Update in GDR, The Genome Database for Rosaceae
S Jung, T Lee, S Ficklin, CH Cheng, I Cho, P Zheng, K Evans, C Peace, N Oraguzie, A Abbott, D Layne, M Olmstead, F Gmitter, C Chen, L Mueller and D Main
Topics• New Data in GDR
• The whole genome sequence and annotation of strawberry, in addition to peach and apple
• Large-scale phenotyping and genotyping data from RosBreed are now available through Breeders Toolbox in GDR.
• SNP markers included in the apple 9K, peach 9K and cherry 6K illumina SNP arrays, as well as all candidates SNPs.
• QTL data and more genetic map and polymorphism data• New Functionality
• Breeders Toolbox has been updated to include more search sites and analysis tools for breeders to access their private data that is integrated with public GDR data.
• GBrowse_Syn to display syntenic regions• QTL search site
Search Tools
Marker Details
Search for syntenic regions in strawberry using Gbrowse_Syn
• A secure site where breeders can access their private data (pedigree, phenotyping and genotyping) and analyze them in combination with other public GDR data through an advanced search interface.
• Now available for RosBREED public breeding data• Functionality
– Search by dataset, variety, trait, parentage, marker, allele– Online tools for breeders - generating inputs for breeding
software and crossing decision tool
Breeders Toolbox
Breeders Toolbox
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Browse Datasets
Phenotyping Data Search
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Variety Detail Page
Genotyping Data Search
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Tools – Generate Input files for Pedimap, a breeding software
CrossAssist: Generates a list of parents and the number of seedlings to get the progeny with desired traits
Acknowledgements
• Project coPIs- Dorrie Main (PI), Bert Abbott, Cameron Peace, Kate Evans, Des Layne, Nnadozie Oraguzie, Mercy Olmstead, Fred Gmitter, the RosBREED and Cacao teams
• Rosaceae, Citrus, Cacao and Bioinformatics Community
• USDA NIFA SCRI, NSF Plant Genome Program, MARS, USDA-ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute