The Triticeae Toolbox (T3) is the web portal for data generated by the Triticeae Coordinated Agricultural Project (T-CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). It also contains data from US Uniform Regional Nurseries, supported by the US Wheat and Barley Scab Initiative. The database was initially developed as The Hordeum Toolbox (THT) to hold barley data generated by the Barley CAP project (2006-2010). T3 Barley hods data generated for Hordeum vulgare L. T3 Wheat holds data generated for Triticum spp. T3 Oat holds data generated for Avena. All are being enhanced in database performance, community curation and user tools. T3 contains germplasm line information, pedigree, genotype and phenotypic data from breeding programs participating in the CAP and core germplasm collections maintained by the USDA National Small Grains Collection.
Dataset Acknowledgments9K wheat iSelect assay
The 9,000 SNP wheat iSelect assay was designed by research groups funded by the USDA National Institute of Food and Agriculture (grant CRIS0219050; PI: E. Akhunov; co-PIs: S. Chao, G. Brown-Guedira, D. See, M. Sorrells) and the Grains Research and Development Corporation (GRDC), Australia (PI: Matthew Hayden). The details of assay design can be obtained from the USDA wheat SNP development project and International Wheat SNP Working Group websites.
|Jean-Luc Jannink||USDA-ARS, NAA, RWHCAH, Ithaca, NY||Project coordinator|
|Mark Sorrells||Cornell University, Ithaca, NY||Project coordinator|
|Clay Birkett||USDA-ARS, NAA, RWHCAH, Ithaca, NY||Database programming and development|
|Clare Saied||Cornell University, Ithaca, NY||Data curator|
|Dave Matthews||Cornell University, Ithaca, NY||Database development, GrainGenes collaborator|
|Shiaoman Chao||USDA-ARS Biosciences Research Lab, Fargo, ND||SNP data production and curation|
|Peter Bradbury||USDA-ARS, NAA, RWHCAH, Ithaca, NY||Pedigree information and links to TASSEL|
|Mike Bonman||USDA-ARS, Aberdeen, ID||GRIN collaboration|
|Harold Bockelman||USDA-ARS, Aberdeen, ID||GRIN collaboration|
|Tim Close||Botany and Plant
University of California
|Assembly and SNP context information from HarvEST: Barley|
|T-CAP Participants||Throughout the U.S.A.||Data collection and contribution|
|Julie A. Dickerson||Electrical and Computer Engineering, Iowa State University||Principal Investigator|
|Roger P. Wise||USDA-ARS|
Department of Plant Pathology
Iowa State University
|Jennifer Kling||Dept. of Crop and Soil Science Oregon State University||Phenotype and pedigree data curation|
|Shreyartha Mukherjee||Bioinformatics and Computational Biology, Iowa State University||Developer/Bioinformatics|
|Kartic Ramesh||Computer Science, Iowa State University||Developer|
|Gavin Monroe||Software Engineering, Iowa State University||Developer|
|Ethan Wilder||Computer Engineering, Iowa State University||Developer|
|Yong Huang||Bioinformatics and Computational Biology, Iowa State University||Developer/Bioinformatics|
CollaboratorsThe James Hutton Institute Development Team (David Marshall, Paul Shaw)
PLEXdb Development Team at Iowa State University (Ethy Cannon and Sudhansu Dash)
Gramene Database (Doreen Ware)
GrainGenes Database (David Matthews) USDA/ARS, Cornell University
Software availabilityThe T3 software is available under the GNU General Public License (LICENSE) and may be downloaded from GitHub.
It requires Linux, Apache, MySQL, and PHP. Details are in the INSTALL document.
A list of recent changes to the T3 software are in the Change Log document.
The database schema in .sql format is here. Graphical diagrams are available in MySQL Workbench (.mwb) format and .png format.