Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition

Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition | 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 Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition Peng Yu, Nan-Nan Li, Guoliang Li, Danning Wang, Lige Ma, Xiaofang Huang, and 21 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6521565/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 03 Feb, 2026 Read the published version in Nature Plants → Version 1 posted You are reading this latest preprint version Abstract The microbiome influences the performance and fitness of the host plant. Nevertheless, the biotic interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here, we generated 1,341 paired datasets, including root transcriptomes, rhizosphere prokaryotic taxa, and root ionomes, to conduct multi-omics analyses of the host-microbe associations at the root-soil interface using 175 rapeseed ( Brassica napus L.) ecotypes that were resequenced and evaluated at two field environments. We observed the high prediction ability of nitrogen uptake, with a prediction accuracy of 0.67, accounting for about 45% of the variance in nitrogen levels among natural ionomic variations. This significant proportion of explained variance was driven by the overall transcriptome-wide gene expression and 203 highly heritable microbial amplicon sequence variants (ASVs). These microbial variations were strongly associated with root nitrogen uptake, underscoring the role of the microbiome in plant nutrition. We also identified significant genome-wide associations for the 203 heritable ASVs at multiple genetic loci, regulated by eQTL hotspots, particularly those involved in carbon and nitrogen metabolism. These associations involved a dominant bacterial genus, Sphingopyxis , which exhibited a strong gene regulatory effect on its variation, regulated by the eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected the isolated bacterial isolate to whole-genome sequencing. Finally, targeted plant metabolite profiling of auxin biosynthesis and root confocal imaging assays demonstrated that Sphingopyxis regulates lateral root development and impacts plant nitrogen nutrition. These results suggest a host-microbiome regulatory effect that connects bacterial abundance with plant root architecture and nutrient acquisition. In summary, this study reveals the genetic basis of host-microbiome trait associations across transcriptional, nutritional and environmental domains and suggests that the potential of bacterial microbiome might have consistent effects on root development with implications towards the breeding of nutrient-efficient crops. Biological sciences/Plant sciences/Plant development Biological sciences/Genetics/Genetic association study Biological sciences/Microbiology Biological sciences/Plant sciences/Plant genetics Brassica napus eQTL GWAS ionome rhizosphere microbiome root transcriptome Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementalinformation.docx Supplementary figures 1-15 and Supplementary Table 1 SupplementaryDatasets.xlsx Supplementary Datasets 1-10 Cite Share Download PDF Status: Published Journal Publication published 03 Feb, 2026 Read the published version in Nature Plants → 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-6521565","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":451147993,"identity":"a6beae90-e9b2-4647-b206-2d8ae64bacc4","order_by":0,"name":"Peng 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and nitrogen acquisition","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Brassica napus, eQTL, GWAS, ionome, rhizosphere microbiome, root transcriptome","lastPublishedDoi":"10.21203/rs.3.rs-6521565/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6521565/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe microbiome influences the performance and fitness of the host plant. Nevertheless, the biotic interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here, we generated 1,341 paired datasets, including root transcriptomes, rhizosphere prokaryotic taxa, and root ionomes, to conduct multi-omics analyses of the host-microbe associations at the root-soil interface using 175 rapeseed (\u003cem\u003eBrassica napus\u003c/em\u003e L.) ecotypes that were resequenced and evaluated at two field environments. We observed the high prediction ability of nitrogen uptake, with a prediction accuracy of 0.67, accounting for about 45% of the variance in nitrogen levels among natural ionomic variations. This significant proportion of explained variance was driven by the overall transcriptome-wide gene expression and 203 highly heritable microbial amplicon sequence variants (ASVs). These microbial variations were strongly associated with root nitrogen uptake, underscoring the role of the microbiome in plant nutrition. We also identified significant genome-wide associations for the 203 heritable ASVs at multiple genetic loci, regulated by eQTL hotspots, particularly those involved in carbon and nitrogen metabolism. These associations involved a dominant bacterial genus, \u003cem\u003eSphingopyxis\u003c/em\u003e, which exhibited a strong gene regulatory effect on its variation, regulated by the eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected the isolated bacterial isolate to whole-genome sequencing. Finally, targeted plant metabolite profiling of auxin biosynthesis and root confocal imaging assays demonstrated that \u003cem\u003eSphingopyxis\u003c/em\u003e regulates lateral root development and impacts plant nitrogen nutrition. These results suggest a host-microbiome regulatory effect that connects bacterial abundance with plant root architecture and nutrient acquisition. In summary, this study reveals the genetic basis of host-microbiome trait associations across transcriptional, nutritional and environmental domains and suggests that the potential of bacterial microbiome might have consistent effects on root development with implications towards the breeding of nutrient-efficient crops.\u003c/p\u003e","manuscriptTitle":"Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-05-05 05:38:30","doi":"10.21203/rs.3.rs-6521565/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-plants","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"nplants","sideBox":"Learn more about [Nature Plants](http://www.nature.com/nplants/)","snPcode":"","submissionUrl":"","title":"Nature Plants","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Research","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"96cf1c55-6d16-4577-8f9b-429d15f5f35d","owner":[],"postedDate":"May 5th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":47999917,"name":"Biological sciences/Plant sciences/Plant development"},{"id":47999918,"name":"Biological sciences/Genetics/Genetic association study"},{"id":47999919,"name":"Biological sciences/Microbiology"},{"id":47999920,"name":"Biological sciences/Plant sciences/Plant genetics"}],"tags":[],"updatedAt":"2026-02-04T08:19:13+00:00","versionOfRecord":{"articleIdentity":"rs-6521565","link":"https://doi.org/10.1038/s41477-025-02210-7","journal":{"identity":"nature-plants","isVorOnly":false,"title":"Nature Plants"},"publishedOn":"2026-02-03 05:00:00","publishedOnDateReadable":"February 3rd, 2026"},"versionCreatedAt":"2025-05-05 05:38:30","video":"","vorDoi":"10.1038/s41477-025-02210-7","vorDoiUrl":"https://doi.org/10.1038/s41477-025-02210-7","workflowStages":[]},"version":"v1","identity":"rs-6521565","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6521565","identity":"rs-6521565","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}