Juanillas V. auteur aut IRD Dereeper Alexis auteur aut IRD Beaume N. auteur aut IRD Droc G. auteur aut IRD Dizon J. auteur aut IRD Mendoza J. R. auteur aut IRD Perdon J. P. auteur aut IRD Mansueto L. auteur aut IRD Triplett L. auteur aut IRD Lang J. auteur aut IRD Zhou G. auteur aut IRD Ratharanjan K. auteur aut IRD Plale B. auteur aut IRD Haga J. auteur aut IRD Leach J. E. auteur aut IRD Ruiz M. auteur aut IRD Thomson M. auteur aut IRD Alexandrov N. auteur aut IRD Larmande Pierre auteur aut IRD Kretzschmar T. auteur aut IRD Mauleon R. P. auteur aut IRD text journalArticle eng text/pdf reformatted digital access 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. 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. 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. specialized rice breeding workflow genomes high-density genotypes reproducibility single-nucleotide polymorphism genome-wide association studies Galaxy project 076 122 020 8 5 giz028 [14 p.] 2019 2047-217X https://www.documentation.ird.fr/hor/fdi:010076213 10.1093/gigascience/giz028 2047-217X [F B010076213] https://www.documentation.ird.fr/hor/fdi:010076213 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers19-07/010076213.pdf IRD - Base Horizon / Pleins textes 2019-08-05 2019-08-05 fdi:010076213 fre