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We consider the problem of detecting and estimating the strength ofassociation between a trait of interest and alleles or haplotypes in a smallgenomic region (e.g. a gene or a gene complex), when no direct information onthat region is available but the values of neighbouring DNA-markers are athand. We argue that the effects of the non-observable haplotypes of the genomicregions can and should be represented by factors representing disjoint groupsof marker-alleles. A theoretical argument based on a hypothetical phylogenetictree supports this general claim.  The techniques described allow to identify and to infer the number ofdetectable haplotypes in the genomic region that are associated with a trait.The methods proposed use an exhaustive combinatorial search coupled with themaximization of a version of the likelihood function penalized for the numberof parameters. This procedure can easily be implemented with standardstatistical methods for a moderate number of marker-alleles.

An efficient strategy to characterize alleles and complex haplotypes using DNA-markers