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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2011 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
To start barley genomic selection (GS), 48 crosses were made by our collaborator last fall to construct the cycle 1 population for the winter barley GS breeding project. The parental lines were genotyped with 1,536 SNPs. We analyzed the crosses and SNPs to identify an optimal subset of 384 SNP. We have trained different genomic selection models on agronomic, disease, and grain quality traits obtained from the Barley CAP. In cross-validation tests, correlation between the predicted and observed phenotypes ranged between 0.5 (for yield) and 0.7 (for plant height) using training populations of 300 individuals. Steps were also made to improve the Triticeae Toolbox (T3) database system. The entry web site for T3 was developed at It links to The Hordeum Toolbox for barley and to a functionally identical wheat database for wheat. The following improvements have been implemented or will shortly be ready: 1. Database programmer hired to work on line selection based on clustering genotypic data, haplotype searches, and to implement downloads in new formats enabling use by other analysis platforms. 2. A data curator hired to debug and document upload procedures to the database using XL templates and upload and assure quality of datasets coming in from other collaborators. 3. A user group has been assembled to propose, describe, and prioritize data access, analysis, and visualization tools, test new applications and identify educational needs.

4. Accomplishments

Last Modified: 2/23/2016
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