Abstract
Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the acreage. These requirements for improved plant cultivars can be supported by the broader exploitation of plant genetic resources (PGR) as inputs for genomics-assisted breeding. To support this process we have developed BRIDGE, a data warehouse and exploratory data analysis tool for genebank genomics of barley (Hordeum vulgare L.). Using efficient technologies for data storage, data transfer and web development, we facilitate access to digital genebank resources of barley by prioritizing the interactive and visual analysis of integrated genotypic and phenotypic data. The underlying data resulted from a barley genebank genomics study cataloging sequence and morphological data of 22,626 barley accessions, mainly from the German Federal ex situ genebank. BRIDGE consists of interactively coupled modules to visualize integrated, curated and quality checked data, such as variation data, results of dimensionality reduction and genome wide association studies (GWAS), phenotyping results, passport data as well as the geographic distribution of germplasm samples. The core component is a manager for custom collections of germplasm. A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic data in MIAPPE-compliant ISA-Tab files. BRIDGE is accessible at the following URL: https://bridge.ipk-gatersleben.de.
Highlights
Cereal grasses like barley, rye and wheat are the main nutrition source for human calorie intake in the world (FAO, 2018)
Except for the parameter “perplexity” the function was called with default the TSNE() function, the variant call format (VCF) file was converted into a NumPy values for all parameters
Much of BRIDGE has been designed with a novice user in mind and we guide them with our interactive help function
Summary
Rye and wheat are the main nutrition source for human calorie intake in the world (FAO, 2018). The necessary continued crop improvement can be achieved by modern plant breeding methods like marker assisted selection (Varshney et al, 2005; Crossa et al, 2017), reverse breeding (Dirks et al, 2009), and genome engineering/editing (Voytas and Gao, 2014). These methods allow to increasingly benefit from the putative advantageous alleles of the PGRFA, which have not yet been used in recent breeding efforts. Based on the integrated datasets of these information systems, decisions for the optimization of the breeding process and curation of passport data can be derived
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