update in gdr, the genome database for rosaceae s jung, t lee, s ficklin, ch cheng, i cho, p zheng,...

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

Go Live

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