Comparison of RSAP, SRAP and SSR markers for genetic analysis in hot pepper

Abstract

The restriction site amplified polymorphism (RSAP), combining simplicity, reliability and moderate throughput ratio was used to assess the genetic divergence between different hot pepper (Capsicum annuum L.) inbred lines. The utility of RSAP markers was compared to that of sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers. The result suggested that RSAP was significantly informative among the three genetic marker systems studied on hot pepper genetic divergence. The highest number of polymorphic bands per assay ratio and the highest marker index was obtained using it. The clusters of RSAP and SSR were found to have of pepper inbred lines representing similar geographic origins, as well as reflecting important role of fruit characteristics in pepper classification. The correlations of genetic relationships were significantly high between RSAP datasets and SSR markers, but very low between SRAPs and SSRs, which corresponded to the polymorphic regions detected by different marker systems.