Optimizing expected cross value for genetic introgression

Optimizing expected cross value for genetic introgression | 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 Optimizing expected cross value for genetic introgression Charles Chen, Pouya Ahadi, Balabhaskar Balasundaram, Juan Borrero This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3932291/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Jul, 2024 Read the published version in Heredity → Version 1 posted 8 You are reading this latest preprint version Abstract In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross, in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of target traits and evaluates the combination of the genomic information of the pair of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for a gamete produced by two individuals of the population selected as parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected parents. We extend the approach in two directions: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve the efficiency of genetic introgression while maintaining genetic diversity in a breeding program. Biological sciences/Biological techniques/Bioinformatics Biological sciences/Genetics/Agricultural genetics Full Text Additional Declarations There is no duality of interest Supplementary Files HeredityECVSupplementary.pdf ECV Supplementary Material Cite Share Download PDF Status: Published Journal Publication published 02 Jul, 2024 Read the published version in Heredity → Version 1 posted Editorial decision: revise 13 Mar, 2024 Review # 2 received at journal 08 Mar, 2024 Review # 1 received at journal 22 Feb, 2024 Reviewer # 2 agreed at journal 19 Feb, 2024 Reviewer # 1 agreed at journal 09 Feb, 2024 Reviewers invited by journal 08 Feb, 2024 First submitted to journal 05 Feb, 2024 Editor assigned by journal 05 Feb, 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-3932291","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":271812068,"identity":"d5cdad28-1f7d-4b5a-b8c4-335996852834","order_by":0,"name":"Charles Chen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA/ElEQVRIiWNgGAWjYDACCSB+AGN8YEiAiTPj15IAZTDOADJ5IKqJ1MLMQ4wW/tnNzz4kVNSBGMce21Sk2duznz/4gKHCOrEBlyV3jhnPSDhzGMRIN845k5PYw5PMbMBwJh2nFgOJBGOGxLYDQEaOmXRuW0UCD0MymwRj22E8WtI/MyT+qwMy8r9JW7ZV2PPwP2b/wfgPn5YcoC0NzCAGmzRjWw5jj0QyGwNjA24tEjdyihkSjh3mkbiRZibZcyYtsefGY2OJBKDHcGnhn5G+meFDTZ0c/4zkZxI/KpLt2fsTH374UGMti0sLDPCgchMIKB8Fo2AUjIJRgB8AAHqkUdNdBKqsAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-2203-0433","institution":"Oklahoma State University","correspondingAuthor":true,"prefix":"","firstName":"Charles","middleName":"","lastName":"Chen","suffix":""},{"id":271812069,"identity":"fa78b161-37d8-4e9c-8170-9481a349bfb8","order_by":1,"name":"Pouya Ahadi","email":"","orcid":"","institution":"Georgia Institute of Technology","correspondingAuthor":false,"prefix":"","firstName":"Pouya","middleName":"","lastName":"Ahadi","suffix":""},{"id":271812070,"identity":"1ba50c3c-61ee-4b9c-8b2a-21a88c04a2d3","order_by":2,"name":"Balabhaskar Balasundaram","email":"","orcid":"","institution":"Oklahoma State University","correspondingAuthor":false,"prefix":"","firstName":"Balabhaskar","middleName":"","lastName":"Balasundaram","suffix":""},{"id":271812071,"identity":"ff5d4b51-20f7-4b13-b66f-78347ec4fb38","order_by":3,"name":"Juan Borrero","email":"","orcid":"","institution":"Oklahoma State University","correspondingAuthor":false,"prefix":"","firstName":"Juan","middleName":"","lastName":"Borrero","suffix":""}],"badges":[],"createdAt":"2024-02-06 01:10:19","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3932291/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3932291/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41437-024-00697-y","type":"published","date":"2024-07-02T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":59554891,"identity":"6e68a6a5-46f3-49d0-aa21-a95bc9a00dc1","added_by":"auto","created_at":"2024-07-03 07:10:10","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":356905,"visible":true,"origin":"","legend":"Article File","description":"","filename":"HeredityECV.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3932291/v1_covered_07655b00-4328-4558-a9fa-a74040d22607.pdf"},{"id":50982458,"identity":"027a6f00-42d7-49d0-a4b8-1c269c6aafbd","added_by":"auto","created_at":"2024-02-12 06:22:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":255122,"visible":true,"origin":"","legend":"ECV Supplementary Material","description":"","filename":"HeredityECVSupplementary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3932291/v1/84bd464edc2176b46acca93a.pdf"}],"financialInterests":"There is no duality of interest","formattedTitle":"Optimizing expected cross value for genetic introgression","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-3932291/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3932291/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. 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