Visualization and visual analytics tools for improved crop breeding
Term: 4 years, starting in 2020
Status: Ongoing
Funding Amount: $110,918
Lead Researcher(s): Dr. Carl Gutwin (University of Saskatchewan)
Funding Partners: Western Grains Research Foundation, Saskatchewan Ministry of Agriculture -Agriculture Development Fund (ADF)
Project Description
The main problems with current tools for visualizing crop genetics and supporting marker-assisted selection are the: lack of availability and usability for real-world breeding programs, lack of explicit support for polyploidy crops including wheat (whole-genome duplication), and lack of scalability to the size of datasets that are now available. Thus, this project will focus on developing new visual-analytics tools for Saskatchewan crop breeders using genomic data from four important Saskatchewan crop including wheat, that will improve marker-based selection and genomic exploration to a greater extend.
The researchers will design and build new visualization tools for the breeders and genomicists to identify candidate markers to better understand the gene expression and mechanisms of control over crop traits. Several new tools will be developed in the following three areas: Tools to show and compare markers and genetic variation; Tools for visualizing and comparing duplicated genes (to show similarities across multiple species, and will add capabilities to support tasks for breeders of polyploid crops in understanding where genes are duplicated, comparing gene function across these sites, and investigation of multiple lines simultaneously); and Tools for big-data analytics (that can efficiently show huge networks and allow breeders to interact with the data, enabling new kinds of research hypotheses and new discoveries about how genes control desired traits).
The new tools will allow breeders to efficiently use marker-assisted selection, planning crosses, selecting lines and adding traits more quickly, which will accelerate the development of new varieties.