Identification of high-resolution microsatellites without a priori knowledge of genotypes using a simple scoring approach
Article first published online: 3 SEP 2013
© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 11, pages 1076–1082, November 2013
How to Cite
Eschbach, E., Schöning, S. (2013), Identification of high-resolution microsatellites without a priori knowledge of genotypes using a simple scoring approach. Methods in Ecology and Evolution, 4: 1076–1082. doi: 10.1111/2041-210X.12101
- Issue published online: 6 NOV 2013
- Article first published online: 3 SEP 2013
- Accepted manuscript online: 23 JUL 2013 09:36AM EST
- Manuscript Accepted: 18 JUL 2013
- Manuscript Received: 16 APR 2013
- German Ministry of Education and Research. Grant Number: 01UU0907
- genetic resolution;
- Large numbers of microsatellite loci for many species are increasingly made available from public data bases or through de novo isolation with next generation sequencing methods. However, the challenge remains to identify the subset of loci with suitable polymorphism for the populations of interest. This normally requires genotyping individuals in a representative subset of populations.
- Here, we present an approach that does not require individual genotypes, but instead uses the presence and absence of alleles in pooled DNA samples to estimate within-population variation (WPV, i.e. polymorphism) and among-population variability (APV, i.e. rare alleles). From these, we developed a scoring procedure to rank individual loci and thereby identify those most suitable for individual genotyping.
- We used multiplex PCR of 20 pooled individuals from each of 12 populations to screen a total of 80 published and unpublished microsatellite loci in the Northern pike Esox lucius, a species known to exhibit low genetic variability, thus predisposing it as a model species to test our approach. The screening of pooled samples revealed extremely different levels of microsatellite variability, ranging from 1·0 to 27·5 alleles per microsatellite (WPV) and from 1·4 to 12 populations per allele (APV). Scoring placed microsatellites with high WPV and medium APV at the highest ranks.
- We validated this outcome by genotyping individuals of two pike populations from geographically close areas. A strong differentiation potential (measured as Weir's & Cockerham's FST) as well as a better resolving power of higher over lower-ranked microsatellites (measured as Nei′s DA and probability of identity) proved that the method presented here is suitable for rapid and inexpensive identification of appropriate microsatellites without a priori knowledge of genotypes.
- Our scoring procedure is generally applicable to all population genetic studies based on microsatellites and is particularly recommended, if species with low genetic variability are to be investigated.