Welcome to the first issue of the GDR newsletter in 2015. This newsletter is issued to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news via http://www.rosaceae.org/contact.
- Funding and Governance
- New genome assemblies and annotations
- New gene database
- New map, marker and QTL data
- New Malus species data and photos of Malus germplasm
- New search interfaces for haplotype data
- Updates in data submission page
- New page for downloading GDR presentation
- New page for data contributors
- Work in progress
- Employment opportunities
- Community News
- GDR will be continuously supported by new grants from the USDA NIFA Specialty Crop Research Program (2009-2019), USDA NIFA National Research Support Project 10 (2014-2019), and the Washington Tree Fruit Research Commission (2008-2016), as well as by Clemson University, University of Florida and Washington State University.
RosEXEC will be the official steering committee for GDR. Quarterly reports are submitted to the committee ahead of the quarterly RosEXECs meetings.
2. New genome assemblies and annotations
- Prunus persica Genome V2.0.a1 (IPGC 2015): View assembly in GBrowse/JBrowse, search genes from gene/sequence search page, access assembly with annotations and the GDR functional annotations from the genome page, or access through NCBI BLAST or Batch BLAST tools.
- Fragaria vesca Genome V1.1.a2 (Darwish et al., 2015): View assembly in GBrowse/JBrowse and access assembly with annotations from the genome page.
- Fragaria vesca Genome V2.0.a1 (Tennessen et al., 2014): View assembly in GBrowse/JBrowse and access assembly with annotations from the genome page.
- Malus x domestica V3.0.a1 View assembly in GBrowse and access assembly with annotations from the genome page.
- Genes with gene symbol, assigned by individual investigators, usually with known or predicted function or phenotype, can be searched in gene search page or sequence search page. These genes with gene symbols in GDR are obtained by parsing NCBI nr database and submission from individual investigators. The gene sequences are aligned to the reference genomes when possible, and also directly linked to the corresponding predicted genes when assigned by individual investigators.
- Genes predicted from the whole genome assembly can be searched in sequence search page.
To facilitate standardization of gene names, gene naming guidelines, put together by Rosaceae Gene Name Standardization Subcommittee of RosIGI, is available in GDR. The current list of Gene Class symbols and the template to submit the gene/gene class data are also available from GDR.
7. Updates in data submission page
Templates and guidelines for gene/gene class data and whole genome data are available in the data submission page, in addition to templates for genetic map data, QTL map data, diversity data and breeding data.
GDR and related presentations can be downloaded in presentations page.
- Addition of more map, marker and QTL data: We are continuously adding more map, marker and QTL data from publications to keep up-to-date database.
- Developing a new annotation for Fragaria vesca Genome V2.0.a2: A consensus gene set of V2.0.a1 and genes from V1.1.a2 will be developed using our GenSAS program.
- Peach breeder Ksenjia Gasic (GDR CoPI) is evaluating the use of the FieldBook App (from Jesse Polands lab) for electronic recording of tree fruit breeding data.
- A breeding tools needs assessment workshop (afternoon of July 30th, 2015) is being organized by the GDR team in conjunction with the National Association of Plant Breeders annual meeting (Pullman, WA, July 27-30).
- We are modifying the breeders toolbox to provide better interfaces and also converting to Tripal to share with other databases.
- Working on converting the breeders toolbox to Tripal and adding more functionality
- We are developing further terms for Trait Ontology to describe Rosaceae traits.
Funding: “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars project” has been funded from USDA NIFA Specialty Crop Research Program (2009-2019). For more information contact Amy Iezzoni of Michigan State University or Cameron Peace of Washington State University.
- XIV Eucarpia Symposium on Fruit Breeding and Genetics will be held in Bologna, Italy on June 14-18, 2015
- ASHS 2015 Annual Conference will be held in New Orleans, Louisiana, USA on August 4–7, 2015
- The 8th International Rosaceae Genomics Conference is scheduled to be held in Angers, France in June, 2016. More details will be posted in the GDR conferences page as they become available.