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Rice Galaxy: an open resource for plant science

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, im...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527052/
https://www.ncbi.nlm.nih.gov/pubmed/31107941
http://dx.doi.org/10.1093/gigascience/giz028
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author 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
author_facet 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
author_sort Juanillas, Venice
collection PubMed
description 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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spelling pubmed-65270522019-05-28 Rice Galaxy: an open resource for plant science 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 Gigascience Technical Note 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. Oxford University Press 2019-05-18 /pmc/articles/PMC6527052/ /pubmed/31107941 http://dx.doi.org/10.1093/gigascience/giz028 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
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
Rice Galaxy: an open resource for plant science
title Rice Galaxy: an open resource for plant science
title_full Rice Galaxy: an open resource for plant science
title_fullStr Rice Galaxy: an open resource for plant science
title_full_unstemmed Rice Galaxy: an open resource for plant science
title_short Rice Galaxy: an open resource for plant science
title_sort rice galaxy: an open resource for plant science
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527052/
https://www.ncbi.nlm.nih.gov/pubmed/31107941
http://dx.doi.org/10.1093/gigascience/giz028
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