ArticleDatabase : the journal of biological databases and curation2016
Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Divergent genetic architecture of cold stress tolerance inFrontiers in plant science · 2025Article
- Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization.Frontiers in genetics · 2022Article
- Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces.BMC plant biology · 2021Article
- Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.Horticulture research · 2021Article
- Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- Vis/NIR hyperspectral imaging distinguishes sub-population, production environment, and physicochemical grain properties in rice.Scientific reports · 2020Article
- TeaMiD: a comprehensive database of simple sequence repeat markers of tea.Database : the journal of biological databases and curation · 2020Article
- Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective.Rice (New York, N.Y.) · 2019Review
- Haplotype Characterization of the sd1 Semidwarf Gene in United States Rice.The plant genome · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- Association Analysis of Three Diverse Rice (The plant genome · 2019Article
- Rice Genomics: over the Past Two Decades and into the Future.Genomics, proteomics & bioinformatics · 2018Review
- The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa.The New phytologist · 2017Article
- Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis.PloS one · 2017Article
Corrections and comments
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice.
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Registered trials
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