The Triticeae Toolbox (T3): From the Ground Up

The Triticeae Toolbox (http://triticeaetoolbox.org; T3) are two distinct databases for wheat and barley enabling plant breeders and researchers to combine, visualize and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP). T3 users can use in-house software for ‘Genome Wide Association’ and ‘Genomic Prediction’, to identify germplasm carrying favorable alleles through a ‘Search by Haplotype’ tool, to visualize genetic relatedness of a population through the ‘Cluster by Genotype’ tool in 2D or 3D, and more. User-defined data sets combining phenotype trial results with run-specific or consensus genotyping scores can alternatively be downloaded from T3 in formats compatible with the external tools TASSEL, Flapjack, and R. T3 tools to assist plant breeders include a ‘Selection Index Generator’ and applications using the Android OS, with a ‘Field Plot Layout Designer’ in development. Researchers using T3 will soon enjoy the ability to design training sets, define core germplasm sets and perform multivariate analysis. An increased collaboration with GrainGenes and integration with reference sequence resources will place T3 in a pivotal role for on-the-fly data analysis with instant access to the knowledge databases for wheat and barley. T3 software is available under the GNU General Public License and is freely downloadable from github.  An overview of the advanced T3 tools and installation requirements for installing a T3-like database will be discussed.  TCAP and T3 are supported by the Agriculture and Food Research Initiative Competitive Grant no. 2011-68002-30029 from the USDA National Institute of Food and Agriculture (NIFA).