ARS | Publication request: SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of specialty crops

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract
Publication Acceptance Date: January 14, 2008
Publication Date: January 14, 2008
Citation: Kuhn, D.N., Meerow, A.W., Borrone, J.W., Motamayor, J.C., Schnell Ii, R.J. 2008. Sscp markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of specialty crops. Plant and Animal Genome Conference.

Technical Abstract: For well studied species where whole genome sequence and extensive EST data is available, SNP markers are the logical choice for both targeted genotyping or whole genome association studies. However, SNP markers do not necessarily address the needs of a researcher working on a plant specialty crop with limited available genomic information, small or nonexistent populations (which eliminates the need for high-throughput), and where the concern for development time and costs overrides that of analysis. Traditionally, microsatellite markers have been employed in such cases due to their robustness, yet they suffer from a long and difficult development phase that may result in a low yield of polymorphic markers. Single-strand conformation polymorphism (SSCP) markers, like microsatellites, are PCR-based and scored by electrophoretic mobility but, because they are based on SNPs rather than length differences, are much more common and easier to develop. We have examined how well correlated the estimation of genetic diversity and genetic distance are in a population or germplasm collection when measured by 13 highly polymorphic microsatellite markers or 20 newly developed SSCP markers. Our results demonstrate a significant correlation in pairwise genetic distances of 95 individuals in an international cacao germplasm collection as measured by SSCP markers and microsatellite markers (Mantel test Rxy = 0.593, p < 0.0001 for 9999 permutations) and provide strong support for the use of SSCP markers in the genotyping of specialty crops or other plant species where development of microsatellites would be difficult or expensive.