Article ID: 25J01
Genomic information is inherently large and complex, making it difficult to understand the big picture based on polymorphism data alone. We have developed “Genome Painting”, a Python and R-based visualization method, to address this issue. This tool compares the genomes of two rice varieties to the ‘Nipponbare’ reference genome, representing the twelve chromosomes as rectangles and polymorphisms as colored lines. The method uses VCF (Variant Call Format) files to visualize and compare polymorphisms between specific varieties. This tool enabled more accurate identification of substitution regions containing target genes and residual genetic background in near-isogenic lines. By comparing visualizations between pedigrees, it facilitated the understanding of gene and genetic region transfer. It also enabled the discovery of new correlations and relationships by analyzing genomic relationships between varieties. This comprehensive visualization approach improves the accessibility of whole genome data for rice breeders in the selection and variety evaluation processes. It also provides rice geneticists and molecular biologists with a tool to better understand and interpret complex genomic information. “Genome Painting” thus bridges the gap between complex genomic data and its practical application in rice breeding and research.
