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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE

Location: Plant, Soil and Nutrition Research

Title: The hordeum toolbox - the barley CAP genotype and phenotype resource

Authors
item Blake, Victoria
item Kling, Jennifer -
item Hayes, Patrick -
item Jannink, Jean-Luc
item Jillella, Suman -
item Lee, John -
item Matthews, David
item Chao, Shiaoman
item Close, Timothy -
item Muehlbauer, Gary -
item Smith, Kevin -
item Wise, Roger
item Dickerson, Julie -

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 10, 2012
Publication Date: July 19, 2012
Citation: Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.

Interpretive Summary: The paper describes the creation and use of The Hordeum Toolbox (THT), an online database and analysis tool collection. THT was developed to serve as a data repository for the multi-institution USDA-NIFA funded Barley CAP grant. Tools were created for users to define data sets of germplasm, phenotype and genotype information, and then download these data into files ready to use for association analysis or graphical genotyping. This ability to create user-defined data sets is novel and is emphasized in the paper. Other web-based analytical tools developed for THT are described and used in examples, for instance, the ‘Cluster by Genotype’ tool allows users to select germplasm that carry specific versions of genes-of-interest. Data held in THT, including the contributing breeding programs and specific phenotypic trials and locations are reported in several tables.

Technical 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. Thus, 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. THT 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.

Last Modified: 9/2/2014