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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
OutlineOutline
• Introduction• Data and function overview• Work in progress• Future development• Acknowledgements
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
www.coolseasonfoodlegume.org
Species PagesSpecies Pages
Data Overview Data Overview
Data Submission Data Submission
Contact usContact us
Mailing ListMailing List
Please subscribe so we can send you newsletters highlighting new data and functionality and community news
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
Search TraitsSearch Traits
Trait Search ResultsTrait Search Results
QTL Details PageQTL Details Page
Search MarkersSearch Markers
Search MarkersSearch Markers
Search MarkersSearch Markers
Search MarkersSearch Markers
Search MarkersSearch Markers
Marker Search ResultsMarker Search Results
Will also add map position and germplasm
Marker Details PageMarker Details Page
Will also add more data where it is available, genetic map, location on genome(s)
Sequence SearchSequence Search
Sequence Search ResultsSequence Search Results
Search Details PageSearch Details Page
Genome Viewer: GBrowseGenome Viewer: GBrowse
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
• 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
www.rosaceae.org
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)