Update info.Tools - Reference - Detail
Reference Detail
| Reference | ||
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| Author | Naithani S., Mohanty B., Elser J., D'Eustachio P., Jaiswal P. | |
| Title | Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (<i>Oryza sativa</i>). | |
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Abstract: Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement. |
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| Journal | Plants (Basel) | |
| Country | USA | |
| Volume | 12(11) | |
| Pages | ||
| Year | 2023 | |
| PubMed ID | 37299125 | |
| PubMed Central ID | 10255735 | |
| DOI | 10.3390/plants12112146 | |
| URL | - | |
| Relation | ||
| Gene | BBX17 BOP3 BSRD1 DCA1 ERF61 ERF66 ERF67 HOX12 ILI2 LA1 MYB45 NAC1 ONAC300 OSH1 OSKN2 PCF8 RLB SUB1B TCP18 WRKY1 WRKY16 WRKY24 WRKY55 WRKY70 WRKY71 WRKY74 WRKY8 YAB6 _ _ _ | |
| INSD | - | |
| Strain | Wild Core Collection | - |
| Induced Mutation Lines(NIG Collection) | - | |
| Sterile Seed Strain | - | |
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Lethal Embryo Mutantion Strain |
- | |
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Stages in Each Organ - Muant Lines (Gene) |
- | |
| Cultivated Varieties(NIG Collection) | - | |
| Stages in Each Organ | - | |
