Update in GDR The Genome Database for Rosaceae

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 Ros. Breed are now available through Breeders Toolbox in GDR. • SNP markers included in the apple 9 K, peach 9 K and cherry 6 K 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

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Search Tools

Marker Details

Search for syntenic regions in strawberry using Gbrowse_Syn

Breeders Toolbox • 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 Ros. BREED 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

Browse Datasets 13

Phenotyping Data Search 14

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Variety Detail Page

Genotyping Data Search 17

Tools – Generate Input files for Pedimap, a breeding software

Cross. Assist: Generates a list of parents and the number of seedlings to get the progeny with desired traits

Acknowledgements • Project co. PIs- Dorrie Main (PI), Bert Abbott, Cameron Peace, Kate Evans, Des Layne, Nnadozie Oraguzie, Mercy Olmstead, Fred Gmitter, the Ros. BREED and Cacao teams • Rosaceae, Citrus, Cacao and Bioinformatics Community • USDA NIFA SCRI, NSF Plant Genome Program, MARS, USDAARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute