Molecular diversity analysis of Asparagus racemosus and its adulterants using random amplified polymorphic DNA (RAPD)
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Abstract:
Leaves of 28 genotypes of 4 species of the genus Asparagus, namely: Asparagus racemosus, Asparagus falcatus, Asparagus officinalis and Asparagus plumosus were analyzed for genetic diversity by random amplified polymorphic DNA (RAPD). Out of one hundred 10-mer RAPD primers screened, 25 were selected for comparative analysis of different accessions of A. racemosus and its closely related species. High genetic variations were found between the different Asparagus species studied. Among a total of 296 RAPD fragments amplified, 287 bands (96.95%) were found polymorphic in the four species. Average polymorphic information content (PIC) value for the amplification product was 0.23. Fourteen species-specific bands were found in A. racemosus species. These species-specific RAPD markers could potentially be used for identifying authentic A. racemosus spp. and could be sequenced for conversion to a sequence-characterized amplified region (SCAR) marker so as to serve as species specific marker. Jaccard’s genetic similarity co-efficient varied from 0.19 to 0.85. The unweighted pair group method with arithmetic average (UPGMA) dendrogram was constructed on the basis of Jaccard’s genetic similarity co-efficient values that separate the three other species of Asparagusfrom A. racemosus accessions. Results of this study will facilitate authentic A. racemosusidentification, thereby aiding drug standardization, its collection, management and conservation.
Key words: Medicinal herb, genetic diversity, molecular marker, authentication, conservation.Keywords:
Asparagus racemosus
Jaccard index
Asparagus
UPGMA
Dendrogram
Molecular marker
Twenty accessions of Asparagus racemosus from ten agro-ecological zones of Kerala were evaluated for genetic diversity using Random Amplified Polymorphic DNA markers. Twenty random primers were selected based on reproducibility and clarity of bands. A total of 1209 bands were scored out of which, 1181 loci were found to be polymorphic (97.75%). Efficiency parameters of primers viz., Total Number of Loci, Total Number of Polymorphic Loci, Percentage of Polymorphism, Polymorphism Information Content (PIC), Resolving Power, Marker Index and Number of Unique Bands were estimated. Value of PIC varied from 0.059 to 0.209 and OPI19 is proved to be most polymorphic marker. Evaluation of relationship among seven efficiency parameters revealed positive and significant (P<0.01) correlation of Total Number of Loci with Total number of Polymorphic Loci, Resolving Power and Unique Bands. Jaccard’s similarity coefficient varied from 0.118 to 0.566. It indicates presence of large genetic variations within the accessions. The UPGMA dendrogram data revealed genetic relationships within accessions and there is no geographic isolation in the clustering. The present observations suggest that RAPD markers can be used as an effective tool for deriving intra-species genetic diversity among A. racemosus accessions.
UPGMA
Jaccard index
Dendrogram
Asparagus racemosus
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Fifteen species of the genus Dendrobium were analyzed, using RAPD (random amplified polymorphic DNA) technique. Ten decanucleotide primers (10 bp) were selected from 70 primers, and 99 bands of amplification were obtained, which were used for RAPD analysis. Based on the RAPD profile, a dendrogram of cluster analysis of the species studied was constructed according to their similarity coefficients. It is concluded that RAPD is effective in characterizing Dendrobium species. The high percentage of polymorphic loci ((84.85%)) in the species indicates that this genus is highly diverse genetically.
Dendrobium
Dendrogram
Similarity (geometry)
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The genetic diversity and phylogenetic relationships of eleven herbaceous peonies grown in Korea were analyzed by random amplified polymorphic DNA (RAPD). Twenty-four decamer RAPD primers were used in a comparative analysis of these Korean peony species. Of the 142 total RAPD fragments amplified, 124 (87.3%) were found to be polymorphic. The remaining 18 fragments were found to be monomorphic (12.7%) shared by individuals of all 11 peony species. Cluster analysis based on the presence or absence of bands was performed by Jaccard's similarity coefficient, based on Unweighted Pair Group Method with Arithmetic Averages. Genetic similarity range was 0.39 to 0.90 with a mean of 0.64. This study offered a rapid and reliable method for the estimation of variability among different peony species which could be utilized by the breeders for further improvement of the local peony species. Also, the results propose that the RAPD marker technique is a useful tool for evaluation of genetic diversity and relationship amongst different peony species.
Jaccard index
Herbaceous plant
Similarity (geometry)
Phylogenetic relationship
Genetic similarity
UPGMA
Genetic relationship
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The random amplified polymorphic DNA (RAPD) markers were applied to detect the genetic relationships and diversity among 33 accessions of Curcuma species in China, which involved six medicinal species. A total of 115 products were amplified by 21 primers, among which 106 products (92.17%) were found to be polymorphic. 3 to 8 polymorphic bands were amplified by each polymorphic primer, with an average of 5.48 bands. The data of 115 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. The results show that the genetic similarity coefficient relatively of these six species is large, from the cluster diagram, the genetic relationships are not associated with their geographical distributions.
Key words: Curcuma, cluster analysis, genetic diversity, random amplified polymorphic DNA, similarity coefficient.
UPGMA
Dendrogram
Jaccard index
Similarity (geometry)
Primer (cosmetics)
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To identify 8 medicinal species of Selaginella with method of molecular marker and to explore their genetic relationship.8 primers were selected from 60 random primers to amplify the total DNA extracts of 17 samples with RAPD method and then the amplified were analyzed.A total of amplified 58 bands and RAPD map were obtained. Based on them, a Jaccard's genetic similarity matrix and a dendrogram for the 8 plants were established using SPSS 11.5 software.The method revealed distinct differences of different species and the variation of the same species of Selaginella from different habitats. It can provide with genetic proof for authentication of some species and units below species.
Jaccard index
Dendrogram
Selaginella
Similarity (geometry)
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Germ plasm
UPGMA
Jaccard index
Genetic similarity
Genetic relationship
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The species of Asparagus are very important as they are used for ornamental, vegetable and medicinal purposes since ancient time. In the present study, random amplified polymorphic DNA (RAPD) markers were used to evaluate genetic diversity among nine species of Asparagus and six cultivars of Asparagus officinalis L. RAPD analysis using seven random oligonucleotide primers yielded a total amplification of 245 bands, among which 220 (89.80%) were polymorphic with an average of 31.4 bands per primers. Highest number of 39 (97.50%) polymorphic bands were obtained with primer OPC-07, while minimum polymorphic bands were 18 (69.23%) with primers OPA-01. Genetic similarity coefficient ranged from 0.75 to 0.96 with an average of 0.85. Phenogram clustered all Asparagus species and A. officinalis L. cultivars into two clear clusters. One cluster comprised of all cultivars of A. officinalis L. while the second cluster comprised of all the Asparagus species. The present study reveals that RAPD markers were more convincing for analyzing genetic diversity among Asparagus species and cultivars of A. officinalis L. Key words: Asparagus officinalis L., genetic diversity, random amplified polymorphic DNA (RAPD), Phenogram.
Asparagus
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Dendrogram
UPGMA
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Genetic inter-relationship of nine Cinnamomum species was estimated using randomly amplified polymorphic DNA (RAPD) markers. The 15 selected RAPD primers out of 2 primers were amplified in all cinnamon species. Cinnamomum verum has very close similarity (87%) with C. citronella and another two species of C. camphora and C. glucens. Our results suggested that genetic relationships in Cinnamomum species using RAPD banding data may be useful for plant improvement and an efficient way to conserve genetic resources of Cinnamomum species, in addition to their effective medicinal uses.
Cinnamomum camphora
Cinnamomum
Genetic similarity
Genetic relationship
Genetic distance
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Objective: Genetic diversity among 12 species of Clematis L.were analyzed,and the result was the foundation information for identification of medicinal plants.Methods: Random amplified polymorphic DNA(RAPD)technique was used to analyze genetic diversity,and the dendrogram was constructed by UPGM.Results: Ten RAPD primers were selected to apply for random amplification.A total of 89 DNA bands were detected,all which were polymorphic.The dendrogram by using UPGM claimed that the differences among most of species were dominant,and the differences among different distribution site of the same species could be identified,however,it was not easy to identify the same species at the same site.Conclusion: RAPD markers was suitable for identification of species of Clematis.But whether it was used for phylogenetics was not sure.
Dendrogram
Clematis
Identification
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