ArticleDatabase : the journal of biological databases and curation2009
Gramene QTL database: development, content and applications.
Article in Database : the journal of biological databases and curation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Disruption of the OsWRKY71 transcription factor gene results in early rice seed germination under normal and cold stress conditions.BMC plant biology · 2024Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- The Mining of Genetic Loci and the Analysis of Candidate Genes to Identify the Physical and Chemical Markers of Anti-Senescence in Rice.Plants (Basel, Switzerland) · 2023Article
- Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice.International journal of molecular sciences · 2022Article
- Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services.Nucleic acids research · 2022Article
- Comparison of Transcriptional Response of CFrontiers in plant science · 2021Article
- Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture.International journal of molecular sciences · 2020Article
- Technological Innovations for Improving Cassava Production in Sub-Saharan Africa.Frontiers in genetics · 2020Review
- Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective.Rice (New York, N.Y.) · 2019Review
- Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress.Functional & integrative genomics · 2019Article
- The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Rapid gene cloning in cereals.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Computational aspects underlying genome to phenome analysis in plants.The Plant journal : for cell and molecular biology · 2019Review
- Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice.Plant diversity · 2018Article
- QTLTableMinerBMC bioinformatics · 2018Article
- Statistical Approach for Gene Set Analysis with Trait Specific Quantitative Trait Loci.Scientific reports · 2018Article
- The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Nucleic acids research · 2018Article
- Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice.Current genomics · 2018Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.
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Registered trials
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.