Publications des scientifiques de l'IRD

Juanillas V., Dereeper Alexis, Beaume N., Droc G., Dizon J., Mendoza J. R., Perdon J. P., Mansueto L., Triplett L., Lang J., Zhou G., Ratharanjan K., Plale B., Haga J., Leach J. E., Ruiz M., Thomson M., Alexandrov N., Larmande Pierre, Kretzschmar T., Mauleon R. P. (2019). Rice Galaxy : an open resource for plant science. Gigascience, 8 (5), p. giz028 [14 p.]. ISSN 2047-217X.

Titre du document
Rice Galaxy : an open resource for plant science
Année de publication
2019
Type de document
Article référencé dans le Web of Science WOS:000474856100019
Auteurs
Juanillas V., Dereeper Alexis, Beaume N., Droc G., Dizon J., Mendoza J. R., Perdon J. P., Mansueto L., Triplett L., Lang J., Zhou G., Ratharanjan K., Plale B., Haga J., Leach J. E., Ruiz M., Thomson M., Alexandrov N., Larmande Pierre, Kretzschmar T., Mauleon R. P.
Source
Gigascience, 2019, 8 (5), p. giz028 [14 p.] ISSN 2047-217X
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Sciences du monde végétal [076] ; Informatique [122]
Localisation
Fonds IRD [F B010076213]
Identifiant IRD
fdi:010076213
Contact