A Large-Scale Multi-Environment Study Dissecting Stripe Rust Resistance Haplotypes in Australian Wheat Breeding Populations

A Large-Scale Multi-Environment Study Dissecting Stripe Rust Resistance Haplotypes in Australian Wheat Breeding Populations | 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 A Large-Scale Multi-Environment Study Dissecting Stripe Rust Resistance Haplotypes in Australian Wheat Breeding Populations Natalya Vo Van-Zivkovic, Eric Dinglasan, Jingyang Tong, Calum Watt, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4665427/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 13 Mar, 2025 Read the published version in Theoretical and Applied Genetics → Version 1 posted 5 You are reading this latest preprint version Abstract Wheat stripe rust ( Puccinia striiformis ) is a fungal disease responsible for substantial yield losses globally. To maintain crop productivity in future climates, the identification of genetics offering durable resistance across diverse growing conditions is crucial. To stay one-step ahead of the pathogen, Australian wheat breeders are actively selecting for adult plant resistance (APR), which is considered more durable than seedling resistance. However, deploying resistance that is stable or effective across environments and years is challenging as expression of underling APR loci often interact with environmental conditions. To explore the underlying genetics and interactions with the environment for stripe rust resistance, we employ haplotype-based mapping using the local GEBV approach in elite wheat breeding populations. Our multi-environment trial (MET) analyses comprising 35,986 inbred lines evaluated across 10 environments revealed significant genotype by environment (GxE) interactions for stripe rust. A total of 32 haploblocks associated with stripe rust resistance were identified, where 24 were unique to a specific environment and 7 were associated with stable resistance across environments. Population structure analysis revealed commercial or advanced breeding lines carried desirable resistance haplotypes, highlighting the opportunity to continue to harness and optimise resistance haplotypes already present within elite backgrounds. Further, we demonstrate that in-silico stacking of multiple resistance haplotypes through a whole-genome approach has the potential to substantially improve resistance levels. This represents the largest study to date exploring commercial wheat breeding populations for stripe rust resistance and highlights the breeding opportunities to improve stability of resistance across and within target environments. resistance breeding genotype by environment interaction haplotype mapping multi-environment trial disease resistance Full Text Supplementary Files VoVanZivkovicetal.supplementaryfiles.docx Cite Share Download PDF Status: Published Journal Publication published 13 Mar, 2025 Read the published version in Theoretical and Applied Genetics → Version 1 posted Editorial decision: Major revisions 03 Oct, 2024 Reviewers agreed at journal 11 Aug, 2024 Reviewers invited by journal 06 Aug, 2024 Editor assigned by journal 02 Jul, 2024 First submitted to journal 30 Jun, 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-4665427","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":336519640,"identity":"93983428-5580-4412-9030-f3289966876f","order_by":0,"name":"Natalya Vo Van-Zivkovic","email":"","orcid":"","institution":"The University of Queensland - Saint Lucia Campus: The University of Queensland","correspondingAuthor":false,"prefix":"","firstName":"Natalya","middleName":"Vo","lastName":"Van-Zivkovic","suffix":""},{"id":336519641,"identity":"54f8d37b-6f3a-430a-9a0e-efef91057e85","order_by":1,"name":"Eric Dinglasan","email":"","orcid":"","institution":"The University of Queensland - 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