A Comparison of ITS Nuclear rDNA Sequence Data and AFLP Markers for Phylogenetic Studies in Phyllostachys (Bambusoideae, Poaceae)

Abstract

Two contrasting molecular techniques, namely DNA sequences and amplified fragment length polymorphisms (AFLP) were used to investigate phylogenetic relationships of Phyllostachys, a large, economically important genus of woody bamboos. DNA sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) were used in a parsimony analysis. PhyrrOStachys was well supported as monophyletic with Chimonobambusa as its closest allied genus. The 5s spacer region of nrDNA was investigated but found unsuitable for this purpose. The AFLP analysis showed much higher discriminating power between species and was more useful for phylogenetic reconstruction at this taxonomic level. The combined data were used to review the previous infra-generic classifications. Section Heteroclada Wang & Ye is strongly supported and can be further divided into sub-groups. A group within section Phyllosachys is strongly supported, but a further group of taxa previously included in this section is difficult to place. The ability of the methods to help separate species such as P.sulphurea and investigate genetic diversity at the infra-specific level was also assessed. It is argued that AFLPs could often be the method of choice for phylogenetic studies of closely related taxa for which DNA sequence data provide insufficient resolution.

Using AFLP markers for species differentiation and assessment of genetic variability of in vitro-cultured Papaver bracteatum (section Oxytona)

“…AFLP fingerprints are highly reproducible and generally produce a large number of polymorphic markers (Becker et al, 1995;Ridout and Donini, 1999;Hodkinson et al, 2000). We have demonstrated that they can be applied to the study of genetic variation in poppies.…”

“…AFLP fingerprinting is based on the selective amplification of restriction fragments from a digest of genomic DNA. The resulting complex fingerprints are reproducible and provide a wide number of informative markers derived from the many loci dispersed throughout the genome (Ridout and Donini, 1999 Hodkinson et al, 2000). AFLP has been used to detect genetic variation in highly inbred lines of cereal crops and for the study of clonal variation in plants (Mackill et al, 1996;Paul et al, 1997;Waugh et al, 1997;Hodkinson et al, 2002).…”

“…AFLP has been used to detect genetic variation in highly inbred lines of cereal crops and for the study of clonal variation in plants (Mackill et al, 1996;Paul et al, 1997;Waugh et al, 1997;Hodkinson et al, 2002). It has also been used for species differentiation in a range of higher plant species such as Phyllostachys (Hodkinson et al, 2000), but not in Papaver section Oxytona.…”

Molecular Characterization of Fusarium globosum Strains from South African Maize and Japanese Wheat

“…It was suggested that AFLPs be the method of choice for phylogenetic studies of closely related organisms when other characters (e.g. morphological characters) are identical [3,16]. An advantage of the AFLP procedure is the fact that the whole genome is used as the source of information for the banding patterns.…”

Use of fluorescent-based amplified fragment length polymorphism to resolve phylogenetic relationships of Colchicum species from Turkey

“…However, the power of this region fails to resolve the phylogenetic assessments (Després et al, 2003). AFLP emerges as an efficient technique to solve difficulties whereas cpDNA is not sufficient to identify phylogenies, particularly among closely related species or at the intraspecific level (Hodkinson et al, 2000;Koopman et al, 2001;Xu and Sun, 2001;Zhang et al, 2001;Karakaş et al, 2013). AFLP analysis can detect high levels of polymorphism and has high repeatability and speed of analysis.…”