Genome-wide association study reveals influence of cell-specific gene networks on Soybean root system architecture

Genome-wide association study reveals influence of cell-specific gene networks on Soybean root system architecture | 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 Genome-wide association study reveals influence of cell-specific gene networks on Soybean root system architecture Todd Michael, Ying Sun, Charlotte Miller, Ashish Rajurkar, Anthony Alyward, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6719211/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Root system architecture (RSA), the three-dimensional arrangement of roots in soil, is a critical determinant of plant productivity, resource use efficiency, and resilience to environmental stress. Despite its agronomic importance, RSA remains a largely untapped breeding target due to historical technical barriers in root phenotyping. We present RADICYL (Root Architecture 3D Cylinder), a scalable, non-invasive, gel-based platform enabling high-throughput, high-resolution quantification of 15 RSA traits in intact root systems. Applying RADICYL to a genetically diverse panel of 371 soybean accessions, we combined 3D phenotyping with genome-wide association studies (GWAS), single-nucleus RNA sequencing (snRNA-seq), and gene co-expression network (GCN) analysis to identify RCE1 and NPR3 as central regulators of RSA, suggesting auxin and salicylic acid-mediated signaling impacts RSA in specific root tissues. Functional validation in Arabidopsis mutants revealed conserved effects on root width and lateral root development. Our findings position the endodermis and metaphloem as key regulatory cell types and demonstrate how multi-omic frameworks can accelerate the discovery of functional genes underlying complex traits. This study establishes a foundation for cell-type-targeted genome editing and climate-smart crop engineering, offering actionable genetic targets to optimize root systems for improved nutrient acquisition, drought resilience, and deep carbon sequestration. By bridging genotype, cellular context, and phenotype, this work redefines RSA as a tractable and transformative trait for the future of crop improvement. Biological sciences/Plant sciences/Plant molecular biology Biological sciences/Plant sciences/Plant biotechnology/Agricultural genetics genome-wide association study (GWAS) Soybean (Glycine max) root system architecture 28 (RSA) metaphloem endodermis lateral root length Full Text Additional Declarations Yes there is potential Competing Interest. T.P.M. and W.B. are founders of the carbon sequestration company Cquesta. Supplementary Files SoyGWASSupplementaryTables051625.xlsx Supplementary Tables 1 - 17 Cite Share Download PDF Status: Posted 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-6719211","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":467855057,"identity":"37457ae2-26c6-421a-9bfe-256566f3804e","order_by":0,"name":"Todd 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metaphloem, endodermis, lateral root length","lastPublishedDoi":"10.21203/rs.3.rs-6719211/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6719211/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Root system architecture (RSA), the three-dimensional arrangement of roots in soil, is a critical determinant of plant productivity, resource use efficiency, and resilience to environmental stress. Despite its agronomic importance, RSA remains a largely untapped breeding target due to historical technical barriers in root phenotyping. We present RADICYL (Root Architecture 3D Cylinder), a scalable, non-invasive, gel-based platform enabling high-throughput, high-resolution quantification of 15 RSA traits in intact root systems. Applying RADICYL to a genetically diverse panel of 371 soybean accessions, we combined 3D phenotyping with genome-wide association studies (GWAS), single-nucleus RNA sequencing (snRNA-seq), and gene co-expression network (GCN) analysis to identify RCE1 and NPR3 as central regulators of RSA, suggesting auxin and salicylic acid-mediated signaling impacts RSA in specific root tissues. Functional validation in Arabidopsis mutants revealed conserved effects on root width and lateral root development. Our findings position the endodermis and metaphloem as key regulatory cell types and demonstrate how multi-omic frameworks can accelerate the discovery of functional genes underlying complex traits. This study establishes a foundation for cell-type-targeted genome editing and climate-smart crop engineering, offering actionable genetic targets to optimize root systems for improved nutrient acquisition, drought resilience, and deep carbon sequestration. 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