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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 » Publication #331998
Title: The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding

Author
item BLAKE, VICTORIA - Montana State University
item Birkett, Clayton
item Matthews, David
item HANE, DAVID - University Of California
item Bradbury, Peter
item Jannink, Jean-Luc

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2015
Publication Date: 6/15/2015
Citation: Blake, V., Birkett, C.L., Matthews, D.E., Hane, D., Bradbury, P., Jannink, J. 2015. The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding. The Plant Genome. doi: 10.3835/PlantGenome2014.12.0099.

Interpretive Summary: The Triticeae Toolbox (http://triticeaetoolbox.org; T3) is a database with a web-base user interface that enables plant breeders and researchers to find, combine, and visualize the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP). T3 enables users to define specific data sets for download in formats compatible with the external tools or to analyze on the T3 server for operations such as Genome Wide Association and Genomic Prediction. New T3 tools to assist plant breeders include a Selection Index Generator, analytical tools to compare phenotype trials using common or user-defined indices, and a histogram generator for nursery reports, with applications using the Android OS, and a Field Plot Layout Designer in development. Researchers using T3 can design training sets for genomic prediction, define core germplasm sets, and perform multivariate analysis. An increased collaboration with GrainGenes and integration with small grains reference sequence resources facilitate users generating hypotheses about their datasets and following these up by accessing publicly available genomic information with instant access to knowledge databases for wheat and barley. T3 software is available under the GNU General Public License and is freely downloadable.

Technical Abstract: The Triticeae Toolbox (http://triticeaetoolbox.org; T3) is the database schema 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 enables users to define specific data sets for download in formats compatible with the external tools TASSEL, Flapjack, and R; or to use by software residing on the T3 server for operations such as Genome Wide Association and Genomic Prediction. New T3 tools to assist plant breeders include a Selection Index Generator, analytical tools to compare phenotype trials using common or user-defined indices, and a histogram generator for nursery reports, with applications using the Android OS, and 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 the small grains 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.