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

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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

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)