The identification of genes and quantitative trait loci (QTLs) and DNA markers that are linked to them is accomplished via QTL mapping experiments. QTL mapping thus represents the foundation of the development of markers for MAS.
Previously, it was generally assumed that markers could be directly used in MAS. However, there are many factors that influence the accuracy of QTL mapping such as population size and type, level of replication of phenotypic data, environmental effects and genotyping errors. These factors are particularly important for more complex quantitative traits with many QTLs each with relatively small effects (e.g. drought tolerance, yield).