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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2012 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:
Start barley genomic selection (GS). 48 crosses were made by our collaborator in fall 2010 to construct the cycle 1 population for the winter barley GS breeding project. We trained genomic selection models on agronomic, winter hardiness, disease, and grain quality traits obtained from the Barley CAP. 800 progeny were developed and their performance predicted using these models. Selections were made based on these predictions and they have been crossed. Progeny were also plant in head rows in the fall of 2011. A correlation of 0.5 was observed between predicted and observed winter survival. Improve the Triticeae Toolbox (T3) database system The user interface and portal to access the T3 database ( has been enhanced and developed. An improved link between T3 and the analysis package TASSEL has been made such that TASSEL can be called directly from T3. We have improved visualization of clustering based on genotypes. All the while improvements in the efficiency of the database have been made and provisions to include more and more types of marker data. Six User Group meetings have been convened using online meeting software over the course of the year.

4. Accomplishments

Last Modified: 05/28/2017
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