Clonal genetic diversity and populational genetic differentiation in Phragmites australis distributed in the Songnen Prairie in northeast China as revealed by amplified fragment length polymorphism and sequence-specific amplification polymorphism molecular markers

Genetic variation within and between four naturally occurring Phragmites australis land populations, DBS, QG, SS1 and SS2 (named after locality), which colonise distinct habitats (different edaphic conditions) in the Songnen Prairie in northeast China, were investigated by amplified fragment length polymorphism (AFLP) and sequence-specific amplification polymorphism (S-SAP) markers. It was found that the selected primer combinations of both markers were highly efficient in revealing the inter-clonal genetic diversity and inter-populational genetic differentiation in P. australis from a molecular ecological perspective. Cluster analysis categorised the plants into distinct groups (DBS, QG and SS groups), which were in line with their localities, albeit the two SS group populations (SS1 and SS2) showed a lower degree of inter-populational differentiation. These results were strongly supported by multiple statistical analysis including Mantel's test, principal coordinate analysis, allocation test and analysis of molecular variance, which further suggested that gene flow, genetic drift and differences in as yet unidentified edaphic factors may all underpin the inter-clonal genetic diversity and inter-populational differentiation at the nucleotide sequence level. Analysis of intra-population clonal diversity also revealed that the QG population harboured a strikingly lower amount of within-population variation compared with those of the other three populations, presumably being caused by genetic drift and followed by physical and/or biological isolation. Homology analysis of a subset of population-specific or population-private AFLP and S-SAP bands suggested that regulatory genes and retroelements might play important roles in the ecological adaptation and differentiation of the P. australis populations. Possible causes for and implications of the extensive genetic variability in P. australis were discussed for its future genetic conservation and use in ecological revegetation.