Rapid screening and comparison of human microsatellite markers in baboons: allele size is conserved, but allele number is not.

We have developed a rapid screening method for cross-species amplification of homologous microsatellite loci and studied some of the characteristics of those loci in the species of origin (human) and the test species (baboon). We tested a matrix of 64 combinations of magnesium concentration and annealing temperature, and after screening over 750 markers with that system, we found that 32 of those combinations account for >99% of the loci that could be amplified across species. This number of test conditions can be further reduced to 6 conditions when a touchdown PCR profile is used instead of traditional 3-step PCR. When the test primers are used to amplify batched DNA samples, and fluorescently labeled dNTPs are incorporated into the PCR product, the products from the best set of conditions can be loaded directly onto an automated sequencer, and the number of alleles, allele size range, and approximate allele frequencies can be estimated from one lane per locus. We were able to optimize conditions for automated microsatellite genotyping in baboons for 24.3% of the loci screened, resulting in a panel of over 280 genetic markers suitable for genetic analysis of baboons. Analysis of 139 markers for which we had completed human and baboon genotyping indicated that there was no correlation between numbers of alleles in humans and in baboons, but a high correlation between median allele sizes. There is no indication of directional selection for increased human microsatellite size.