Simplified 3D genome and gap-less CC group Oryza genome reveal genetic dynamics of rice triploid lines from distant hybridization

Simplified 3D genome and gap-less CC group Oryza genome reveal genetic dynamics of rice triploid lines from distant hybridization | 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 Simplified 3D genome and gap-less CC group Oryza genome reveal genetic dynamics of rice triploid lines from distant hybridization Hui Guo, Fangping LI, Jiaxuan Chen, Can Chen, jieying Liu, Haifei Hu, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6200142/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Intergeneric hybridization and domestication breeding is an efficient means for utilizing wild rice germplasm resources. In this study, we constructed gap-less genome assemblies for two CC, two BBCC and one CCDD wild rices to explore the role of the C subgenome in rice diversification. Furthermore, we assembled the genome of a cultivated rice (AA) and further developed A/C hybrids with enhanced resistance to BPH using an efficient hybrid embryo rescue system. To facilitate the tracking of chromosomes in backcross and selfed progeny of these hybrids, we developed a streamlined 3D genome method, enabling an ultra-rapid and low-cost Hi-C library construction process (sHi-C). By integrating these resources with whole-genome resequencing and genome assembly, we effectively tracked chromosomal dynamics in A/C hybrids and their progeny with cultivated rice. For the first time, we characterized the gamete segregation features and preferences in the progeny of distant hybrid lines and redrew the subgenome dynamics. We revealed that the progeny of A/C hybrids tend to exist predominantly as multiple types of euploid triploids, but also exhibit coexistence of triploids and diploids. Furthermore, we identified chromosomal exchanges between A and C subgenomes in selfed progeny, which may key for fertile offspring development. Preliminary gene identification also highlighted the activity of the C subgenome in progeny and its contribution to insect resistance. Our findings provide a robust framework for harnessing beneficial alleles from CC wild rice through distant hybrid breeding and open new opportunities for rice improvement. Biological sciences/Plant sciences/Plant genetics/Plant hybridization Biological sciences/Plant sciences/Plant biotechnology Biological sciences/Plant sciences/Plant genetics/Polyploidy in plants Full Text Additional Declarations There is NO Competing Interest. Supplementary Files 250310SPFDecodingWildRiceOryzaofficinalis.docx 250310SPTDecodingWildRiceOryzaofficinalis.docx.xlsx Cite Share Download PDF Status: Under Review 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-6200142","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":428913736,"identity":"c7966358-8a37-4a33-9a18-34c1a9998aa0","order_by":0,"name":"Hui 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