Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea

Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea | 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 Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea Yongfu Tao, Shichao Sun, Chuanzheng Wei, Sofie Pearson, Alan Cruickshank, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7597787/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 Cowpea ( Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assembled 20 high-quality genomes representing cowpea global diversity and constructed a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) were uncovered, affecting thousands of coding sequences and gene expression. Notably, thousands of SVs were found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpointed key SVs underlying variation in pod length and seed number per pod. Two SV clusters appeared to modulate pod length through altering expression and function of VuWAK and VuGA2ox2 genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement. Biological sciences/Plant sciences/Plant breeding Biological sciences/Genetics/Genome/Genetic variation/Structural variation Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementarytables.xls Supplementary tables SupplementaryFigures.docx Supplementary Figures 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. 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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-7597787","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":541887644,"identity":"e1a1544f-c263-4c26-ad43-eabd737e592c","order_by":0,"name":"Yongfu 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