Abstract:

Quantitative trait locus (QTL) mapping is a powerful method for identifying genetic regions associated with complex traits. The availability of high-throughput genotyping and phenotyping data has made QTL mapping a popular method for identifying the genetics of complex and quantitative traits. However, the analysis of QTLs can be challenging, especially when working with experimental populations. In such cases, R/qtl, an interactive environment for QTL mapping, can be an invaluable tool for data analysis and method, model and parameter selection. The R software interface may be difficult for beginners to use; for this reason, we propose a practical tutorial as an introduction to the use of the R/qtl package. The tutorial will cover the basics of data preparation, including the input file format and required information. Participants will also learn how to use various functions and parameters of R/qtl, including the selection of the most appropriate model for each data and methods for estimating genetic maps. The tutorial will introduce a practical example of a set of eggplant (Solanum melongena) advanced backcrosses (ABs) materials with introgressions of a wild relative, which have been phenotyped and genotyped. Once the QTL analysis is performed, R/qtl can provide a variety of useful outputs, including LOD scores of significant molecular markers, LOD, and effect plots for identified QTLs. These outputs can assist in the dissection of the genetic basis of complex traits and provide valuable information for breeding and selection programs. The practical approach will allow participants with limited programming experience to analyze their data and gain a deeper understanding of QTL mapping methods.

Keywords:

Association analysis, QTL, R/qtl, LOD score, effect plot.