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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2013 Annual Report

1a. Objectives (from AD-416):
1. Expand “The Hordeum Toolbox” database to house wheat data and expanded genotypic data; 2. Curate data coming from the “Improving barley and wheat germplasm for changing environments” project to populate the database; 3. Develop interface tools allowing breeders to upload and download project data and data from their own breeding programs directly; and 4. Develop interfaces to analysis tools for association mapping and genomic selection.

1b. Approach (from AD-416):
1. A database called “The Hordeum Toolbox” is already hosted on GrainGenes and houses data from the past Barley Coordinated Agricultural Project. This database will be expanded to enable it to house wheat data. It will be renamed “The Triticeae Toolbox” or T3. To allow the storage or large amounts of sequence data that will be produced by the project, fields called “binary large objects” (BLOBs) will be added to the schema. 2. A dedicated data curator will be hired by the project. This data curator will communicate with all project participants to ensure timely data submission. The curator will also lead training sessions to teach participants to submit their own data using online tools. 3. Encouraging breeders to transition from storing their data in spreadsheets to a functional relational database is an important goal of the project. To that end, user-friendly interface tools will be implemented to allow breeders to use T3 to store data from their own projects. Training sessions will be organized and an online tutorial developed. 4. Statistical analysis methods to perform association mapping and genomic selection are increasingly well described and understood, but software to perform these analyses is not always available. Since the T3 database will house all of the data necessary for such analyses, it will be natural to also allow it to run some of them and provide the output in interpretable format for breeders. One of the personnel hired with the funds sought in this proposal will be responsible for integrating existing analysis software with T3.

3. Progress Report:
Implement barley genomic selection (GS). Two further cycles of selection have been performed since the last annual report. Each cycle has comprised 800 selection candidates genotyped with 384 SNP markers. In the second of these two cycles, a high number of markers have become monomorphic (they are no longer variable and thus do not provide predictive information), requiring that we develop new markers going forward. Using the TCAP database, “The Triticeae Toolbox”, phenotypic information from the selection candidates of the first cycle were added to the training population for predicting cycles 2 and 3. Improve the Triticeae Toolbox (T3) database system. The user interface and portal to access the T3 database ( continues to be enhanced and developed. User Group meetings have been convened on a regular basis using web conferencing. New features can be categorized as interface, data type, and analysis function improvements. There are new interfaces to select lines, genetic maps and for data quality control filtering. New data types include presence / absence markers, genetic characteristics of lines, and the ability to store and analyze plot-level data. New analysis functions include the ability to generate data histograms, to compare line performance in different trials, to calculate indices based on canopy spectral reflectance data, and to launch large genome-wide association studies in the background. Web analytics data show that T3 users come from 42 of the 50 US states, and that about 25% of T3 traffic is international.

4. Accomplishments

Last Modified: 10/19/2017
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