Fine mapping and cloning of QTL
Markers allow a QTL to be manipulated in a breeding programme, but they seldom give any clues as to function or molecular mechanism. To obtain this information, it is necessary to clone the QTL, which requires it to be first mapped to a much higher resolution position. This is achieved by a combination of larger population size (up to a few thousand) and additional markers known - or discovered - to map in the region of the QTL.
See Tuberosa et al. 2007 for a good discussion of this, and Frary et al. 2000 for an example.