Resources for genomics, genetics and breeding research in GDR, the Genome Database for Rubus

Authors: Bassil, Nahla; JUNG, SOOK - Washington State University; LEE, TAEIN - Washington State University; CHENG, CHUN-HUAI - Washington State University; ZHENG, PING - Washington State University; BUBBLE, KATHERYN - Washington State University; YU, JING - Washington State University; HUMANN, JODI - Washington State University; HOUGH, HEIDI - Washington State University; MAIN, DORRIE - Washington State University

Submitted to: International Rubus Ribes Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2023
Publication Date: 7/20/2023
Citation: Bassil, N.V., Jung, S., Lee, T., Cheng, C., Zheng, P., Bubble, K., Yu, J., Humann, J., Hough, H., Main, D. 2023. Resources for genomics, genetics and breeding research in GDR, the Genome Database for Rubus. International Rubus Ribes Symposium.

Interpretive Summary: The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is a comprehensive online resource dedicated to facilitate basic, and applied research for crops in the Rose Family, including red raspberry, black raspberry, and blackberry. It aims to provide a one-stop platform that offers integrated data, accessible through user-friendly web interfaces and tools. GDR offers a wide range of curated and integrated data, including genome sequences, genes, genetic maps, markers, traits, germplasm, and publications, made accessible to browse, query and download through easy-to-use web interfaces and tools. Whole genome sequence data, along with functional annotation provided by the GDR team, are available for the three versions of the black raspberry genome, two cultivars of red raspberry (Joan J and Anitra), and one blackberry cultivar (Hillquist). Whole genome data for a traditional Chinese medicinal plant in this genus is also available. Various tools are provided to facilitate data access and analysis. For breeders, GDR offers the Breeding Information Management System (BIMS), a secure and comprehensive management system that aids in the organization and handling of breeding-related information. In this presentation, we will highlight new features and future development as well as provide an overview of existing resources in GDR for research in these berry crops.

Technical Abstract: The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is a comprehensive online resource dedicated to facilitate basic, translational and applied research for rosaceous crops, including Rubus crops such as red raspberry, black raspberry, and blackberry. It aims to provide a one-stop platform that offers integrated data, accessible through user-friendly web interfaces and tools. GDR offers a wide range of curated and integrated data, including genome sequences, genes, transcripts, orthologs, genetic maps, markers, QTL, traits, germplasm, and publications, made accessible to browse, query and download through easy-to-use web interfaces and tools. Whole genome assembly data, along with functional annotation provided by the GDR team, are available for the three versions of the blackberry genome Rubus occidentalis, two cultivars of red raspberry Rubus idaeus (Joan J and Anitra), and black raspberry Rubus argutus Hillquist. Whole genome data for Rubus chingii Hu, a traditional Chinese medicinal plant, is also available. Various tools are provided to facilitate data access and analysis. Users can utilize search pages, BLAST, and JBrowse to explore the genome data. MegaSearch allows powerful and flexible searches across all data types in GDR, enabling users to build datasets based on different categories and customize data fields for viewing and downloading. Conserved syntenic regions across rosaceous genomes, identified using MCScanX, are accessible through the synteny viewer and ortholog/paralog search, facilitating data transfer across species. GDR also provides pathway data through RubusCyc, which is constructed using predicted genes from the Rubus occidentalis v3.0 genome assembly via PathwayTools. For breeders, GDR offers the Breeding Information Management System (BIMS), a secure and comprehensive management system that aids in the organization and handling of breeding-related information. In this presentation, we will highlight new features and future development as well as provide an overview of existing resources in GDR for Rubus research.