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

## TL;DR

GCCVision is a new tool that helps plant breeders track and visualize how much DNA comes from each parent in offspring, speeding up crop improvement.

## Contribution

GCCVision introduces an integrated toolkit combining a Python backend and web-based frontend for analyzing and visualizing parental genome contributions in plant breeding.

## Key findings

- GCCVision processes VCF files from biparental crosses to calculate parental genome contributions.
- The tool generates customizable genotype maps with color-coded chromosome segments by parental origin.
- GCCVision streamlines breeding decisions like backcrossing and F2 analysis, reducing breeding cycles.

## Abstract

Tracking parental genome contributions in segregating populations is crucial for accelerating genetic gain in plant breeding. We introduce GCCVision (Genome Contribution Calculator and Visualizer), an integrated bioinformatics toolkit to simplify this process. GCCVision uses an efficient Python-based backend and a user-friendly web-based frontend to analyze Variant Call Format (VCF) files from biparental crosses. The software identifies informative single-nucleotide polymorphisms (SNPs), calculates parental contribution rates, and generates clear, customizable graphical genotype maps where chromosome segments are color-coded by parental origin. By providing clear visualizations of genomic composition, GCCVision assists breeders in selection decisions for backcrossing, F2 analysis, quality control of hybrid seeds, and other breeding programs. This streamlined workflow shortens breeding cycles and accelerates the development of improved crop varieties.

•An integrated toolkit for parental genome contribution analysis•Directly processes standard VCF files from biparental crosses•Combines a Python backend with an interactive web-based visualizer•Streamlines selection in breeding programs like backcrossing and F2 analysis

An integrated toolkit for parental genome contribution analysis

Directly processes standard VCF files from biparental crosses

Combines a Python backend with an interactive web-based visualizer

Streamlines selection in breeding programs like backcrossing and F2 analysis

Biocomputational method; Genomic analysis; Plant bioinformatics; Plant genetics; Techniques in genetics