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Updates to the Cool Season Food Legume Genome Database

Updates to the Cool Season Food Legume Genome Database. Dorrie Main, Chun- Huai Cheng, Rebecca McGee, Clarice Coyne, Stephen Ficklin , Taein Lee, Sook Jung, Marwa Sanad , Ping Zheng , Yu Ma, Keithanne Mockaitis NAPIA Meeting , October 31st, 2013. Outline. Introduction

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Updates to the Cool Season Food Legume Genome Database

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  1. Updates to the Cool Season Food Legume Genome Database Dorrie Main, Chun-Huai Cheng, Rebecca McGee, Clarice Coyne, Stephen Ficklin, Taein Lee, Sook Jung, MarwaSanad, Ping Zheng, Yu Ma, KeithanneMockaitis NAPIA Meeting, October 31st, 2013

  2. Outline • Introduction • Data and function overview • Work in progress • Future development • Acknowledgements

  3. What is the CSFL Genome Database? • A pulse database focusing on providing centralized access to tools and data to enable basic, translational and applied research in pea, chickpea and lentil. • Built using the open-source, user-friendly, Tripal database infrastructure used by several other databases. • Collaborative module development and data exchange with LIS and KnowPulse

  4. www.coolseasonfoodlegume.org

  5. Species Pages

  6. Data Overview

  7. Data Submission

  8. Contact us

  9. Mailing List Please subscribe so we can send you newsletters highlighting new data and functionality and community news

  10. Trait/Marker Data and Tools • Collecting all publicly available trait (MLT/QTL) and marker data for pea, chickpea and lentil • Add associated markers • Assign plant ontology to traits • QTL search site available • Marker search site available • Obtain associated map data and more detailed marker information from authors

  11. Search Traits

  12. Trait Search Results

  13. QTL Details Page

  14. Search Markers

  15. Search Markers

  16. Search Markers

  17. Search Markers

  18. Search Markers

  19. Marker Search Results Will also add map position and germplasm

  20. Marker Details Page Will also add more data where it is available, genetic map, location on genome(s)

  21. Sequence Search

  22. Sequence Search Results

  23. Search Details Page

  24. Genome Viewer: GBrowse

  25. Work in Progress - 2013 • Collecting all publicly available trait (MLT/QTL) and marker data for pea, chickpea and lentil • Adding the chickpea desi-type genome sequence • Update the Medicago genome data (v4.0) • Adding tutorials • Adding a publications search site • Adding the Kauret al., 2011 lentil transcriptome • Adding more chickpea transcriptome data • Developing a quarterly newsletter

  26. Future Developments - 2013 • Demo CSFL Genome database at PAG in Jan • Submit an NRSP for core development of Tripal and database support for 22 crops • Adding a gene search site • Generating a pea unigene v3 • Adding genomic/genetic data for fava bean • Continue to add genomic/genetic data for pea, chickpea and lentil • Start to create a breeders toolbox

  27. www.rosaceae.org

  28. Acknowledgements • Mainlab Bioinformatics Team • USDA Grain Legumes Team • USDA Plant Introduction Team • WSUDepartment of Horticulture • Legume Information System • University of Saskatchewan Pulse Crop Research Group • USDA Specialty Crop ResearchProgram grants for tfGDR andRosBREED (2009-2013)

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