Visualization and visual analytics tools for improved crop breeding

Posted on 22.02.2021 | Last Modified 10.04.2024
Lead Researcher (PI): Carl Gutwin
Institution: University of Saskatchewan
Total WGRF Funding: $110,917
Co-Funders: Agriculture Development Fund, Saskatchewan Wheat Development Commission
Start Date: 2020
Project Length: 4 Years

To develop tools for marker-based breeding and comparative genomic analyses in crop genomes. To develop tools for visualizing synteny (duplicated regions) within and between crop genomes. To develop tools for big-data analysis of connection networks.

Project Summary:

Genomic data in agriculture is being generated at an unprecedented rate due to the emergence of new sequencing systems. The increased availability of high-resolution genomic data has aided researchers and breeders in tackling a range of questions in crop development. The overall goal of this research project is to develop new tools for visualizing crop genetics that are usable by breeders and genomic researchers, and that are valuable for breeding programs that involve major Saskatchewan crops. We have created new tools in close collaboration with several breeder and genomic-research groups to advance the science of genomics and plant breeding. The motivating problem for this research is that although many genomic visualization systems exist, few are capable of supporting the interactive exploration that is now required in a modern genomic-focused breeding program. Within this context, we developed new visualization tools in four areas that provide interaction techniques to support exploration and complex analyses. The four areas are: visualizing synteny, comparative genomic analyses, tools for marker-assisted breeding, and tools for big-data genomic analysis. Over the course of the project, we have identified new requirements for interactive genomics visualization systems, and have developed more than a dozen web-based applications to support these objectives. The tools are freely available to breeders and researchers, and are deployed at the website

Extension Messages

• Genomics visualization tools are increasingly become an integral part of crop breeding programs
• Interaction with visualization systems is becoming an important part of genomic analysis
• Close collaboration with breeder and genomic-research teams is critical for understanding the specific interaction requirements for the development of new tools in the genomics domain
• We have provided several freely-available tools at