GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data

Authors: WILKEY, ANDREW - OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION (ORISE); BROWN, ANNE; Cannon, Steven; Cannon, Ethalinda

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/9/2020
Publication Date: 11/23/2020
Citation: Wilkey, A., Brown, A.V., Cannon, S.B., Cannon, E.K. 2020. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. Biomed Central (BMC) Genomics. 21. Article 822. https://doi.org/10.1186/s12864-020-07217-2.
DOI: https://doi.org/10.1186/s12864-020-07217-2

Interpretive Summary: Plant breeders and other researchers work with diverse genetic material in order to combine desirable genetic features from two or more varieties. Determining how two varieties differ is challenging. This work describes a software program, GCViT (Genotype Comparison Visualization Tool) for viewing the genetic locations of differences between two or more varieties of organisms across all chromosomes. The software can be used with any species that has the right kind of genetic variant data. It can be used in a stand-alone instance on a private workstation, or in online instances. Online instances for the software are available for soybean, chickpea, common bean, peanut, and maize (corn). This software will help researchers to identify regions of interest for breeding projects and other basic research.

Technical Abstract: Large genotyping data sets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping data sets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such data sets, to assess characteristics such as overall differences between accessions, and regional anomalies across the genome. This work describes GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping data sets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or in stand-alone instances for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among selected accessions, identifying allele differences and similarities between accessions and a user selected reference, with visualizations through histogram, heat map, or haplotype views. Resulting analyses and images can be exported in various formats. This software will help researchers to identify regions of interest for breeding projects and other basic research.