Use of rice SSR markers as RAPD markers for genetic diversity analysis in Zingiberaceae

Abstract

Species of Zingiberaceae display a diversity in habitat, ethnobotanical use and morphology. However, little is known about the genetic relationships among taxa and genetic diversity, primarily due to the lack of suitable molecular markers. We tested the cross-amplification potential of microsatellite markers among taxa to identify a larger number of genetic markers. To assess the applicability of rice microsatellite markers to the Zingiberaceae, we tested 12 microsatellite markers for 14 genotypes from three genera of this family: Zingiber, Alpinia and Curcuma. The origin of the genotypes was diverse, covering eight Asian countries. Four microsatellite primer sets failed to amplify fragments in all genotypes studied, whereas the other primer sets amplified all the genotypes. Among the 141 bands, that could be scored, 140 (99.5%) were polymorphic. On the average, each microsatellite primer set amplified 17.6 DNA fragments. In general, amplified fragments were larger than the original rice fragments including the microsatellite region, although in some cases, the amplified bands were similar in size. Though sequence analysis of these bands confirmed the absence of target repeat motif, amplification of a large number of polymorphic bands provided the basis to perform an analysis of genetic diversity. Primers could generate enough polymorphism for possible use in diversity studies, based on provisional multivariate analyses such as cluster analysis and principal component analysis (PCA). The whole set of genotypes based on molecular data was classified into four clusters after cluster analysis. Genotypes from the Curcuma and Alpinia genera were grouped into clusters I and II, respectively. Clusters III and IV comprised genotypes from the genus Zingiber. PCA led to a similar classification. The high polymorphism documented in the present study indicated that the rice microsatellite primers were useful for genetic diversity studies among genera in the family Zingiberaceae.