Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-053-000-D
Project Type: In-House Appropriated
Start Date: Apr 1, 2023
End Date: Mar 31, 2028
Objective:
Objective 1: Conduct research to simplify getting data into T3 and to expand T3 functionality for users.
Sub-objective 1.A: Sample tracking with the small grains genotyping labs.
Sub-objective 1.B: Data upload through Android Field Book, Coordinate, and Intercross apps.
Sub-objective 1.C: Spatial analysis of individual field trials.
Sub-objective 1.D: Target population of environments (TPE) determination.
Sub-objective 1.E: Determine the value to selection gain from weighting field evaluations by their genetic correlation to the long-run TPE average.
Sub-objective 1.F: Genomic mate selection (GMS).
Objective 2: Develop and incorporate analyses into T3 that strengthen initial data curation.
Sub-objective 2.A: Practical haplotype graph incorporation.
Objective 3: Strengthen T3 interoperability with other biological databases.
Sub-objective 3.A: Creation of private instances of T3.
Sub-objective 3.B: Ensure T3 remains compliant with the BrAPI specification
Objective 4: Assemble a T3 User Group to advise developers on advances in the breeding process and on data management feature needs.
Sub-objective 4.A: Host a meeting of the T3 Advisory User Group (TAUG) twice each year.
Approach:
Research and development work on Objective 1 to simplify getting data into T3 and to expand T3 functionality includes some small subobjectives and some larger ones. We will develop interfaces to track samples coming from the small grains genotyping labs and to better interface with digital data acquisition devices like tablet apps. We will add functionality to run spatial analyses on phenotyping trials that have field layouts. These features will culminate in better data to determine target populations of environments (TPE) for breeding programs. With the TPE defined, we will seek to use multi-year and multi-location trail data to better weight data from trials in for selection. Finally, we will implement genomic mate selection.
Work on Objective 2 really focuses on harmonizing marker data across genotyping platforms or protocols. We will do this by integrating the practical haplotype graph into T3. Over time, we have come to acknowledge that breeders do not always want their data to be made public rapidly. In Objective 3 to avoid that putting data into T3 forces that, we will create private instance of T3. Nevertheless, to ensure ongoing T3 interoperability with open-source breeding data analysis packages, we will ensure that T3 remains compliant with the BrAPI specification.
Finally, we know T3 has faults that we are not fully aware of. To better appreciate and be able to address these faults, in Objective 4, we will assemble a T3 User Group to advise developers on advances in the breeding process and on data management feature needs. We will convene this group twice each year.
