Transcript Resources for Fragaria Research in GDR

Resources Available for Fragaria
Research through the Genome Database
for Rosaceae
Dorrie Main, Sook Jung, Chun-Huai Cheng, Stephen Ficklin, Taein Lee, Jodi Humann,
Jing Yu, Ping Zheng, Cameron Peace, Kate Evans, Ksenjia Gasic, Mercy Olmstead,
Lisa Wasko DeVetter, Michael Kahn, Jim McFerson, Albert Abbott, Nahla Bassil*
8th International Strawberry Symposium
August 13-17, 2016
Quebec, Canada
Introduction
• GDR was initiated in 2003 to
– curate, house and integrate emerging Rosaceae
genomics, genetics and breeding data
– provide access to data mining tools
– facilitate comparative genomics within the
family
• Funded through 2019 (USDA SCRI, NRSP10, NSF)
• Fragaria genomic and genetic data in GDR is
provided by the community and collected from
publications.
New GDR Design
Species Overview Page - vesca
Species Overview Page – ananassa
Links to published NCBI SRA
For the RNASeq data we are creating Reference Transcriptomes for all the major genera
and major species in GDR (see Rubus)
Many of the search features on GDR have been modified and
short audio visual and text tutorials are available for each
search page and the site overview.
From the gene details page, find out all the associated genome
location, functional annotation, sequence, alignments,
analyses etc for that gene.
New synteny analysis between
apple, peach, strawberry and pear
Choose the synteny analysis depending on
what version of the genome assembly you are
working with – v2.0 or v1.1
peach
strawberry
apple
strawberry
pear
The Breeders Toolbox provides
access to current RosBREED 1 data
for strawberry. New comprehensive
Breeding Information Management System
being developed in GDR
Browse or search available phenotype, genotype or haplotype data
And finally …..
• Explore GDR to find all the data and functionality
available for Fragaria research – contact us about
using FieldBook App for phenotype data collection
• Join our GDR mailing list to find out what is new,
receive newsletters events etc.
• Let us know if you have any problems, request
new or improved functionality
• Attend our 2 hr training workshop at PAG where
most presentations will be by users of GDR
• If you use GDR please site us (Jung et al., 2014)
• As always thanks for your continued support of
GDR 
Acknowledgements
• USDA SCRI, USDA NRSP10, NSF Plant Genome Program,
USDA-ARS, SAAEDS, Washington Tree Fruit Research
Commission, Cotton Incorporated, USA Dry Pea and Lentil
Commission, Northern Pulse Growers, Mars Inc.
• Mainlab bioinformatics team and various projects CoPIs/PIs
• Rosaceae, Citrus, Blueberry, Legume, Cacao, Cotton and
Bioinformatics Communities
• US Land Grant University researchers and extension agents