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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #351331

Research Project: Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

Title: Updates to the Cool Season Food Legume Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding

item JUNG, SOOK - Washington State University
item HUMANN, JODI - Washington State University
item CHENG, CHUN-HUAI - Washington State University
item LEE, TAEIN - Washington State University
item ZHENG, PING - Washington State University
item MORGAN, FRANK - Washington State University
item MCGAUGHEY, DEAH - Washington State University
item SCOTT, KRISTEN - Washington State University
item BUBLE, KATHRYN - Washington State University
item YU, JING - Washington State University
item HOUGH, HEIDI - Washington State University
item Coyne, Clarice - Clare
item McGee, Rebecca
item MAIN, DOREEN - Washington State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: none

Technical Abstract: The Cool Season Food Legume Genome database (CSFL, is an online resource for genomics, genetics, and breeding research for chickpea, lentil,pea, and faba bean. The user-friendly and curated website allows for all publicly available map,marker,trait, gene,transcript, germplasm, and genome data to be easily searched and retrieved as downloadable tables and files. CSFL now utilizes the Tripal BLAST module which allows for hyperlinks from the results to JBrowse, NCBI, and data detail pages in CSFL. The available BLAST databases include chickpea, lotus, Medicago, and soybean genome assemblies; annotated reference transcriptomes (RefTrans) and unigenes assemblies for pea, chickpea, lentil and faba bean; and ESTs from NCBI for each of the four crops. CSFL also has several tools for data exploration such as JBrowse for viewing chickpea and related model organism genomes and the corresponding annotations or alignments and PathwayTools for viewing predicted metabolic pathways in the Cicer genomes. CSFL features a new integrated genetic MapViewer module that replaces CMap and allows for easier comparison, display and retrieval of all map and associated data. MapViewer pulls data from the CSFL Chado database and integrates the maps into the CSFL genetic map details pages and allows users to zoom and select regions dynamically through clicking and dragging. MapViewer also allows users to compare linkage groups from the same map or different maps and display the corresponding markers in both maps. In the near future CSFL will also utilize the Tripal Breeding Information Management System (BIMS) module and allow for breeders to manage their private data and use tools that will assist with marker-assisted breeding. This project is supported by USDA NRSP10, the USA Dry Pea and Lentil Council, Northern Pulse Growers Association, USDA-ARS and Washington State University.