Bridging the genetic and genotypic gain gap for Eucalyptus: the critical role of inbreeding and dominance effects in breeding strategies

Bridging the genetic and genotypic gain gap for Eucalyptus: the critical role of inbreeding and dominance effects in breeding strategies | 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 Article Bridging the genetic and genotypic gain gap for Eucalyptus: the critical role of inbreeding and dominance effects in breeding strategies Marcio Araujo, David Bush, Evandro Tambarussi This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4712132/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Aug, 2025 Read the published version in Heredity → Version 1 posted 8 You are reading this latest preprint version Abstract Understanding the mating system of Eucalyptus species is necessary to accurately estimate genetic parameters and improve breeding programs. Eucalyptus species often exhibit mixed mating systems, leading to complex relationships among progenies. Traditional tree breeding programs that assume a half-sibling relationship for open-pollinated (OP) trials may overestimate genetic gains by neglecting the effects of inbreeding and dominance. This study focuses on Eucalyptus pellita, a species with a mixed mating system, to quantify the impact of selfing and dominance on breeding strategies. We simulated OP trial growth data for 100 randomly selected families in a randomized complete block design, using published data for diameter at breast height (DBH). Our analysis indicated that marker-based models, particularly those incorporating dominance effects, provide more accurate genetic parameter estimates and higher predicted genetic gains than pedigree-based models. Furthermore, we identified significant genetic and genotypic gain gaps when traditional models were used, underscoring the need to consider non-additive genetic effects in breeding programs. These findings highlight the importance of using marker-based approaches to enhance genetic improvement and achieve sustainable forestry. Biological sciences/Genetics/Plant breeding Biological sciences/Genetics/Plant genetics Full Text Additional Declarations There is no duality of interest Cite Share Download PDF Status: Published Journal Publication published 21 Aug, 2025 Read the published version in Heredity → Version 1 posted Editorial decision: revise 30 Sep, 2024 Review # 1 received at journal 16 Sep, 2024 Review # 2 received at journal 01 Sep, 2024 Reviewer # 2 agreed at journal 01 Sep, 2024 Reviewer # 1 agreed at journal 30 Aug, 2024 Reviewers invited by journal 25 Jul, 2024 Editor assigned by journal 09 Jul, 2024 First submitted to journal 09 Jul, 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. 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-4712132","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":331715005,"identity":"d7ae23dc-d538-44c5-ac56-e2a391eef5d5","order_by":0,"name":"Marcio Araujo","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5UlEQVRIiWNgGAWjYLCCBCCWYG8++BjMY2ZuIFILz7FkYwYGA6AWRiK0gICEhI+aNFgLAwEtuu1nH354UMEgJzmDh626oOJPNH87UMuPim04tZidSTeWSDjDYCwt3Xvs9owzBrkzDjM2MPacuY1by4E0NobENobEeTLn0m7zthnkNgC1MDO24dFy/hlUi0SOWTFIy3yCWm5AbZkN1MIM0rKBsJZnzGC/SPYcS5bmOWOcuxGo5SBev5xPY/z4AxhiEsebD37mqZDLnXf+8MEHPypwa4GC/6jcA4TUj4JRMApGwSjADwBvklXHDxFCkQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0001-7218-3879","institution":"Abacusbio","correspondingAuthor":true,"prefix":"","firstName":"Marcio","middleName":"","lastName":"Araujo","suffix":""},{"id":331715006,"identity":"945bd61d-d6f1-4032-8144-8727b02c7fb0","order_by":1,"name":"David Bush","email":"","orcid":"","institution":"CSIRO","correspondingAuthor":false,"prefix":"","firstName":"David","middleName":"","lastName":"Bush","suffix":""},{"id":331715007,"identity":"ae2f3218-d3ce-4c76-b595-e62289a4bb39","order_by":2,"name":"Evandro Tambarussi","email":"","orcid":"https://orcid.org/0000-0001-9478-5379","institution":"Faculdade de Ciências Agronômicas, Universidade Estadual Paulista","correspondingAuthor":false,"prefix":"","firstName":"Evandro","middleName":"","lastName":"Tambarussi","suffix":""}],"badges":[],"createdAt":"2024-07-09 12:41:06","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4712132/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4712132/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41437-025-00792-8","type":"published","date":"2025-08-21T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":89634479,"identity":"9590b518-fe06-464f-9228-2ab24822ed57","added_by":"auto","created_at":"2025-08-22 07:06:50","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2111154,"visible":true,"origin":"","legend":"","description":"","filename":"DraftSelfingOP2024ERN.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4712132/v1_covered_a9f271bf-f768-4aaa-bb70-b10ae80db44b.pdf"}],"financialInterests":"There is no duality of interest","formattedTitle":"Bridging the genetic and genotypic gain gap for Eucalyptus: the critical role of inbreeding and dominance effects in breeding strategies","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":"heredity","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"hdy","sideBox":"Learn more about [Heredity](http://www.nature.com/hdy/)","snPcode":"41437","submissionUrl":"https://mts-hdy.nature.com/cgi-bin/main.plex","title":"Heredity","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-4712132/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4712132/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Understanding the mating system of Eucalyptus species is necessary to accurately estimate genetic parameters and improve breeding programs. 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