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Protocols

GDR specifications

Information


Unique identifier OMICS_04489
Name GDR
Alternative name Genome Database for Rosaceae
Restrictions to use None
Community driven Yes
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Dorrie Main

Publications for Genome Database for Rosaceae

GDR citations

 (48)
call_split

Morphometrics Reveals Complex and Heritable Apple Leaf Shapes

2018
Front Plant Sci
PMCID: 5758599
PMID: 29354142
DOI: 10.3389/fpls.2017.02185
call_split See protocol

[…] the variance, or the number of independent SNPs. The inferred Meff used to calculate the significance threshold was 91,667 SNPs.We searched the regions surrounding any significant GWAS SNPs using the Genome Database for Rosaceae GBrowse tool for Malus × domestica v1.0 p genome (Jung et al., ). We used a window of ±5,000 bp (10 kb) surrounding the significant SNP to check for genes, and when identi […]

library_books

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

2017
PMCID: 5727400
DOI: 10.1093/database/bax092

[…] g adoption by many communities. Some example databases using Tripal include GeneNetEngine (), the Banana Genome Hub (http://banana-genome.cirad.fr/) (), CottonGen (https://www.cottongen.org/) (), the Genome Database for Rosaceae (GDR, http://www.rosaceae.org) (), Knowpulse: Pulse Crop Genomics & Breeding (http://knowpulse2.usask.ca/portal) (), the Hardwood Genomics Database (http://www.hardwoodgen […]

library_books

XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues

2017
BMC Genomics
PMCID: 5678779
PMID: 29115918
DOI: 10.1186/s12864-017-4255-8

[…] The annotated Fragaria vesca genome V1.0 (fvesca_v1.0_genemark_hybrid.faa.gz) available at the Genome Database for Rosaceae (GDR) [] (https://www.rosaceae.org/species/fragaria/fragaria_vesca) was used. Sequences were re-interrogated in F. vesca genome V1.1 [], and annotated sequences were analy […]

library_books

Global Identification, Classification, and Expression Analysis of MAPKKK genes: Functional Characterization of MdRaf5 Reveals Evolution and Drought Responsive Profile in Apple

2017
Sci Rep
PMCID: 5647345
PMID: 29044159
DOI: 10.1038/s41598-017-13627-2

[…] le databases were performed in order to identify members of the MAPKKKs. MAPKKKs sequences for Arabidopsis and rice were used as queries to perform repetitive blast searches against the GDR database (Genome Database for Rosaceae: http://www.rosaceae.org/). Additionally, all protein sequences of proteins were then used as queries to perform multiple database searches against proteome and genome fil […]

library_books

CHASE Containing Histidine Kinase Receptors in Apple Tree: From a Common Receptor Structure to Divergent Cytokinin Binding Properties and Specific Functions

2017
Front Plant Sci
PMCID: 5611679
PMID: 28979279
DOI: 10.3389/fpls.2017.01614

[…] To identify MdCHK receptors, BLAST searches were performed against the Genome Database for Rosaceae (GDR; ) using A. thaliana cytokinin receptor sequences as queries (AHK2, AHK3, and AHK4). Five sequences were identified based on genome analysis and corresponding cDNA we […]

library_books

Response of miR156 SPL Module during the Red Peel Coloration of Bagging Treated Chinese Sand Pear (Pyrus pyrifolia Nakai)

2017
Front Physiol
PMCID: 5545762
PMID: 28824447
DOI: 10.3389/fphys.2017.00550

[…] tely conserved miRNAs and to 5 for novel and candidate miRNAs (Xia et al., ). The apple consensus gene set from AppleGFDB and the annotation information for miRNA target genes were retrieved from the Genome Database for Rosaceae (Zhang et al., ). Degradome data were normalized to transcripts per million values. Based on the number of degradome sequences and their abundance values, the cleavage sit […]

Citations

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GDR institution(s)
Department of Horticulture, Washington State University, Pullman, WA, USA; Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA; Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, USA; Department of Computer Science, Saginaw Valley State University, University Center, MI, USA; Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
GDR funding source(s)
Supported by the USDA National Institute of Food and Agriculture-Specialty Crop Research initiative projects [2009-51181-06036, 2009-51181-05808]; Washington Tree Fruit Research Commission, Clemson University, University of Florida, Boyce Thompson Institute for Plant Research and Washington State University.

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