Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata–D.cayenensis)

Abstract

Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results.

Molecular Analysis of Phylogenetic Relationships among Myrmecophytic Macaranga Species (Euphorbiaceae)

“…Both types of assay were carried out in a total volume of 17 l, including 0.9 U Taq DNA polymerase (QIAGEN) in the reaction buffer system supplied by the manufacturer (including 1ϫ Q-Solution to reduce scoring problems due to DNA secondary structures) and final concentrations of 2-5 mM MgCl 2 , 0.2 mM dNTP, 0.8 M primer, and 2-25 ng of template DNA. Amplifications were performed in a PerkinElmer 9700 thermocycler under the cycling conditions described by Ramser et al (1997) , banding profiles were resolved on 1.5% agarose gels in TBE buffer (Sambrook et al, 1989), stained with ethidium bromide, and photographed under UV light with a red filter. Homology of comigrating bands was exemplarily tested by Southern blot hybridization (Ramser et al, 1997).…”

“…Amplifications were performed in a PerkinElmer 9700 thermocycler under the cycling conditions described by Ramser et al (1997) , banding profiles were resolved on 1.5% agarose gels in TBE buffer (Sambrook et al, 1989), stained with ethidium bromide, and photographed under UV light with a red filter. Homology of comigrating bands was exemplarily tested by Southern blot hybridization (Ramser et al, 1997). For this, two individual RAPD and two MP-PCR bands were excised from the gel, each purified with a QIAquick Gel Extraction Kit (QIAGEN), reamplified with the respective primer, and labeled with 32 P by random priming (Sambrook et al, 1989).…”

“…The related MP-PCR technique makes use of microsatellite-specific primers to amplify genomic interrepeat regions and should be, due to longer primer sequences, better reproducible than RAPD amplification (Wolfe and Liston, 1998). RAPD and MP-PCR data have been used extensively in phylogenetic reconstruction of closely related taxa (e.g., Adams and Demeke, 1993;Harrier et al, 1997;Ramser et al, 1997;Friesen et al, 1999).…”

Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata

“…Some authors consider them as part of a complex called D. cayenensis/D. rotundata (Dansi et al, 1999;Mignouna et al, 2002), while others consider them as two distinct species (Ramser et al, 1997;Mignouna et al, 2005).…”

Estimation of genetic diversity of the Kenyan yam (Dioscorea spp.) using microsatellite markers

“…On the basis of phylogenic studies using RFLP analysis in chloroplast and nuclear ribosomal DNA, it was suggested that D. cayenensis is a variety of D. rotundata (Terauchi et al, 1992). More recent studies based on isozyme (Dansi et al, 2000a) and molecular markers (Ramser et al, 1997;Mignouna et al, 1998Mignouna et al, , 2005 support the separate identity of the two species.…”