On the relative importance of marker heterozygosity and intermarker distance in gene mapping

Molecular biologists are often confronted with the problem of whether they should try to generate large numbers of very closely linked markers of low heterozygosity or smaller numbers of less closely linked markers of high heterozygosity. In other words, What is more important for gene mapping, high marker heterozygosity or dense marker spacing? We investigated that problem by analytically computing the expected lod score per meiosis in which the new locus is informative and phase known. We also looked at the length of the 1-unit-of-lod-score support interval for the expected lod score from 100 such meioses. We found that while both quantities have an influence on the number of meioses needed to find linkage, the length of the support interval is almost entirely dependent on the intermarker distance, for heterozygosities between 20 and 100%. However, the probability of any given meiosis being phase known and the ability to develop an accurate map of the markers are functions of marker heterozygosity, further complicating the issue.