Ongoing mapping efforts and increasingly efficient techniques for detecting QTL in both breeding and targeted mapping populations are providing a rapid increase in the number markers available for use in breeding. With large numbers of markers, population sizes required to combine desirable alleles across all of these loci can be prohibitive. Choice of the most efficient strategies can reduce populations sizes required to recover a target genotype by orders of magnitude and extend our ability to combine large numbers of target alleles.

Currently, most breeding crosses will be varying both for well mapped, often simply inherited, traits and others for which no marker association has been established. Even with ongoing discovery of marker-trait associations, genetic progress will continue to depend on introducing new genetic variation and at least initially, the value of this new variation will be unknown. In both instances, there will be a need to balance selection for known desirable alleles already present in breeding populations with phenotypic selection to retain desirable new alleles and allelic combinations. Strategies allowing for, or maximizing the probability of reducing, linkage drag in combination with selection for known target alleles is likely to be important in effective exploitation of this unmapped genetic variation.

Strategies to efficiently combine large numbers of target alleles and balance marker and phenotypic selection will be discussed using examples from our breeding program. The effects of incomplete linkage of markers with genes, use of flanking markers and coupling and repulsion phase linkages between target loci will be considered.