ArticleProceedings of the National Academy of Sciences of the United States of America2011
Genetic dissection of the biotic stress response using a genome-scale gene network for rice.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 190 citations in OpenAlex.
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Benchmarking ensemble and deep learning models for drought-responsive gene prioritisation in rice using multi-omics data.PloS one · 2026Article
- Global Protein Interactome Mapping in Rice Using Barcode-Indexed PCR Coupled with HiFi Long-Read Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Floral Development onPlants (Basel, Switzerland) · 2023Article
- Genome-Wide Identification of MADS-Box Genes inInternational journal of molecular sciences · 2023Article
- Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Plants (Basel, Switzerland) · 2023Article
- Population genetic analysis and scans for adaptation and contemporary selection footprints provide genomic insight intoJournal of genetics · 2023Article
- An open source plant kinase chemogenomics set.Plant direct · 2022Article
- Comparison of anther transcriptomes in response to cold stress at the reproductive stage between susceptible and resistant Japonica rice varieties.BMC plant biology · 2022Article
- Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides.Chemical reviews · 2022Review
- Integration of probabilistic functional networks without an external Gold Standard.BMC bioinformatics · 2022Article
- Systems biology for crop improvement.The plant genome · 2021Review
- The rice PALE1 homolog is involved in the biosynthesis of vitamin B1.Plant biotechnology journal · 2021Article
- Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants.Frontiers in plant science · 2021Article
- In silico analysis of functional linkage among arsenic induced MATE genes in rice.Biotechnology reports (Amsterdam, Netherlands) · 2020Article
- A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots.Plant physiology · 2020Article
- Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars.BMC genomics · 2020Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
Abstract
Rice is a staple food for one-half the world's population and a model for other monocotyledonous species. Thus, efficient approaches for identifying key genes controlling simple or complex traits in rice have important biological, agricultural, and economic consequences. Here, we report on the construction of RiceNet, an experimentally tested genome-scale gene network for a monocotyledonous species. Many different datasets, derived from five different organisms including plants, animals, yeast, and humans, were evaluated, and 24 of the most useful were integrated into a statistical framework that allowed for the prediction of functional linkages between pairs of genes. Genes could be linked to traits by using guilt-by-association, predicting gene attributes on the basis of network neighbors. We applied RiceNet to an important agronomic trait, the biotic stress response. Using network guilt-by-association followed by focused protein-protein interaction assays, we identified and validated, in planta, two positive regulators, LOC_Os01g70580 (now Regulator of XA21; ROX1) and LOC_Os02g21510 (ROX2), and one negative regulator, LOC_Os06g12530 (ROX3). These proteins control resistance mediated by rice XA21, a pattern recognition receptor. We also showed that RiceNet can accurately predict gene function in another major monocotyledonous crop species, maize. RiceNet thus enables the identification of genes regulating important crop traits, facilitating engineering of pathways critical to crop productivity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.