Abstract:

The development of experimental populations, such as introgression lines (ILs), is crucial for studying traits of interest in plant breeding. Efficient selection and identification of desirable traits in these populations require a correct visualization of plant genotyping data. However, obtaining graphical genotypes of chromosomes with different introgressions can be complex and challenging due to the amount of data points and the need to have the data in the appropriate format for each software used in the analysis. To address this issue, we present a step-by-step guide on how to generate chromosome graphical genotypes with different introgressions using the Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) and the Graphical GenoTypes (GGT2) software. Our approach uses as a case study the genotyping of a set of advanced backcrosses (ABs) with introgressions from an eggplant wild relative in the background of cultivated eggplant (Solanum melongena) to visualize the 12 chromosomes of the eggplant genome. In the tutorial, we provide images of the programs to facilitate their use, and we explain the parameters to choose the best one for each analysis and visualization. First, the filtering of the genotyping data is performed using TASSEL to identify the introgressions of interest. Then, the GGT2 software is used to generate a graphical representation of the chromosomes with the introgressions marked. The tutorial also includes essential information on the necessary intermediate adaptation between the two software, practical examples, and tips to overcome common challenges during the process. This guide is aimed at students with basic knowledge of genotyping data analysis and bioinformatic tools. The methodology presented can help to improve the accuracy and efficiency of chromosome graphical genotypes generation for studies related to plant breeding, genome evolution, and genetic diversity.

Keywords:

Chromosome, introgression, TASSEL, GGT2, data visualization.