The Genome Database for Rosaceae is a curated and integrated web-based relational database providing data mining tools and publicly available genomics, genetics and breeding data for Rosaceae (almond, apple, blackberry, cherry, peach, pear, plum, raspberry, rose, and strawberry), to aid basic, translational and applied research in this economically important family. GDR contains whole genome sequences of apple, peach and strawberry available to browse or download with a range of annotations including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs, and association of InterPro protein domains, GO terms, and KEGG pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse or JBrowse. EST unigene sets are available for major genera and Pathway data is available through FragariaCyc, AppleCyc, and PeachCyc databases. Synteny among four sequenced genomes can be viewed using GBrowse_Syn. Markers, genetic maps, and extensively curated qualitative/Mendelian and quantitative trait loci are available as are phenotype and genotype data from breeding projects and genetic diversity projects. Search pages are available for genes, sequences, markers, trait loci, trait evaluation, genetic diversity, and publications . New search tools for breeders enable selection comparison and assistance with breeding decision-making. GDR also provides online analysis tools such as a NCBI BLAST and Batch BLAST, primer3 and a sequence retrieval tool. In July 2016, we redesigned the GDR theme and organization and implmented in Tripal version 2.1,
- Funding for GDR comes from the following sources: USDA Specialty Crop Research Initiative (2009-2019, Award #2014-51181-2237 and Award # 2009-51181-0603), the USDA National Research Support Project 10 (2015-2019), the NSF Plant Genome Research Program (2016-2019 Award # 444573, 2003-2008, Award #0320544) and the Washington Tree Fruit Research Commission.
- If you use GDR data or tools, please reference us
Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace, Albert G. Abbott, Lukas A. Mueller, Mercy A. Olmstead and Dorrie Main. The Genome Database for Rosaceae (GDR): year 10 update. Nucl. Acids Res. (2014) Jan 1; 42(1):D1237-44
Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, and Dorrie Main. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Research, 2008 January; 36(Database issue): D1034–D1040.
Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins and Dorrie Main. 2004. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 2004, 5:130.
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