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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Improving Barley and Wheat Germplasm for Changing Environments

Location: Genomics and Gene Discovery

2012 Annual Report


1a.Objectives (from AD-416):
A genetic database for called The Triticeae Toolbox (T3) will be created, developed, populated with all data from the USDA NIFA Triticeae CAP project, and served on the Internet for free public access. T3 will hold the experimental results from 60,000 wheat and barley lines which will be phenotyped for 100 traits and genotyped for an average of 10,000 mapped SNP markers. It will provide flexible queries for extracting desired datasets for analysis as well as integrated analytical tools.


1b.Approach (from AD-416):
Two separate databases will be implemented, T3 Wheat and T3 Barley. A server machine will be purchased, designed to optimize searching large databases, computing statistical functions on large datasets, and serving the results via Internet. Five years of system administration support will be provided for the machine including installation of required software, all security administration, data and software backup maintenance, and upgrades of hardware, software and operating system. Physical support will be provided in a server room with refrigeration, high-speed network switching and failover electric supplies.


3.Progress Report:

The Triticeae Toolbox (T3) databases for wheat and barley are now running on the GrainGenes server in Albany, California, at address http://triticeaetoolbox.org. Software enhancements have been added for the curator to load data, and for users to analyze it and to download it. The Triticeae CAP (Coordinated Agricultural Project) curator has begun loading both phenotype and genotype (molecular marker allele) data for both species. The wheat database which was initially empty, but now has both kinds of data for over 4000 wheat lines, including 25 million genotyping data points. The barley database has grown similarly, in addition to inheriting all the data from the predecessor Barley CAP project. A new, more powerful server machine purchased by the Triticeae CAP as part of the collaboration has been installed in the same server room by this project's system administrator, and became a production server as of 21 July 2012. This research is contributing to parent project Sub-objectives 1.B. (integration of genetic maps from linkage disequilibrium analysis of small grains diversity data) and 1.C. (integration of genotyping and phenotyping results, both from advanced breeding lines and germplasm collections.)


Last Modified: 7/23/2014
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