Graph-based Pangenome Analysis Reveals the Genetic Control of Root Development in Cynanchum Species

Graph-based Pangenome Analysis Reveals the Genetic Control of Root Development in Cynanchum Species | 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 Graph-based Pangenome Analysis Reveals the Genetic Control of Root Development in Cynanchum Species Tae-Jin Yang, Sae Hyun Lee, Insu Lim, Min Jeong Kang, Hyeji Lee, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7014984/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 The roots of three Cynanchum species—Cynanchum wilfordii (CW), C. auriculatum (CA), and C. rostellatum (CR)—are widely used for medicinal purposes in Northeast Asia. Unlike CW and CA, CR lacks storage roots and features long, slender roots. To explore these species' genomes and support breeding efforts, we assembled nearly complete pseudo-haploid reference genomes with centromere and telomere repeats for all three, along with 28 haplotype-resolved genomes from nine CW, three CA, and two CR accessions. Graph-based pangenome integration and association scans identified key genes involved in root diversity in CW. Additionally, the Cynanchum pangenome and expression data indicated lower abscisic acid (ABA) biosynthesis in CR due to structural variation in ABSCISIC ALDEHYDE OXIDASE 3. ABA deficiency hampers stomatal control, while extremely long roots likely adapt to water loss. Our findings offer insights into root development and aid genomics-based breeding of these valuable root crops. Biological sciences/Genetics/Genomics Biological sciences/Plant sciences/Plant genetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files 2Supplementarydata.xlsx Supplementary Tables 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-7014984","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":485913589,"identity":"c9648c32-d74b-4fbc-9ae8-79065eb52535","order_by":0,"name":"Tae-Jin 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