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

Abstract

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.

Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers

“…As such, this species is distributed widely across the Songnen Prairie in northeastern China. P. australis often grows as a companion species in alkalized meadows but forms monodominant communities in local low-lying areas or saline-rich/alkaline patches (Li et al, 2009). This species is used as a major forage grass in the Songnen Prairie due to its high level of productivity and high protein content.…”

“…However, little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale (Pellegrin and Hauber, 1999;Guo et al, 2003;Gao et al, 2012). A preliminary investigation of the genetic diversity of this reed in the Songnen Prairie showed extensive genetic variability across a certain geographic range (Li et al, 2009). However, the within-and between-habitat genetic diversity and differentiation on a small spatial scale in the Songnen Prairie have not yet been studied.…”

Epigenetic polymorphisms could contribute to the genomic conflicts and gene flow barriers resulting to plant hybrid necrosis

“…In the same thought, it seems that human assisted hybrids breeding and also microbial genomic attacks in plants could at times lead to deleterious epigenetic interactions in plants that can cause hindrances in gene flow in plants. This can also trigger other epigenetically induced regulatory genes and elements like retrotransposons in diverse populations as was observed in Phragmites australis populations (Li et al, 2009). Such interactive implications can provide an explanation in the search for full understanding of the molecular basis of hybrid necrosis.…”

Genetic Diversity, Habitat Fragmentation and Epigenetic Variations

“…Such habitat fragmentation and other physical barriers like mountains, human activities, shielding vegetations and accumulation of valleys could influence the flow of wind and movement of dispersal agents. Further more, recent studies by Li et al, 2009, showed a remarkable observation in their cluster analysis indicating that the soil condition and the proximal distance between the populations have a significant influence in the genetic www.intechopen.com diversity analysis. Hence, it is now conceivable that the occurrence and spectra of genetic variations both within a plant population and among populations can be caused by three distinct as well as interlaced factors.…”

“…These could interfere with wind and pollinator movements (Li et al, 2009) causing homogenization of clones. This possibility was evidenced by an exceptionally low level of gene flow between two populations of L. chinensis (Zhang et al, 2009).…”