Rice Galaxy: an open resource for plant science

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.

Keywords: Galaxy project; breeding; genome-wide association studies; genomes; high-density genotypes; reproducibility; rice; single-nucleotide polymorphism; workflow.

Figure 1:

Rice Galaxy at IRRI with customized analysis tools for genetics, breeding, and custom data sources (i.e., 3000 Rice Genomes project).

Figure 2:

Genome-wide association studies analysis (implemented by TASSEL software) in Rice Galaxy.

Figure 3:

Genome-wide association studies analysis workflow in SNiPlay as implemented in Rice Galaxy.

Figure 4:

Oghma genomic prediction and selection tools in Rice Galaxy with various classifier tools installed.

Figure 5:

Genomic selection analysis workflow as implemented by Oghma tool suite.

Figure 6:

Workflow for classifier evaluation in the genome prediction tool suite implemented by Oghma.

Figure 7:

Overview schematic showing the integration of the 3K Rice Genomes project genotyping database and rapid extraction of subset SNPs by RAVE module for use by analysis workflows installed in Rice Galaxy.

Figure 8:

Rice Galaxy SNiPlay workflow for diversity and population structure analyses using various software tools.

Figure 9:

Uniqprimer comparative genomics−based diagnostic primer design tool for microbial pathogen detection installed in Rice Galaxy.

Figure 10:

The components (A) and the flow of digital objects (DOs) from upload to discoverability (B) in the prototype Rice Galaxy OA.

Figure 11:

Rice Galaxy Toolshed with the various available tools.