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 Data and function overview Work in progress Future development Acknowledgements

What is the CSFL Genome Database? pea chickpealentil A pulse database focusing on providing centralized access to tools and data to enable basic, translational and applied research in pea, chickpea and lentil. Tripal 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

Species Pages

Data Overview

Data Submission

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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

Search Traits

Trait Search Results

QTL Details Page

Search Markers

Marker Search Results Will also add map position and germplasm

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

Sequence Search

Sequence Search Results

Search Details Page

Genome Viewer: GBrowse

Work in Progress 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

Acknowledgements 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 Research Program grants for tfGDR and RosBREED ( )