Linkage disequilibria between pairs of loci within a highly polymorphic region of chromosome 2Q.

A recently described region on chromosome 2q contains seven restriction fragment length polymorphisms (RFLPs) revealed by single-copy probes isolated from a 20-kilobase (kb) segment of a single cosmid insert. Analysis of six of these loci demonstrates modest amounts of linkage disequilibrium. This reflects the presence of a substantial number of different haplotypes in this chromosome region and indicates that the region could be used as one highly polymorphic locus. No consistent relationship is found between the amount of linkage disequilibrium and the physical distance between pairs of loci. For seven of the 10 pairs of diallelic loci studied, the observed disequilibrium can be attributed primarily to the absence of the minor haplotype from the population. These results suggest that, for small regions of the genome, factors such as mutation, genetic drift, and population admixture may have effects that outweight those of recombination. In addition, results are reviewed which show that estimates of linkage disequilibrium coefficients for tightly linked loci are very imprecise. Thus, the inference of gene order from linkage disequilibrium values must be regarded with caution.