Rice Galaxy: an open resource for plant science

  1. Venice Juanillas
  2. Alexis Dereeper
  3. Nicolas Beaume
  4. Gaetan Droc
  5. Joshua Dizon
  6. John Robert Mendoza
  7. Jon Peter Perdon
  8. Locedie Mansueto
  9. Lindsay Triplett
  10. Jillian Lang
  11. Gabriel Zhou
  12. Kunalan Ratharanjan
  13. Beth Plale
  14. Jason Haga
  15. Jan E Leach
  16. Manuel Ruiz
  17. Michael Thomson
  18. Nickolai Alexandrov
  19. Pierre Larmande
  20. Tobias Kretzschmar
  21. Ramil P Mauleon

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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 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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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz028

    Venice Juanillas 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexis Dereeper 2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexis DereeperNicolas Beaume 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicolas BeaumeGaetan Droc 3CIRAD, UMR AGAP, F-34398 Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gaetan DrocJoshua Dizon 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohn Robert Mendoza 8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJon Peter Perdon 8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLocedie Mansueto 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLindsay Triplett 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lindsay TriplettJillian Lang 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jillian LangGabriel Zhou 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKunalan Ratharanjan 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kunalan RatharanjanBeth Plale 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Beth PlaleJason Haga 5National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 1,1-1-1 Umezono, Tsukuba, Ibaraki 305-8560 JAPANFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason HagaJan E. Leach 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jan E. LeachManuel Ruiz 3CIRAD, UMR AGAP, F-34398 Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Thomson 1International Rice Research Institute, Manila, Philippines6Department of Soil and Crop Sciences, Texas A&M University, Houston, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNickolai Alexandrov 1International Rice Research Institute, Manila, Philippines10Inari Agriculture Inc., 200 Sidney St, Cambridge, Massachusetts, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre Larmande 2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pierre LarmandeTobias Kretzschmar 1International Rice Research Institute, Manila, Philippines9Southern Cross Plant Science, Southern Cross University, Lismore, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRamil P. Mauleon 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ramil P. Mauleon

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz028 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101705 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101706

  2. Version published to 10.1093/gigascience/giz028
  3. Version published to 10.1101/358754v1 on bioRxiv