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, 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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Subjects: | F30 - Génétique et amélioration des plantes, C30 - Documentation et information, U10 - Informatique, mathématiques et statistiques, riz, Oryza, génome, génotype, diffusion de l'information, application des ordinateurs, banque de données, http://aims.fao.org/aos/agrovoc/c_6599, http://aims.fao.org/aos/agrovoc/c_5435, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_3225, http://aims.fao.org/aos/agrovoc/c_3860, http://aims.fao.org/aos/agrovoc/c_24009, http://aims.fao.org/aos/agrovoc/c_24833, |
Online Access: | http://agritrop.cirad.fr/592539/ http://agritrop.cirad.fr/592539/1/giz028.pdf |
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dig-cirad-fr-5925392024-01-29T01:59:18Z http://agritrop.cirad.fr/592539/ http://agritrop.cirad.fr/592539/ Rice Galaxy: An open resource for plant science. Juanillas Venice, Dereeper Alexis, Beaume Nicolas, Droc Gaëtan, Dizon Joshua, Mendoza John Robert, Perdon Jon Peter, Mansueto Locedie, Triplett Lindsay R., Lang Jillian M., Zhou Gabriel, Ratharanjan Kunalan, Plale Beth, Haga Jason, Leach Jan E., Ruiz Manuel, Thomson Michael J., Alexandrov Nickolai, Larmande Pierre, Kretzschmar Tobias, Mauleon Ramil P.. 2019. GigaScience, 8 (5) : 1-14.https://doi.org/10.1093/gigascience/giz028 <https://doi.org/10.1093/gigascience/giz028> Rice Galaxy: An open resource for plant science Juanillas, Venice Dereeper, Alexis Beaume, Nicolas Droc, Gaëtan Dizon, Joshua Mendoza, John Robert Perdon, Jon Peter Mansueto, Locedie Triplett, Lindsay R. Lang, Jillian M. Zhou, Gabriel Ratharanjan, Kunalan Plale, Beth Haga, Jason Leach, Jan E. Ruiz, Manuel Thomson, Michael J. Alexandrov, Nickolai Larmande, Pierre Kretzschmar, Tobias Mauleon, Ramil P. eng 2019 GigaScience F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/592539/1/giz028.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1093/gigascience/giz028 10.1093/gigascience/giz028 info:eu-repo/semantics/altIdentifier/doi/10.1093/gigascience/giz028 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1093/gigascience/giz028 |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 Juanillas, Venice Dereeper, Alexis Beaume, Nicolas Droc, Gaëtan Dizon, Joshua Mendoza, John Robert Perdon, Jon Peter Mansueto, Locedie Triplett, Lindsay R. Lang, Jillian M. Zhou, Gabriel Ratharanjan, Kunalan Plale, Beth Haga, Jason Leach, Jan E. Ruiz, Manuel Thomson, Michael J. Alexandrov, Nickolai Larmande, Pierre Kretzschmar, Tobias Mauleon, Ramil P. Rice Galaxy: An open resource for plant science |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques riz Oryza génome génotype diffusion de l'information application des ordinateurs banque de données http://aims.fao.org/aos/agrovoc/c_6599 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3860 http://aims.fao.org/aos/agrovoc/c_24009 http://aims.fao.org/aos/agrovoc/c_24833 |
author |
Juanillas, Venice Dereeper, Alexis Beaume, Nicolas Droc, Gaëtan Dizon, Joshua Mendoza, John Robert Perdon, Jon Peter Mansueto, Locedie Triplett, Lindsay R. Lang, Jillian M. Zhou, Gabriel Ratharanjan, Kunalan Plale, Beth Haga, Jason Leach, Jan E. Ruiz, Manuel Thomson, Michael J. Alexandrov, Nickolai Larmande, Pierre Kretzschmar, Tobias Mauleon, Ramil P. |
author_facet |
Juanillas, Venice Dereeper, Alexis Beaume, Nicolas Droc, Gaëtan Dizon, Joshua Mendoza, John Robert Perdon, Jon Peter Mansueto, Locedie Triplett, Lindsay R. Lang, Jillian M. Zhou, Gabriel Ratharanjan, Kunalan Plale, Beth Haga, Jason Leach, Jan E. Ruiz, Manuel Thomson, Michael J. Alexandrov, Nickolai Larmande, Pierre Kretzschmar, Tobias Mauleon, Ramil P. |
author_sort |
Juanillas, Venice |
title |
Rice Galaxy: An open resource for plant science |
title_short |
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_sort |
rice galaxy: an open resource for plant science |
url |
http://agritrop.cirad.fr/592539/ http://agritrop.cirad.fr/592539/1/giz028.pdf |
work_keys_str_mv |
AT juanillasvenice ricegalaxyanopenresourceforplantscience AT dereeperalexis ricegalaxyanopenresourceforplantscience AT beaumenicolas ricegalaxyanopenresourceforplantscience AT drocgaetan ricegalaxyanopenresourceforplantscience AT dizonjoshua ricegalaxyanopenresourceforplantscience AT mendozajohnrobert ricegalaxyanopenresourceforplantscience AT perdonjonpeter ricegalaxyanopenresourceforplantscience AT mansuetolocedie ricegalaxyanopenresourceforplantscience AT triplettlindsayr ricegalaxyanopenresourceforplantscience AT langjillianm ricegalaxyanopenresourceforplantscience AT zhougabriel ricegalaxyanopenresourceforplantscience AT ratharanjankunalan ricegalaxyanopenresourceforplantscience AT plalebeth ricegalaxyanopenresourceforplantscience AT hagajason ricegalaxyanopenresourceforplantscience AT leachjane ricegalaxyanopenresourceforplantscience AT ruizmanuel ricegalaxyanopenresourceforplantscience AT thomsonmichaelj ricegalaxyanopenresourceforplantscience AT alexandrovnickolai ricegalaxyanopenresourceforplantscience AT larmandepierre ricegalaxyanopenresourceforplantscience AT kretzschmartobias ricegalaxyanopenresourceforplantscience AT mauleonramilp ricegalaxyanopenresourceforplantscience |
_version_ |
1792499742688673792 |