2013 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.
The Triticeae Toolbox (T3) databases for wheat and barley are now running on the GrainGenes server in Albany, California, (http://triticeaetoolbox.org). Extensive modifications to the T3 database have added more utility in being able to compare breeding lines with trait data. The interface now makes good use of statistical programs which allow select data selection and analysis. The Triticeae CAP (Coordinated Agricultural Project) curator has begun loading both phenotype and genotype (molecular marker allele) data for both species. The TCAP projects also yielded an increase in datasets for wheat and barley including many National Small Grains Collection datasets; over 25 million genotyping data points have been collected each for wheat and barley representing over 390 thousand phenotypes scores. Many of these studies may have utility in germplasm improvement; basically accessed by the research public and using interactive tools via the web browser interface. Efforts have also moved forward to formalize the data set vocabulary describing the trait phenotypes and software enhancements have been added for efficient curator activities to load data and curate data. Users can now download their analyses after using the on-board interactive tools. A new, more powerful server machine purchased by the Triticeae CAP as part of the collaboration has been installed within the GrainGenes project server room. This research is contributing to parent project Objectives 2. (Integrate genotyping and phenotyping results from the Triticeae Coordinated Agricultural Project (T-CAP) including the T3 database, the National Small Grains Collection and GRIN database, and Gramene, to enhance support for trait analysis by association mapping and trait improvement by genomic selection).