How useful are microsatellites?

February 29, 2016
Schematic representation of the repeats, flanking regions, and fragment length -- the basis of the three data sets in this study. The four shades of gray correspond to the four different nucleotides. The number of repeats is calculated as the difference between the fragment length (from genotyping) and the flanking region (from sequencing). Credit: Germain-Aubrey, C. C., C. Nelson, D. E. Soltis, P. S. Soltis, and M. A. Gitzendanner. 2016. Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae). Applications in Plant Sciences 4(2): 1500115. doi:10.3732/apps.1500115.

Understanding genetic diversity and evolutionary dynamics of organisms can have important implications for designing successful conservation efforts and understanding potential effects of future climate change. For scientists seeking to illuminate these dynamics and uncover genetic diversity within plant species, microsatellites are an often-used tool. These repeated segments of DNA sequences offer a glimpse into the evolutionary history of organisms at a very fine scale, providing a valuable data source for population-level studies.

"These markers aren't without potential problems, however," warns Dr. Charlotte Germain-Aubrey, a scientist in the Florida Museum of Natural History and lead author of a study in a recent issue of Applications in Plant Sciences. The study, a collaboration between scientists at the University of Florida, aims to provide a deeper understanding of the utility—and problems—of using fragment lengths, repeats, and flanking regions of for conservation genetic studies.

"Several studies have examined and reported biases associated with the use of microsatellite genotyping," says Germain-Aubrey. "The widespread use of these markers for genetic studies led us to further explore the utility and problems associated with using microsatellites. We used an endangered , Polygala lewtonii, as a test case."

The problem with microsatellites essentially boils down to whether or not you can confidently infer the relative number of repeats between individual plants. A problem arises when a mutation in the flanking region causes a change in the overall fragment length. When only considering fragment length, such a mutation can mimic the addition (or deletion) of a repeat, leading to erroneous conclusions. This is termed homoplasy—similarities in fragment length are not due to their shared ancestry but, rather, to an unseen change in an area adjacent to the repeats.

By sequencing the flanking regions, Germain-Aubrey and colleagues were able to quantify the amount of homoplasy in their data set. "Contrary to previous thinking, we found that homoplasy can profoundly affect studies working within even the most recently diverged populations," she explains.

An additional important result from this study is that researchers need to be wary when using microsatellite markers that were designed for a different species. The team found that the amount of homoplasy becomes increasingly problematic when considering multiple species or using markers designed for a taxon other than the target species. "Often, it's tempting to use markers that were previously developed for a closely related species. We strongly suggest that when doing this, researchers take the time to sequence several individuals from their study species using these markers before forging ahead with the study," concludes Germain-Aubrey.

Explore further: Startling genetic similarity in tammar wallabies

More information: Charlotte C. Germain-Aubrey et al. Are Microsatellite Fragment Lengths Useful for Population-Level Studies? The Case of (Polygalaceae) , Applications in Plant Sciences (2016). DOI: 10.3732/apps.1500115

Related Stories

DNA testing to help save corals

May 23, 2014

"We are seriously tackling conservation of coral reefs in Okinawa," said Dr. Chuya Shinzato of the OIST Marine Genomics Unit. Coral reefs face various extinction risks. To avert coral demise, Shinzato is providing his expertise ...

An old genetic tool in plant biology still has value

January 6, 2015

Scientific tools for plant genetics research continuously fade away as newer methods evolve. However, researchers at Mississippi State University have found that one older method, the use of fragmented chloroplast DNA sequences, ...

Recommended for you

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.