The Triticeae Toolbox (T3): New Improvements in Data Delivery and Analysis Tools

The Triticeae Toolbox (T3; http://www.triticeaetoolbox.org) is the public Web database for phenotype and genotype data generated by the US Triticeae Coordinated Agricultural Project (T-CAP; http://www.triticeaecap.org).  There are two independent T3 databases, for barley and wheat.  In addition to the experimental results, T3 contains documentation about the molecular markers used (SNPs) and the germplasm lines evaluated, which include elite lines from breeding programs participating in the T-CAP, core germplasm accessions from the USDA National Small Grains Collection, and nested association mapping (NAM) populations.  More than 75 quantitative agronomic, disease and quality traits have been evaluated in multi-location trials for each crop.  T3 Barley currently holds over 230K phenotype and 33M genotype data points, and T3 Wheat has ca. 140K phenotype and 25M genotype values.  New features in 2012 are 1) a streamlined selection wizard for phenotype/genotype datasets; 2) ability to open the TASSEL analytical software directly using the currently selected data; 3) a download format suitable for import into 'R'; and 4) a BLAST interface to find genotyping markers based on sequence similarity.  Features in development include tools for genomic association and prediction.  T3 is funded by the National Institute for Food and Agriculture (NIFA) of the USDA.