ArticleGigaScience2018
funRiceGenes dataset for comprehensive understanding and application of rice functional genes.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses.BioMed research international · 2019Pooled it
- Mining rare haplotypes to accelerate precision breeding in rice.The plant genome · 2026Article
- RGPA-GCN: Graph convolutional networks for rice gene-phenotype association prediction.Plant biology (Stuttgart, Germany) · 2026Article
- TKC-MC: An Effective Strategy for Generating Heritable Heterozygous Mutations in Essential Genes in Rice.Plant biotechnology journal · 2026Article
- Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance.Nature communications · 2026Article
- ricePSP: a database of rice phase separation-associated proteins.Genome biology · 2025Article
- CRISPR-driven innovations in rice (Oryza sativa L.) breeding: precision development of male sterile lines.Molecular biology reports · 2025Review
- Candidate genes for alkali tolerance identified by genome-wide association study at the seedling stage in rice (Oryza sativa L.).Scientific reports · 2024Article
- Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Biology · 2024Article
- Characterization of the Regulatory Network under Waterlogging Stress in Soybean Roots via Transcriptome Analysis.Plants (Basel, Switzerland) · 2024Article
- Functional differentiation and genetic diversity of rice cation exchanger (CAX) genes and their potential use in rice improvement.Scientific reports · 2024Article
- Review
- Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties.Communications biology · 2024Article
- Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat.Plant biotechnology journal · 2023Article
- Multiple domestications of Asian rice.Nature plants · 2023Article
- The translational landscape of bread wheat during grain development.The Plant cell · 2023Article
- Mining genes regulating root system architecture in maize based on data integration analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations.Plant physiology · 2023Article
- Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice.Frontiers in plant science · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings: We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/). Conclusions: The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice.
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