The use of microsatellite analysis in population biology: background, methods and potential applications.

A promising technique currently emerging for population studies is the analysis of microsatellite DNAs. Microsatellite alleles offer several advantages over other types of molecular markers. They are abundant, highly variable, and can be assayed from minute quantities of DNA using PCR. Their major disadvantage is that it is usually necessary to screen genomic libraries to identify and characterize microsatellite loci for each species under investigation. The first goal of this chapter is to summarize background information having implications for population studies. This information comes primarily from human genome literature and is therefore not easily accessible to many population biologists. Secondly, because microsatellite analysis uses molecular approaches that are new to most population biologists, we attempt to provide a rationale and overview of methodology. Finally, we review population studies to date that have used microsatellite analysis and offer our perspective on the potential for future studies.

Characterization of highly variable (GA/CT) n microsatellites in the bur oak, Quercus macrocarpa.

The objective of this study was to ascertain the usefulness of polymerase chain reaction (PCR)-based microsatellite analysis for studying pollination and parentage in a wind-pollinated temperate tree. A small insert genomic library of the bur oak (Quercus macrocarpa) was constructed and screened for the presence of (CA/GT) n and (GA/CT) n repeats. The proportion of positive clones yielded estimates of 3×10(5) such dinucleotide repeats per genome, roughly comparable to abundances reported in other eukaryotic genomes. Thirteen positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) n motif was more abundant than the (CA/GT) n motif in these clones. The (GA/CT) n repeats also showed longer average repeat length (mean n=16.2 versus 7.3), suggesting that they are better candidates for yielding polymorphic genetic markers in oak genomes. Indeed, a survey of adult bur oaks and offspring in a small stand in northern Illinois at 3 of these (GA/CT) n microsatellite loci revealed Mendelian inheritance and extremely high levels of polymorphism, with the number of alleles at each locus ranging from 11-20 and heterozygosity ranging from 0.66 to 0.75. These results, indicating that (GA/CT) n microsatellites are both abundant and highly polymorphic in the bur oak genome, suggest that such genetic markers have tremendous potential for applications for studies of parentage, pollination and dispersal in temperate trees.