Journal article
Rice Galaxy: an open resource for plant science
Gigascience, Vol.8(5)
2019
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Source: InCites
Abstract
<p>BACKGROUND: Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers.<br />FINDINGS: The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.<br />CONCLUSIONS: Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.</p>
Details
- Title
- Rice Galaxy: an open resource for plant science
- Creators
- Venice Juanillas - International Rice Research Institute, PhillipinesAlexis Dereeper - University of Montpellier, FranceNicolas Beaume - International Rice Research Institute, PhillipinesGaetan DrocJohn R Mendoza - Advanced Science and Technology Institute, PhillipinesJon P Perdon - Advanced Science and Technology Institute, PhillipinesLocedie Mansueto - Southern Cross University, Faculty of Science and EngineeringLindsay Triplett - Colorado State University, USAJillian Lang - Colorado State University, USAGabriel Zhou - Indiana University, USAKunalan Ratharanjan - Indiana University, USABeth Plale - Indiana University, USAJason Haga - National Institute of Advanced Industrial Science and Technology, JapanJan E Leach - Colorado State University, USAManuel RuizMichael Thomson - International Rice Research Institute, PhillipinesNickolai Alexandrov - International Rice Research Institute, PhillipinesPierre Larmande - University of Montpellier, FranceTobias Kretzschmar - Southern Cross University, AustraliaJoshua Dizon - International Rice Research Institute, PhillipinesRamil P Mauleon - Southern Cross University, Australia
- Publication Details
- Gigascience, Vol.8(5)
- Identifiers
- 2043; 991012822200002368
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Resource Type
- Journal article