Rice Galaxy: An open resource for plant science

Juanillas Venice, Dereeper Alexis, Beaume Nicolas, Droc Gaëtan, Dizon Joshua, Mendoza John Robert, Perdon Jon Peter, Mansueto Locedie, Triplett Lindsay R., Lang Jillian M., Zhou Gabriel, Ratharanjan Kunalan, Plale Beth, Haga Jason, Leach Jan E., Ruiz Manuel, Thomson Michael J., Alexandrov Nickolai, Larmande Pierre, Kretzschmar Tobias, Mauleon Ramil P.. 2019. Rice Galaxy: An open resource for plant science. GigaScience, 8 (5) : 1-14.

Quartile : Q1, Sujet : MULTIDISCIPLINARY SCIENCES

Résumé : 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.

Mots-clés Agrovoc : riz, Oryza, génome, génotype, diffusion de l'information, application des ordinateurs, banque de données

Classification Agris : F30 - Génétique et amélioration des plantes
C30 - Documentation et information
U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

• Juanillas Venice, IRRI [International Rice Research Institute] (PHL)
• Dereeper Alexis, CIRAD-BIOS-UMR AGAP (GLP)
• Beaume Nicolas, IRRI [International Rice Research Institute] (PHL)
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269
• Dizon Joshua, IRRI [International Rice Research Institute] (PHL)
• Mendoza John Robert, Advanced Science and Technology Institute (PHL)
• Perdon Jon Peter, Advanced Science and Technology Institute (PHL)
• Mansueto Locedie, IRRI [International Rice Research Institute] (PHL)
• Triplett Lindsay R., Colorado State University (USA)
• Lang Jillian M., Colorado State University (USA)
• Zhou Gabriel, Indiana University (USA)
• Ratharanjan Kunalan, Indiana University (USA)
• Plale Beth, Indiana University (USA)
• Haga Jason, National Institute of Advanced Industrial Science and Technology (JPN)
• Leach Jan E., Colorado State University (USA)
• Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
• Thomson Michael J., IRRI [International Rice Research Institute] (PHL)
• Alexandrov Nickolai, IRRI [International Rice Research Institute] (PHL)
• Larmande Pierre, IRD (FRA)
• Kretzschmar Tobias, IRRI [International Rice Research Institute] (PHL)
• Mauleon Ramil P., IRRI [International Rice Research Institute] (PHL) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/592539/)

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