Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice

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cg.authorship.typesCGIAR and developing country institute
cg.authorship.typesCGIAR and advanced research institute
cg.contributor.affiliationNew York University
cg.contributor.affiliationNational Taiwan University
cg.contributor.affiliationUnited States Department of Agriculture
cg.contributor.affiliationUniversidad Andrés Bello
cg.contributor.affiliationMillennium Institute for Integrative Biology, Chile
cg.contributor.affiliationPontificia Universidad Católica de Chile
cg.contributor.affiliationSalk Institute for Biological Studies
cg.contributor.affiliationInternational Rice Research Institute
cg.contributor.crpExcellence in Breeding
cg.contributor.donorZegar Family Foundation
cg.contributor.donorCGIAR Trust Fund
cg.contributor.donorNational Institutes of Health, United States
cg.contributor.donorLife Sciences Research Foundation
cg.contributor.initiativeAccelerated Breeding
cg.creator.identifierCarly M Shanks: 0000-0001-6229-6845
cg.creator.identifierJi Huang: 0000-0002-4416-7983
cg.creator.identifierMatthew D. Brooks: 0000-0002-6081-6103
cg.creator.identifierJosé M. Alvarez: 0000-0002-5073-7751
cg.creator.identifierAmelia Henry: 0000-0001-6255-5480
cg.creator.identifierGloria M. Coruzzi: 0000-0003-2608-2166
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.3389/fpls.2022.1006044
cg.isijournalISI Journal
cg.issn1664-462X
cg.issue1006044
cg.journalFrontiers in Plant Science
cg.reviewStatusPeer Review
cg.subject.actionAreaGenetic Innovation
cg.subject.impactAreaNutrition, health and food security
cg.volume13
dc.contributor.authorShanks, Carly M.
dc.contributor.authorHuang, Ji
dc.contributor.authorCheng, Chia-Yi
dc.contributor.authorShih, Hung-Jui S.
dc.contributor.authorBrooks, Matthew D.
dc.contributor.authorÁlvarez, José M.
dc.contributor.authorAraus, Viviana
dc.contributor.authorSwift, Joseph
dc.contributor.authorHenry, Amelia
dc.contributor.authorCoruzzi, Gloria M.
dc.date.accessioned2023-01-19T11:11:55Zen
dc.date.available2023-01-19T11:11:55Zen
dc.identifier.urihttps://hdl.handle.net/10568/127525
dc.titleValidation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown riceen
dcterms.abstractNitrogen (N) and Water (W) - two resources critical for crop productivity – are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademics
dcterms.audienceCGIAR
dcterms.audienceDevelopment Practitioners
dcterms.audienceDonors
dcterms.audienceExtension
dcterms.audienceFarmers
dcterms.audienceGeneral Public
dcterms.audienceNGOs
dcterms.audiencePolicy Makers
dcterms.audienceScientists
dcterms.available2022-11-25
dcterms.bibliographicCitationShanks, C.M., Huang, J., Cheng, C.-Y., Shih, H.-J.S., Brooks, M.D., Alvarez, J.M., Araus, V., Swift, J., Henry, A. and Coruzzi, G.M. 2022. Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice. Frontiers in Plant Science 13:1006044.en
dcterms.extent1-18
dcterms.issued2022-11-25
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherFrontiers Media
dcterms.subjectriceen
dcterms.subjectdroughten
dcterms.subjectnitrogenen
dcterms.subjectgenesen
dcterms.typeJournal Article

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