Amplified fragment length polymorphism versus random amplified polymorphic DNA markers: clonal diversity in Saxifraga cernua

Abstract

Random amplified polymorphic DNA (RAPD) markers are sensitive to changes in reaction conditions and may express polymorphisms of nongenetic origin. Taxa with variable chromosome numbers are particularly challenging cases, as differences in DNA content may also influence marker reproducibility. We addressed these problems by comparing RAPD and amplified fragment length polymorphism (AFLP) analyses of clonal identity and relationships in a chromosomally variable arctic plant, the polyploid Saxifraga cernua, which has been thought to be monoclonal over large geographical distances. Fifty-seven plants from four Greenland populations were analysed using a conservative scoring approach. In total, 26 AFLP and 32 RAPD multilocus phenotypes (putative clones) were identified, of which 21 were identical and each of the remaining five AFLP clones was split into two to three very similar RAPD clones. This minor difference can be explained by sampling error and stochastic variation. The pattern observed in Greenland corroborates our previous results from Svalbard, suggesting that rare sexual events in S. cernua are sufficient to maintain high levels of clonal diversity even at small spatial scales. We conclude that although AFLP analysis is superior in terms of efficiency, RAPDs may still be used as reliable markers in small low-tech laboratories.

Clonal structure and reduced diversity of the invasive alien plant Erigeron annuus in Lithuania

“…The second population type is represented by polymorphic populations. A similar situation was described among Saxifraga cernua populations [36]. In a study of S. cernua, 26 AFLP and 32 RAPD multilocus phenotypes (putative clones) were identified, of which 21 were identical and each of the remaining five AFLP clones were split into two to three very similar RAPD clones.…”

“…Only one population (PN16, Vilnius) was characterized as monomorphic by RAPD assay but slightly polymorphic (10.4%) by ISSR assay. The small differences observed between the two types of markers can possibly be explained by stochastic variation in allele assortment in connection with occasional recombination events [36].…”

A Study of Conservation Genetics in Cupressus chengiana, an Endangered Endemic of China, Using ISSR Markers

“…Recently, molecular markers have been frequently applied to ecological genetic and conservation genetic studies (Kjolner et al, 2004;Schonswetter et al, 2004). ISSR (intersimple sequence repeat; Weising et al, 1995;Zietkiewicz et al, 1994) is a modification of the SSR approach (simple sequence repeat) that uses a single primer based on SSR (microsatellites) that are common in the genome.…”

Biogeographical Relationships of the Eel Parasite Anguillicola Crassus Revealed by Random Amplified Polymorphic Dna Markers (Rapds)

“…It is a PCR-based technique using short arbitrary primers to amplify target DNA under low stringency conditions. The utility of RAPDs for genetic characterisation of parasites populations has been demonstrated by several authors (BARRAL et al, 1993;LANGAND et al, 1999, KJØLNER et al, 2004.…”