Rice Galaxy: an open resource for plant science

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Abstract

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.

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  1. Now published in GigaScience doi: 10.1093/gigascience/giz028

    Venice Juanillas 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexis Dereeper 2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexis DereeperNicolas Beaume 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicolas BeaumeGaetan Droc 3CIRAD, UMR AGAP, F-34398 Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID …