (average +7.7% y\u003csup\u003e-1\u003c/sup\u003e), but was accompanied by small decreases in Fe, Zn and SW100. Genomic and single-step models resulted in high accuracy of BLUPs and moderate predictive ability across breeding cycles. The predicted genomic BLUPs for CKT in cycle 2B S\u003csub\u003e0\u003c/sub\u003e seedlings were strongly correlated by rank with their realised genomic BLUPs in S\u003csub\u003e0\u003c/sub\u003e-derived self bulks one year later, especially in a leave-one-trait-out approach in single-step multivariate genomic analysis. Indirect selection in S\u003csub\u003e0\u003c/sub\u003e progeny plants based on correlated and easy-to-measure traits may increase the rate of genetic gain in all traits.\u003c/p\u003e","manuscriptTitle":"Realised genetic gain and predictive ability across breeding cycles for cooking time in common bean based on multivariate genomic selection","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-18 14:55:13","doi":"10.21203/rs.3.rs-8256298/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-03-17T15:00:48+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-26T05:00:38+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-19T22:42:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"88659154988018372580121851382673219899","date":"2026-02-10T07:45:50+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"313553934612264160248327342843178870373","date":"2026-02-09T03:29:25+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"309701518206200012062897009045951764461","date":"2026-02-05T01:09:17+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-04T18:13:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"29931983059085380667254284038410033100","date":"2026-01-15T19:37:12+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"250770736257854167742695268100769313378","date":"2025-12-19T18:17:38+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-12-15T11:03:15+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-12-08T23:20:24+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-12-03T10:46:32+00:00","index":"","fulltext":""},{"type":"submitted","content":"Theoretical and Applied Genetics","date":"2025-12-02T05:39:00+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":"3558c902-3e52-4131-9cc9-6ebf67054198","owner":[],"postedDate":"December 18th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-07T08:13:12+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-18 14:55:13","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8256298","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8256298","identity":"rs-8256298","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}