The Hordeum Toolbox: The Barley Coordinated Agricultural Project Genotype and Phenotype Resource

Abstract

The use of DNA markers in public sector plant breeding is now the norm. Such markers are common across breeding programs and this commonality enables and enhances collaboration. Therefore, large collaborative research projects that measure several phenotypes across multiple environments coupled with the expanding amount of genotype data attainable with current marker technologies are on the rise and these projects demand efficient data delivery. However, development of computational tools for advanced data integration, visualization, and analysis is still a bottleneck, even though these resources have the greatest potential impact for users who are extracting and developing hypothesis-based solutions. The Hordeum Toolbox (THT) was developed as a data resource for the Barley Coordinated Agricultural Project (CAP) with the novel capability of constructing user-defined downloadable sets of phenotype and/or genotype data for downstream analysis. Internal tools in THT enable users to create clusters of a selected group of lines based on genotype data, parse pedigrees, and select germplasm based on haplotype, phenotype, and agronomic properties. The Hordeum Toolbox can be adapted to breeding programs or collaborations to assist researchers in germplasm selection, genotype data visualization, and the integration of complex data sets for statistical analysis.