Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio (Digitaria exilis)

Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio (Digitaria exilis) | 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 Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio ( Digitaria exilis ) Todd Michael, Philip Ozersky, Nolan Hartwick, Kelly Colt, Nick Allsing, and 17 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5743774/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 Fonio ( Digitaria exilis ), known as the "grain of life," is a vital food security crop grown by smallholder farmers across West Africa. Renowned for its short maturity period of 6-8 weeks, fonio provides essential harvests during periods of food scarcity. Its nutritional value, drought resilience, and ability to thrive on marginal soils make it a crucial staple in the region. However, fonio’s yield, averaging less than 0.5 metric tons per hectare, remains significantly lower than major cereals, due to minimal breeding efforts aimed at enhancing agronomic traits. In this study, we generated a high-quality chromosome-resolved, tetraploid (2n=4x=36) genome of a fonio line (PI 349688) available through the United States Germplasm Resource Information Network (GRIN). Time-of-day (TOD) expression profiling revealed sub-genome dominance in pathways associated with key agronomic traits that were also identified in a selective sweep analysis across a panel of 90 fonio accessions that originated from 21 different villages over five regions of Senegal representing eight distinct ethnic groups. Leveraging phenotyping across 14 key agronomic traits, we identified genotype-trait associations for plant height, tillering and panicle yield with genes involved in the circadian clock, light signaling and plant architecture. We demonstrated that fonio is amenable to transformation and gene editing, as evidenced by successful CRISPR-Cas9 modification of the Green Revolution gene REDUCED HEIGHT 1 ( RHT1 ), resulting in lines with increased height, vegetative area, and enhanced tillering. Collectively, the genomic resources developed here pave new avenues for molecular breeding and trait discovery, laying a robust foundation for accelerating fonio improvement to bolster food security, climate resilience, and sustainable agriculture in West Africa. Biological sciences/Plant sciences/Plant biotechnology/Molecular engineering in plants Biological sciences/Genetics/Agricultural genetics Biological sciences/Biotechnology/Genomics/Transcriptomics Biological sciences/Plant sciences/Plant genetics/Transgenic plants Digitaria exilis orphan crop autotetraploidy sub-genome dominance Time-of-day (TOD) expression CRISPR-editing Full Text Additional Declarations Yes there is potential Competing Interest. T.P.M. is a co-founder of Cquesta, a company that works on crop root growth and carbon sequestration. The other authors have nothing to declare. Supplementary Files Foniogenometables123124.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. 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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-5743774","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":398461012,"identity":"21f5eeeb-a84c-4a11-8468-d79fb1036e63","order_by":0,"name":"Todd 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Renowned for its short maturity period of 6-8 weeks, fonio provides essential harvests during periods of food scarcity. Its nutritional value, drought resilience, and ability to thrive on marginal soils make it a crucial staple in the region. However, fonio’s yield, averaging less than 0.5 metric tons per hectare, remains significantly lower than major cereals, due to minimal breeding efforts aimed at enhancing agronomic traits. In this study, we generated a high-quality chromosome-resolved, tetraploid (2n=4x=36) genome of a fonio line (PI 349688) available through the United States Germplasm Resource Information Network (GRIN). Time-of-day (TOD) expression profiling revealed sub-genome dominance in pathways associated with key agronomic traits that were also identified in a selective sweep analysis across a panel of 90 fonio accessions that originated from 21 different villages over five regions of Senegal representing eight distinct ethnic groups. Leveraging phenotyping across 14 key agronomic traits, we identified genotype-trait associations for plant height, tillering and panicle yield with genes involved in the circadian clock, light signaling and plant architecture. We demonstrated that fonio is amenable to transformation and gene editing, as evidenced by successful CRISPR-Cas9 modification of the Green Revolution gene \u003ci\u003eREDUCED HEIGHT 1\u003c/i\u003e (\u003ci\u003eRHT1\u003c/i\u003e), resulting in lines with increased height, vegetative area, and enhanced tillering. 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