Haplotype-resolved genome assembly and resequencing provide insights into the origin and domestication of modern rose

Haplotype-resolved genome assembly and resequencing provide insights into the origin and domestication of modern rose | 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 Haplotype-resolved genome assembly and resequencing provide insights into the origin and domestication of modern rose Junping Gao, Zhao Zhang, Tuo Yang, Yang Liu, Shan Wu, Honghe Sun, and 23 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4727628/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 11 Oct, 2024 Read the published version in Nature Plants → Version 1 posted You are reading this latest preprint version Abstract Modern rose ( Rosa hybrida ) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here, we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida ‘Samantha®’ (‘JACmantha’) and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of ‘Samantha®’ exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis ‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence, and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history and offers unprecedented genomic resources for rose improvement. Biological sciences/Genetics/Genomics Biological sciences/Plant sciences/Plant domestication Biological sciences/Genetics/Plant genetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files RoseSuppNoteFigureR1.pdf Cite Share Download PDF Status: Published Journal Publication published 11 Oct, 2024 Read the published version in Nature Plants → Version 1 posted 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-4727628","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":326872865,"identity":"5fd6809f-431d-416f-b30e-f2d096f31918","order_by":0,"name":"Junping 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Here, we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid \u003ci\u003eR. hybrida\u003c/i\u003e ‘Samantha®’ (‘JACmantha’) and a genome variation map of 233 \u003ci\u003eRosa\u003c/i\u003e accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of ‘Samantha®’ exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild \u003ci\u003eRosa\u003c/i\u003e species to modern roses and highlight that \u003ci\u003eR. odorata\u003c/i\u003e and its derived cultivars are important contributors to modern roses, much like \u003ci\u003eR. chinensis\u003c/i\u003e ‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence, and disease resistance, are identified. 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