Whereas causative polymorphisms give direct information
about genotype for the QTL, the use of indirect
markers for QTL mapping and for selection is based on
the existence of LINKAGE DISEQUILIBRIUM (LD) between the
marker and the QTL.Marker–QTL LD can exist at the
population level but always exists within families, even
between loosely linked loci (BOX 2).Although two loci are
expected to be in population-wide equilibrium in large
random-mating populations, partial population-wide
LD can exist by chance between tightly linked loci in
breeding populations that are under selection.