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Rice Galaxy: An open resource for plant science
- Source :
- GigaScience
- Publication Year :
- 2019
-
Abstract
- BackgroundRice 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 (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL 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.FindingsWe adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) 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.ConclusionsRice 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.
- Subjects :
- 0106 biological sciences
Germplasm
Application des ordinateurs
01 natural sciences
Genome
F30 - Génétique et amélioration des plantes
chemistry.chemical_compound
Molecular marker
Technical Note
riz
2. Zero hunger
0303 health sciences
biology
U10 - Informatique, mathématiques et statistiques
high-density genotypes
food and beverages
single-nucleotide polymorphism
Computer Science Applications
C30 - Documentation et information
Diffusion de l'information
Banque de données
Génotype
workflow
Health Informatics
Computational biology
Quantitative trait locus
Oryza
DNA sequencing
03 medical and health sciences
Genotyping
reproducibility
Genetic association
030304 developmental biology
Genetic diversity
Génome
rice
15. Life on land
biology.organism_classification
chemistry
breeding
genome-wide association studies
genomes
Galaxy project
010606 plant biology & botany
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- GigaScience
- Accession number :
- edsair.doi.dedup.....f02bfb786390c54364b9be11c06966a0