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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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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. |
format | Online Article Text |
id | pubmed-6527052 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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