The teff (Eragrostis tef) pangenome reveals haplotypic diversity and targets for molecular improvement

The teff (Eragrostis tef) pangenome reveals haplotypic diversity and targets for molecular improvement | 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 The teff (Eragrostis tef) pangenome reveals haplotypic diversity and targets for molecular improvement Matteo Dell'Acqua, Worku Kebede Tekle, Ettore Riccucci, Giorgia Di Santolo, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9244157/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 Modern genomic tools can accelerate molecular breeding of underutilized crops such as teff (Eragrostis tef), a gluten-free cereal that is a staple in the Horn of Africa. Here, we report the development of a pangenome comprising chromosome-scale assemblies of 26 teff accessions, including both landraces and improved cultivars, and representing the species’ gene pool. The teff pangenome reveals a highly conserved genome architecture characterized by structural stability across different accessions, with a content of repetitive elements increased by 8% with respect to previous annotations. We describe the features of the pangenome and use it to advance teff biology, targeting seed color, a priority trait for breeding. By defining k-mer-based haplotypes at genomic loci previously known to be associated with the trait, we build a prediction model capable of accurately predicting the color of the seed. Our supervised classification analysis shows that seed color determination cannot be explained by less than four haplotype combinations at loci on chromosomes 4B and 6A. Our results represent a key resource to advance teff breeding and demonstrate that a pangenomic dimension can expand association studies to fully dissect the determination of complex traits. Biological sciences/Plant sciences/Plant genetics Biological sciences/Genetics/Genomics/Comparative genomics Biological sciences/Plant sciences/Plant breeding Full Text Additional Declarations There is NO Competing Interest. Supplementary Files tekleetalsupplementarytables.xlsx Supplementary tables tekleetalsupplementaryfigures.pdf Supplementary Information 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. 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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-9244157","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":614449238,"identity":"41dcfb8c-3839-482f-bd82-e78b33e1caf7","order_by":0,"name":"Matteo 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