Skip to main content
ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #411369
Research Project: Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources

Location: National Clonal Germplasm Repository

Title: Genome database for vaccinium: A community resource for genetics, genomics, and breeding research

Author
item HUMANN, JODI - Washington State University
item CHENG, CHUN-HUAI - Washington State University
item LEE, TAIEN - Washington State University
item BUBLE, KATHERYN - Washington State University
item ZHENG, PING - Washington State University
item JUNG, SOOK - Washington State University
item YU, JING - Washington State University
item GASIC, KSENIJA - Clemson University
item RU, SUSHAN - Auburn University
item Bassil, Nahla
item IORIZZO, MASSIMO - North Carolina State University
item MAIN, DORRIE - Washington State University

Submitted to: International Vaccinium Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2024
Publication Date: 8/24/2024
Citation: Humann, J., Cheng, C., Lee, T., Buble, K., Zheng, P., Jung, S., Yu, J., Gasic, K., Ru, S., Bassil, N.V., Iorizzo, M., Main, D. 2024. Genome database for vaccinium: A community resource for genetics, genomics, and breeding research. International Vaccinium Symposium.

Interpretive Summary:

Technical Abstract: The Genome Database for Vaccinium (GDV, www.vaccinium.org) is an online, community database that enables translational Vaccinium research in genetics, genomics, and breeding by providing tools and published data in one central resource. The database contains curated genetic maps, genetic markers, quantitative trait loci, and genome data from published manuscripts which are searchable through customizable interfaces. GDV includes tools to view genetic maps (MapViewer), genome annotations (JBrowse), synteny (SyntenyViewer) metabolic pathways (PathwayTools), gene expression levels (Expression Heatmap Tool), as well as a BLAST tool for searching genome, transcriptome, and marker sequences. Structural graph data, along with the genome sequences from the Vaccinium Pangenome Project are also available to view and search using tools on GDV. Embedded in GDV is the Breeding Information Management System (BIMS). It can be used to view and search the Vaccinium USDA-GRIN phenotype data and manage private breeding programs. GDV also serves as a community information hub through access to the VacCAP project (www.vacciniumcap.org). The tools and resources available on GDV are based on user input and needs of the research community. Community feedback is always welcome.