Linkage mapping in populations with karyotypic rearrangements

A simulation study was used to examine the consequences of karyotypic rearr angements on molecular genetic map construction, Two groups of 50 datasets were created for F-2 populations segregating for a reciprocal translocation of chromosomal segments or a reciprocal translocation and inversion, Multi ple attempts were made to construct maps for each dataset using MapMaker/EX P, As expected, the markers from segments involved in the translocation for med one linkage group, Maps that corresponded to the known marker order wit hin a segment could be constructed by the following method, The separation of markers distal to the translocation breakpoints into their respective se gments could be made by constructing multiple maps, using distinct orders o f marker entry, and observing the variances in intermarker distances: varia nces between pairs of markers from the same segment were an order of magnit ude less compared to pairs where markers were from different segments, The order of markers within a segment could be determined from combining the pa irwise linkage results from multiple maps, or from maps including all marke rs from a segment. No bias in map distances was observed, These results ind icate that, under conditions similar to those tested, genetic maps correspo nding to the segments conserved in translocations can be constructed.