Submitted to: Electrophoresis
Publication Type: Peer reviewed journal
Publication Acceptance Date: 4/24/2008
Publication Date: 10/1/2008
Citation: Kuhn, D. N., J. C. Motamayor, A. W. Meerow, J. W. Borrone and R. J. Schnell. SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. Electrophoresis29: 4096–4108 . 2008. Interpretive Summary: Researchers working on specialty crops such as cacao where there is limited genetic information need genetic markers to be able to do marker-assisted selection to improve a breeding program. A type of genetic marker that is based on length differences (microsatellite marker) frequently has been used but it can be difficult to identify enough microsatellite markers. We show that a different genetic marker based on mobility changes due to DNA sequence differences (SSCP markers) are more common, easier to develop and function as well as microsatellite markers in genotyping cacao trees. This work is not only important for cacao but should make it easier for scientists working on other specialty crops to develop useful genetic markers.
Technical Abstract: For well-studied plant species with whole genome sequence or extensive EST data, SNP markers are the logical choice for both genotyping and whole genome association studies. However, SNP markers may not address the needs of researchers working on specialty crops with limited available genomic information. Microsatellite markers have been frequently employed due to their robustness, but marker development can be difficult and may result in few polymorphic markers. SSCP markers, like microsatellites, are PCR-based and scored by electrophoretic mobility but, because they are based on SNPs rather than length differences, occur more frequently and are easier to develop than microsatellites. 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. We observed a significant correlation in pairwise genetic distances of 95 individuals in an international cacao germplasm collection (Mantel test Rxy = 0.593, p < 0.0001 for 10,000 permutations). Both sets of markers could distinguish each individual in the population. These data provide strong support for the use of SSCP markers in the genotyping of plant species where development of microsatellites would be difficult or expensive.