Structural haplotypes act as supergene-like additive units that mitigate the genomic prediction cliff in mango

Structural haplotypes act as supergene-like additive units that mitigate the genomic prediction cliff in mango | 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 Structural haplotypes act as supergene-like additive units that mitigate the genomic prediction cliff in mango Mirza Shoaib, Asjad Ali, Bernardo Blanco-Martin, Surya Kant, Matthew J. Hayden This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8961141/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 7 You are reading this latest preprint version Abstract Genomic selection promises to accelerate breeding in perennial crops, yet predictive accuracy often collapses when models cross ancestry boundaries—the “structure cliff.” Whether this collapse is trait-uniform or architecture-dependent remains unresolved. Here, we dissect this question in mango ( Mangifera indica L.), a genetically stratified tree crop, using a 225-accession diversity panel spanning three ancestry groups and 17 previously mapped chromosomal inversions. We show that cross-ancestry portability is governed by concentration of predictive signal in structural haplotypes. Traits anchored by megabase-scale inversions acting as supergene-like, predominantly additive units—shifting blush colour by + 1.12 SD and fruit weight by − 1.10 SD—retain partial predictive signal under leave-cluster-out transfer (r = 0.153–0.192). Conversely, traits with diffuse polygenic architectures collapse to near-zero or negative accuracy. Strikingly, a 17-marker inversion panel recovers 86% of dense-SNP accuracy for blush colour and more than doubles the accuracy of matched random panels under structure-aware validation. Saliency mapping, SHAP attribution, and in silico virtual editing converge on a predominantly additive mechanism, with negligible epistasis within structural blocks (synergy < 0.1% of block effects). We formalise these patterns in a Precision Breeding Hierarchy that ranks traits by transferability and structural concentration and maps each tier to deployment: global KASP assays for portable traits, and locally recalibrated models for ancestry-bound traits. This converts public genomic resources into breeder-ready tools and offers a template for other structured perennial crops, underscoring that portability is an inherent property of trait architecture. Genomic prediction Cross-population portability Structural haplotypes Chromosomal inversions Mango (Mangifera indica) Perennial crop genomics recision breeding hierarchy Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 05 Apr, 2026 Reviewers agreed at journal 26 Mar, 2026 Reviewers agreed at journal 25 Mar, 2026 Reviewers invited by journal 12 Mar, 2026 Editor assigned by journal 02 Mar, 2026 Submission checks completed at journal 25 Feb, 2026 First submitted to journal 24 Feb, 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. 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-8961141","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":605303647,"identity":"0016b120-1bb6-43fc-96b1-230db953a56b","order_by":0,"name":"Mirza Shoaib","email":"data:image/png;base64,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","orcid":"","institution":"Agriculture Victoria","correspondingAuthor":true,"prefix":"","firstName":"Mirza","middleName":"","lastName":"Shoaib","suffix":""},{"id":605303648,"identity":"f1fca7be-ad6c-4c8e-8b09-8d0f36e3f720","order_by":1,"name":"Asjad Ali","email":"","orcid":"","institution":"Queensland Department of Primary Industries","correspondingAuthor":false,"prefix":"","firstName":"Asjad","middleName":"","lastName":"Ali","suffix":""},{"id":605303651,"identity":"0bbf3dad-2a6d-4f6c-91b2-b2dbe8d4d36e","order_by":2,"name":"Bernardo Blanco-Martin","email":"","orcid":"","institution":"Queensland Department of Primary Industries","correspondingAuthor":false,"prefix":"","firstName":"Bernardo","middleName":"","lastName":"Blanco-Martin","suffix":""},{"id":605303654,"identity":"308b234a-f313-4a9e-a3b8-51e28b47bcb2","order_by":3,"name":"Surya Kant","email":"","orcid":"","institution":"La Trobe University","correspondingAuthor":false,"prefix":"","firstName":"Surya","middleName":"","lastName":"Kant","suffix":""},{"id":605303656,"identity":"c3a3e59e-a10a-4fc1-b330-6aea03743633","order_by":4,"name":"Matthew J. 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Here, we dissect this question in mango (\u003cem\u003eMangifera indica\u003c/em\u003e L.), a genetically stratified tree crop, using a 225-accession diversity panel spanning three ancestry groups and 17 previously mapped chromosomal inversions.\u003c/p\u003e \u003cp\u003eWe show that cross-ancestry portability is governed by concentration of predictive signal in structural haplotypes. Traits anchored by megabase-scale inversions acting as supergene-like, predominantly additive units\u0026mdash;shifting blush colour by +\u0026thinsp;1.12 SD and fruit weight by \u0026minus;\u0026thinsp;1.10 SD\u0026mdash;retain partial predictive signal under leave-cluster-out transfer (r\u0026thinsp;=\u0026thinsp;0.153\u0026ndash;0.192). Conversely, traits with diffuse polygenic architectures collapse to near-zero or negative accuracy. 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