Examination of a region showing linkage map discrepancies across sheep breeds.

The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.