Quantitative Trait Locus. A QTL is a hypothesis that a certain region of the chromosome contains genes that contribute significantly to the expression of a complex trait. QTLs are generally identified by comparing the linkage of polymorphic molecular markers and phenotypic trait measurements. The density of the linkage map is important in the accurate and precise location of QTLs; the higher the map density, the more precise the location of the putative QTL, although there is increased likelihood that false positives will be detected. Once QTLs have been mapped to a relatively small chromosomal region, other molecular methods can be used to isolate specific genes.