Difference Between QTL and GWAS
Whereas QTL contain many linked genes, which are then challenging to separate, GWAS produce many unlinked individual genes or even nucleotides, but these studies are riddled with large expected numbers of false positives.
What is QTL mapping used for?The primary purpose of QTL mapping is to localize chromosomal regions that significantly affect the variation of quantitative traits in a population. This localization is important for the ultimate identification of responsible genes and also for our understanding of genetic mechanisms of the variation.