GCCVision: An integrated toolkit for calculating and visualizing parental genome contribution in breeding populations

Area of Science:

• Plant genetics and breeding
• Bioinformatics tools
• Genomic analysis

Background:

• Accelerating genetic gain in plant breeding relies on tracking parental genome contributions.
• Existing methods for analyzing segregating populations can be complex and time-consuming.

Purpose of the Study:

• To introduce GCCVision, an integrated bioinformatics toolkit designed to simplify the analysis of parental genome contributions.
• To provide breeders with a user-friendly tool for visualizing genomic composition in biparental crosses.

Main Methods:

• GCCVision utilizes a Python-based backend and a web-based frontend.
• It analyzes Variant Call Format (VCF) files from biparental crosses.
• The toolkit identifies informative single-nucleotide polymorphisms (SNPs) and calculates parental contribution rates.

Main Results:

• GCCVision generates customizable graphical genotype maps color-coded by parental origin.
• It provides clear visualizations of genomic composition.
• The software streamlines the process of tracking parental genome contributions.

Conclusions:

• GCCVision assists breeders in making informed selection decisions for various breeding programs, including backcrossing and F2 analysis.
• The toolkit accelerates the development of improved crop varieties by shortening breeding cycles.
• GCCVision enhances the efficiency of quality control for hybrid seeds.