HYPERVARIABLE MICROSATELLITES PROVIDE A GENERAL SOURCE OF POLYMORPHICDNA MARKERS FOR THE CHLOROPLAST GENOME

Background: The study of plant populations is greatly facilitated by t he deployment of chloroplast DNA markers. Asymmetric inheritance, lowe r effective population sizes and perceived lower mutation rates indica te that the chloroplast genome may have different patterns of genetic diversity compared to nuclear genomes. Convenient assays that would al low intraspecific chloroplast variability to be detected are required. Results: Eukaryote nuclear genomes contain ubiquitous simple sequence repeat (microsatellite) loci that are highly polymorphic in length; t hese polymorphisms can be rapidly typed by the polymerase chain reacti on (PCR). Using primers flanking simple mononucleotide repeat motifs i n the chloroplast DNA of annual and perennial soybean species, we demo nstrate that microsatellites in the chloroplast genome also exhibit le ngth variation, and that this polymorphism is due to changes in the re peat region. Furthermore, we have observed a nonrandom geographic dist ribution of variations at these loci, and have examined the number and location of such repeats within the chloroplast genomes of other spec ies. Conclusions: PCR-based analysis of mononucleotide repeats may be used to detect both intraspecific and interspecific variability in the chloroplast genomes of seed plants. The analysis of polymorphic micro satellites thus provides an important experimental tool to examine a r ange of issues in plant genetics.