BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics.
Patrick König1, Sebastian Beier1, Martin Basterrechea1
1Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
Frontiers in Plant Science
|June 30, 2020
Summary
Genebanks hold valuable plant genetic resources (PGR) crucial for developing climate-resilient crops. The BRIDGE tool enhances access to barley genomics data, integrating genetic and phenotypic information for improved breeding strategies.
Area of Science:
- Agricultural Science
- Genomics
- Bioinformatics
Background:
- Genebanks preserve vital plant genetic diversity essential for crop improvement.
- Climate change and population growth necessitate the development of stress-resistant cultivars.
- Genomics-assisted breeding requires accessible and integrated plant genetic resources (PGR).
Purpose of the Study:
- To develop BRIDGE, a data warehouse and exploratory analysis tool for barley genebank genomics.
- To facilitate interactive and visual analysis of integrated genotypic and phenotypic data for barley.
- To support the broader exploitation of PGR for developing improved plant cultivars.
Main Methods:
- Developed BRIDGE using efficient data storage, transfer, and web technologies.
- Integrated and curated sequence, morphological, passport, and phenotyping data for 22,626 barley accessions.
- Implemented interactive modules for data visualization, germplasm collection management, and data export.
Main Results:
- BRIDGE provides access to a comprehensive dataset of barley genotypic and phenotypic information.
- The tool visualizes variation data, dimensionality reduction results, GWAS, phenotyping, and geographic distribution.
- Includes modules for searching germplasm and exporting data in VCF and ISA-Tab formats.
Conclusions:
- BRIDGE enhances the utilization of barley genebank resources for genomics-assisted breeding.
- Facilitates interactive exploration of integrated genetic and phenotypic data.
- Supports the development of improved, stress-resistant barley cultivars to meet agricultural demands.
Keywords:
barleydata visualizationdata warehousegenebank genomicsgenotypingphenotypingplant genetic resourcesvisual analyticsMore Related Videos
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