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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
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OutlineOutline
• Introduction• Data and function overview• Work in progress• Future development• Acknowledgements
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What is the CSFL Genome Database?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 peapea, chickpeachickpea and lentillentil.
• Built using the open-source, user-friendly, TripalTripal database infrastructure used by several other databases.
• Collaborative module development and data exchange with LIS and KnowPulse
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www.coolseasonfoodlegume.org
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Species PagesSpecies Pages
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Data Overview Data Overview
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Data Submission Data Submission
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Contact usContact us
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Mailing ListMailing List
Please subscribe so we can send you newsletters highlighting new data and functionality and community news
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Trait/Marker Data and ToolsTrait/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
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Search TraitsSearch Traits
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Trait Search ResultsTrait Search Results
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QTL Details PageQTL Details Page
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Search MarkersSearch Markers
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Search MarkersSearch Markers
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Search MarkersSearch Markers
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Search MarkersSearch Markers
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Search MarkersSearch Markers
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Marker Search ResultsMarker Search Results
Will also add map position and germplasm
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Marker Details PageMarker Details Page
Will also add more data where it is available, genetic map, location on genome(s)
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Sequence SearchSequence Search
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Sequence Search ResultsSequence Search Results
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Search Details PageSearch Details Page
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Genome Viewer: GBrowseGenome Viewer: GBrowse
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Work in Progress - 2013Work 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 Kaur et al., 2011 lentil transcriptome• Adding more chickpea transcriptome data• Developing a quarterly newsletter
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• 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
Future Developments - 2013Future Developments - 2013
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www.rosaceae.org
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AcknowledgementsAcknowledgements
• Mainlab Bioinformatics Team• USDA Grain Legumes Team • USDA Plant Introduction Team• WSU Department of Horticulture• Legume Information System• University of Saskatchewan
Pulse Crop Research Group
• USDA Specialty Crop ResearchProgram grants for tfGDR andRosBREED (2009-2013)