Principles of QTL mapping

The purpose of the phenotyping experiment is to assign a trait value to each mapping population member. This value is then combined with the allele score at the set of marker loci distributed throughout the genome. A datafile is then created which includes all the trait data and all the marker data for the entire population.

Various software applications can be applied to this data file to identify  statistical associations between the presence of alternative alleles and the trait value.