Resources Available for Fragaria Research through the Genome Database for Rosaceae - PowerPoint PPT Presentation

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Resources Available for Fragaria Research through the Genome Database for Rosaceae

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  1. 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, KsenjiaGasic, Mercy Olmstead, Lisa WaskoDeVetter, Michael Kahn, Jim McFerson, Albert Abbott, NahlaBassil* 8th International Strawberry SymposiumAugust 13-17, 2016Quebec, Canada

  2. Introduction • GDR was initiated in 2003 to • curate, house and integrate emerging Rosaceae genomics, genetics and breeding data • provide access to data mining tools • facilitatecomparative 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.

  3. New GDR Design

  4. Species Overview Page - vesca

  5. Species Overview Page – ananassa

  6. 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)

  7. 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.

  8. From the gene details page, find out all the associated genome location, functional annotation, sequence, alignments, analyses etc for that gene.

  9. New synteny analysis between apple, peach, strawberry and pear

  10. Choose the synteny analysis depending on what version of the genome assembly you are working with – v2.0 or v1.1

  11. peach strawberry apple strawberry pear

  12. The Breeders Toolbox provides access to current RosBREED 1 data for strawberry. New comprehensiveBreeding Information Management System being developed in GDR

  13. Browse or search available phenotype, genotype or haplotype data

  14. 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 

  15. 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