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ARS Home Northeast Area Ithaca, New York Robert W. Holley Center for Agriculture & Health Plant, Soil and Nutrition Research Research Publications at this Location





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Title:   Author  item
                                            Blake, Victoriaitem
                                            KLING, JENNIFER - Oregon State Universityitem
                                            HAYES, PATRICK - Oregon State Universityitem
                                            Jannink, Jean-Lucitem
                                            JILLELLA, SUMAN - Iowa State Universityitem
                                            LEE, JOHN - Former ARS Employeeitem
                                            Matthews, Daviditem
                                            Chao, Shiaomanitem
                                            CLOSE, TIMOTHY - University Of Californiaitem
                                            MUEHLBAUER, GARY - University Of Minnesotaitem
                                            SMITH, KEVIN - University Of Minnesotaitem
                                            Wise, Rogeritem
                                            DICKERSON, JULIE - Iowa State University
  Submitted to: The Plant Genome
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 7/10/2012
                                    Publication  Date: 7/19/2012
                                    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.


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