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Rice Galaxy: an open resource for plant science

Venice Juanillas, View ORCID ProfileAlexis Dereeper, View ORCID ProfileNicolas Beaume, View ORCID ProfileGaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, View ORCID ProfileLindsay Triplett, View ORCID ProfileJillian Lang, Gabriel Zhou, View ORCID ProfileKunalan Ratharanjan, View ORCID ProfileBeth Plale, View ORCID ProfileJason Haga, View ORCID ProfileJan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, View ORCID ProfilePierre Larmande, Tobias Kretzschmar, View ORCID ProfileRamil P. Mauleon
doi: https://doi.org/10.1101/358754
Venice Juanillas
1International Rice Research Institute, Manila, Philippines
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Alexis Dereeper
2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
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Nicolas Beaume
1International Rice Research Institute, Manila, Philippines
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Gaetan Droc
3CIRAD, UMR AGAP, F-34398 Montpellier, France
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Joshua Dizon
1International Rice Research Institute, Manila, Philippines
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John Robert Mendoza
8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines
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Jon Peter Perdon
8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines
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Locedie Mansueto
1International Rice Research Institute, Manila, Philippines
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Lindsay Triplett
7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177
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Jillian Lang
7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177
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Gabriel Zhou
4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USA
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Kunalan Ratharanjan
4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USA
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Beth Plale
4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USA
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Jason Haga
5National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 1,1-1-1 Umezono, Tsukuba, Ibaraki 305-8560 JAPAN
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Jan E. Leach
7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177
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Manuel Ruiz
3CIRAD, UMR AGAP, F-34398 Montpellier, France
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Michael Thomson
1International Rice Research Institute, Manila, Philippines
6Department of Soil and Crop Sciences, Texas A&M University, Houston, USA
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Nickolai Alexandrov
1International Rice Research Institute, Manila, Philippines
10Inari Agriculture Inc., 200 Sidney St, Cambridge, Massachusetts, USA
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Pierre Larmande
2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
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Tobias Kretzschmar
1International Rice Research Institute, Manila, Philippines
9Southern Cross Plant Science, Southern Cross University, Lismore, Australia
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Ramil P. Mauleon
1International Rice Research Institute, Manila, Philippines
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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 (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.

Findings

We 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.

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 29, 2018.
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Rice Galaxy: an open resource for plant science
Venice Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay Triplett, Jillian Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil P. Mauleon
bioRxiv 358754; doi: https://doi.org/10.1101/358754
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Rice Galaxy: an open resource for plant science
Venice Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay Triplett, Jillian Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil P. Mauleon
bioRxiv 358754; doi: https://doi.org/10.1101/358754

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