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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Research Project #435035

Research Project: Developing Bioinformatic Pipelines for Genomics-assisted Breeding using Graphical User Interfaces

Location: Sunflower and Plant Biology Research

Project Number: 3060-21000-043-19-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2018
End Date: Aug 31, 2023

Objective:
The goal of this project is to provide technicians, students, and sunflower breeders with a simplified module written in readily available software that provides prediction statistics given a phenotypic and genotypic database for sunflower lines and hybrids. The student on this project will also develop knowledge and abilities in plant breeding and phenotype data collection.

Approach:
An NDSU graduate student in the Plant Sciences Department will work with the Breeding Bioinformatics group in the department to develop genomic selection models for sunflower. This will include work with JMP genomics, and, alternatively, R packages that can handle GCA and SCA effects (multiple random effects) such as ‘BGLR’ for Bayesian GS models and ‘sommer’ for GBLUP. Statistical software will read from the sunflower project’s existing SQL databases. The work will involve working closely with USDA sunflower breeding program personnel to design a solution that is useful to other project personnel not well versed in programming. The student, who has already been hired, has training in computer science and plant breeding and will use best practices to develop the program. The student will also continue to help during the summer months with phenotype data collection and curation in the database.