Basis of QTL Detection
Let’s assume that the same chromosome region contains three loci. M1 and M2 are molecular marker loci that flank a QTL (Fig. 2). For the QTL to be detected, both the QTL and a nearby marker must be polymorphic, that is, the parents must have detectable differences in alleles at those loci.
In the case shown here (Fig. 3), the QTL can be detected because the M1 marker and the QTL are both polymorphic, as shown by different colored bars on the chromosomes. Ideally, M2 or another nearby locus would also be polymorphic.
In this case (Fig. 4), the QTL cannot be detected because neither marker is polymorphic, even though the QTL is polymorphic.
In that situation, one could continue screening additional markers in the vicinity to find one that was polymorphic, as shown by M3 (Fig. 5).
In the situation shown here (Fig. 6), the QTL cannot be detected because the QTL is not polymorphic (both parents have the same allele), even though the flanking markers are both polymorphic.
Another necessary condition for QTL detection is linkage disequilibrium, the tendency for linked alleles to be inherited together in a population rather than to be randomly distributed. This means that the parent A allele at a marker will tend to be inherited together with the parent A allele at a linked QTL. Therefore, a marker can serve as a reliable indicator of the presence of the favorable QTL allele. Because linkage disequilibrium decreases slowly, most mapping populations involving up to a dozen generations will have sufficient linkage disequilibrium for QTL detection.