Rice Galaxy: an open resource for plant science. Issue 5 (18th May 2019)
- Record Type:
- Journal Article
- Title:
- Rice Galaxy: an open resource for plant science. Issue 5 (18th May 2019)
- Main Title:
- Rice Galaxy: an open resource for plant science
- Authors:
- Juanillas, Venice
Dereeper, Alexis
Beaume, Nicolas
Droc, Gaetan
Dizon, Joshua
Mendoza, John Robert
Perdon, Jon Peter
Mansueto, Locedie
Triplett, Lindsay
Lang, Jillian
Zhou, Gabriel
Ratharanjan, Kunalan
Plale, Beth
Haga, Jason
Leach, Jan E
Ruiz, Manuel
Thomson, Michael
Alexandrov, Nickolai
Larmande, Pierre
Kretzschmar, Tobias
Mauleon, Ramil P - Abstract:
- 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,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. … (more)
- Is Part Of:
- GigaScience. Volume 8:Issue 5(2019)
- Journal:
- GigaScience
- Issue:
- Volume 8:Issue 5(2019)
- Issue Display:
- Volume 8, Issue 5 (2019)
- Year:
- 2019
- Volume:
- 8
- Issue:
- 5
- Issue Sort Value:
- 2019-0008-0005-0000
- Page Start:
- Page End:
- Publication Date:
- 2019-05-18
- Subjects:
- rice -- breeding -- workflow -- genomes -- high-density genotypes -- reproducibility -- single-nucleotide polymorphism -- genome-wide association studies -- Galaxy project
Information storage and retrieval systems -- Research -- Periodicals
Biology -- Research -- Periodicals
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570.285 - Journal URLs:
- http://www.gigasciencejournal.com/ ↗
http://www.oxfordjournals.org/ ↗ - DOI:
- 10.1093/gigascience/giz028 ↗
- Languages:
- English
- ISSNs:
- 2047-217X
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
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- 11797.xml