Showing papers on "RAPD published in 2018"

Evaluation of the genetic variability in bamboo using RAPD markers

Abstract: Classical taxonomic studies of the bamboos are based on floral morphology and growth habit, which can cause problems in identification due to erratic flowering. Identification and genetic relationships in 12 species of bamboo were investigated using random amplified polymorphic DNAs (RAPD) technique. Analysis started by using thirty 10-mer primers that allowed us to distinguish 12 species and to select a reduced set of primers. The selected primers were used for identification and for establishing a profiling system to estimate genetic diversity. A total of one hundred thirty seven distinct polymorphic DNA fragments (bands), ranging from 0.4–3.3 kb were amplified by using 10 selected primers. The genetic similar analysis was conducted based on presence or absence of bands, which revealed a wide range of variability among the species. Cluster analysis clearly showed two major clusters belonging to 12 species of bamboo. Two major clusters were further divided into three minor clusters. The species of Bambusa vulgaris and Bambusa vulgaris var. striata were the most closely related and formed the first minor cluster along with Bambusa ventricosa. The variety of Bambusa multiplex var. Silver stripe and Bambusa multiplex were very closely related and there was no variation with Bambusa ventricosa. Another minor cluster was obtained between Bambusa arundinacea, Cephalostachyum pergracil and Bambusa balcooa. The RAPD technique has the potential for use in species identification and genetic relationships between taxa and species of bamboo for breeding program.

Evaluation of genetic diversity of Brassica napus germplasm from China and Europe assessed by RAPD markers

Abstract: The genetic diversity and the relationships among rapeseed germplasm, including a collection of 20 Chinese, 25 Czech, 2 German, 2 French, and 1 English cultivars and breeding materials were evaluated using random amplified polymorphic DNA (RAPD) markers. A total of 79 different polymorphic amplification products were obtained using10 selected decamer primers. RAPDs revealed a significant level of polymorphism among the accessions. The diversity index (DI) ranged from 1.390 to 3.491, showing a sufficient potential of selected primers to differentiate among studied genotypes. Three different metrics were used to assess genetic diversity. The best fit between a priori knowledge about germplasm origin and a posteriori grouping was found using Hamman metrics. Cluster analysis based on Hamman pairwise distance comparison divided the studied accessions into three main clusters. The first group included only accessions from China, the second group only that from Europe with the exception of Zhongshuang No. 2, a Chinese winter rape possessing European cultivars in the pedigree. The third group included accessions both from China and Europe. The results indicate the occurrence of a considerable genetic variation between Chinese and European accessions.

Tracking Multidrug-Resistant Klebsiella pneumoniae from an Italian Hospital: Molecular Epidemiology and Surveillance by PFGE, RAPD and PCR-Based Resistance Genes Prevalence

Abstract: Antimicrobial-resistant Klebsiella pneumoniae represent a global public health concern. K. pneumoniae strains isolated during 2010 and 2014–2016 within a single hospital of Molise Region, Central Italy, were analyzed testing antimicrobial susceptibility, clonality by pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD)-PCR, and prevalence of carbapenem resistance genes by PCR. Forty isolates (23 wild-type in 2010 and 17 non-wild-type in 2014–2016) were collected from hospitalized patients (65.2 ± 18.1 years old, 75% male, 80% from intensive care unit—ICU). K. pneumoniae showed multidrug-resistant profiles and 15 resistotypes were identified (discriminatory power D = 0.88). The 69.6 and 17.4% of isolates in 2010 resulted intermediate and resistant to imipenem, respectively, and 91.3% was sensitive to meropenem, while 88.2% of isolates of 2014–2016 were resistant to both antibiotics. PFGE identified 16 clusters versus 23 by RAPD, 26 pulsotypes versus 33 RAPD patterns (D ≥ 0.97). PFGE separated strains according to isolation period and identified an outbreak occurred in the ICU during December 2014 and January 2015. No strains harbored blaGES, blaIMP, blaNDM−1, and blaOXA−48 genes, as well as AmpC plasmid-mediated beta-lactamases genes. Only K. pneumoniae isolated during 2014–2016 were blaKPC positive. Prevalence of blaVIM was 87 and 76.5% during 2010 and 2014–2016, respectively. No strains colistin-resistant harbored mcr-1 plasmid-mediated resistance gene. The study findings underline an increased circulation of multidrug-resistant K. pneumoniae within the hospital, and the acquisition of carbapenem resistance mechanism. The implementation of surveillance and molecular characterization of isolates are needed to identify outbreaks, reduce the spread of resistance, and guide empirical therapy.

Aluminum-Induced Changes on DNA Damage, DNA Methylation and LTR Retrotransposon Polymorphism in Maize

Abstract: Aluminum (Al) toxicity is a kind of abiotic stresses that causes several damages on plants. In this study, Al-induced DNA damages, DNA methylation alterations and long terminal repeat retrotransposons (LTR RTs) polymorphisms were evaluated in Zea mays seedlings, using random amplified polymorphic DNA (RAPD), coupled restriction enzyme digestion–random amplification (CRED–RA) and inter-retrotransposon amplified polymorphisms assays, respectively. Our results fairly proved that all doses of $$\hbox {AlCl}_{3}$$ (200, 400, 600 and 800 $$\upmu $$ M) caused a reduction in genomic template stability and an increase in RAPD band frequencies (DNA damage). Furthermore, there was an increase in DNA methylation ratio based on CRED–RA results. Five LTR RTs (Nikita-E2647, N57 (Nikita), Sukkula, WLTR 2105 and Stowaway) that were determined in barley genome were investigated in maize genome. Polymorphism was determined under Al stress based on the used LTR primers. It was suggested that this mobilization and methylation status under Al stress might be a part of the defense mechanism in stress.

Comparative analysis of genetic similarity between perennial ryegrass genotypes investigated with AFLPs, ISSRs, RAPDs and SSRs

Abstract: Perennial ryegrass (Lolium perenne L.) is the most important grass species used in temperate grassland agriculture. Our objective was to obtain an overview of the genetic relationships between 20 individual genotypes of perennial ryegrass of diverse origins, using amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and two sets of simple sequence repeat (SSR) markers. All 20 individuals were uniquely fingerprinted by all four marker systems and comparisons were made on the basis of 85 markers each. Mean genetic similarities were estimated at 0.31, 0.43, 0.23 and 0.15 for AFLPs, ISSRs, RAPDs and SSRs, respectively. Cophenetic values resulted in good (AFLP and SSR-B = 0.88) to moderately good fits (ISSR = 0.76, RAPD = 0.70, and SSR-A = 0.79). Comparing the four marker systems to each other, AFLP and SSR-A were correlated best ( r = 0.57). All other comparisons revealed rather low correlation coefficients in the Mantel Z test. With twice as many markers cophenetic values increased to a very good fit for AFLPs (0.90) and SSRs (0.92).

Phytochemical and genetic characterization of five quinoa (Chenopodium quinoa Willd.) genotypes introduced to Egypt.

Abstract: Due to its substantial nutritional value, quinoa (Chenopodium quinoa Willd.) is currently attracting worldwide attention. Quinoa is characterized by a high adaptability to various environmental conditions. This is the first report on the phytochemical and genetic evaluation of quinoa germplasms introduced to Egypt, and the results could be used to implement propagation techniques in the future. For phytochemical characterization, 41 traits, including primary and secondary metabolites, antioxidant molecules, sugars, organic acids and fatty acids, were evaluated. At the same time, 4 RAPD and 7 ISSR markers were used for genetic analysis. UPGMA analysis of RAPD and ISSR polymorphic markers, their combined dataset and phytochemical traits were used to evaluate genetic relationships among genotypes. The quinoa genotypes displayed reasonable variation in the studied phytochemical traits. The results of the genetic analysis confirmed that RAPD and ISSR markers could be used to distinguish effectively quinoa genotypes. The phytochemical and genetic characterization reported herein will be a promising guide for breeding seed quality in quinoa.

Characterization and Identification of Entomopathogenic and Mycoparasitic Fungi using RAPD-PCR Technique

Abstract: BIELIKOVA L., LANDA Z., OSBORNE L.S., CURN V. (2002): Characterization and identification of entomopathogenic and mycoparasitic fungi using RAPD-PCR technique. Plant Protect. Sci., 38: 1–12. Entomopathogenic and mycoparasitic fungi were characterised by RAPD technique, with special attention to evaluate the genetic stability of strains that are used as active ingredients in commercial biopesticides. Strain-specific fingerprints were constru cted for Paecilomyces fumosoroseus – strain PFR 97 Apopka, Gliocladium virens – strain GL 21 and Verticillium lecanii – strain MYCOTAL. Genetic stability and homogeneity was confirmed among re-isolates that were obtained from commercial batches of bio-insecticide PFR 97 TM 20%WDG and bio-fungicide SoilGard TM 12G that had been produced in 1995–1999. RAPD analysis indicated the genetic identity of V. lecanii strains re-isolated from the two different bio-insecticides M YCOTAL ® and VERTALEC ® . The usefulness of RAPD technique was demonstrated when P. fumosoroseus strain PFR 97 Apopka was reliably identified after having passed through adults of the spruce bark beetle Ips typographus, and by analysis of the relationship between fungi of the genus Gliocladium.

Er3 gene, conferring resistance to powdery mildew in pea, is located in pea LGIV

Abstract: Three genes for resistance to Erysiphe pisi, named er1, er2 and Er3 have been described in pea so far. er1 gene is located in pea linkage group VI, while er2 gene has been mapped in LGIII. SCAR and RAPD markers tightly linked to Er3 gene have been identified, but the position of these markers in the pea genetic map was unknown. The objective of this study was to localize Er3 gene in the pea genetic map. Towards this aim, the susceptible pea cv. Messire (er3er3) and a resistant near isogenic line of Messire (cv. Eritreo, Er3Er3) were surveyed with SSRs with known position in the pea map. Three SSRs were polymorphic between “Messire” and “Eritreo” and further surveyed in two contrasting bulks formed by homozygous Er3Er3/er3er3 individuals obtained from a F2 population derived from the cross C2 (Er3Er3) × Messire (er3er3). A single marker, AA349, was polymorphic between the bulks. Subsequently, other ten markers located in the surrounding of AA349 were selected and analysed in Er3Er3 and er3er3 plants. As a results, another SSR, AD61, was found to be polymorphic between Er3Er3 and er3er3 plants. Further linkage analysis confirmed that SSRs AA349 and AD61 were linked to Er3 and to the RAPD and SCAR markers previously reported to be linked to this gene. Er3 gene was located in pea LGIV at 0.39 cM downstream of marker AD61. The location of Er3 gene in the pea map is a first step toward the identification of this gene.

RAPD PCR Profile, Antibiotic Resistance, Prevalence of armA Gene, and Detection of KPC Enzyme in Klebsiella pneumoniae Isolates

Abstract: The increasing prevalence of multidrug-resistant Klebsiella pneumoniae strains isolated from hospitals shows the limitation of recent antibiotics used for bacterial eradication. In this study, 81 K. pneumoniae isolates were collected from three hospitals in Tehran. Antibiotic susceptibility test showed the highest rates of resistance to cefotaxim (85.5%) and ceftazidime (78.3%), and the lowest rates of resistance were detected for colistin (16.9%), streptomycin (16.8%), and chloroamphenicol (21.7%). Eleven different resistance patterns were observed. Sixty-six out of 81 isolates (81.5%) were found to be multidrug resistant (MDR), and 35.8% of them belonged to A3 resistance pattern. 7.4% and 66.7% were KPC enzyme and armA gene positive, respectively. RAPD PCR assay of these bacteria showed 5 clusters, 16 single types, and 14 common types, and there was not any correlation between genetic patterns of the isolates and presence of resistance agents. Simultaneous detection of resistance-creating agents could be an important challenge for combination therapy of MDR K. pneumoniae-caused infections.

RAPD analysis of genetic relatedness among selected quince ( Cydonia oblonga Mill.) accessions from different parts of Turkey

Abstract: Bayazit S., Imrak B., Kuden A., Kemal Gungor M ., 2011. RAPD analysis of genetic relatedness among selected quince ( Cydonia oblonga Mill.) accessions from different parts of Turkey . Hort. Sci. (Prague), 38: 134–141. Quince ( Cydonia oblonga Mill.) is a minor fruit crop, which is primarily used for marmalade, jam, sauce and as root stocks for pears. Different cultivated and local quince genotypes are grown in almost all parts of Turkey for fruit usage. In this study, randomly amplified polymorphic DNA (RAPD) technology was used to study the genetic relationships among 13 quince accessions selected from different parts of Turkey. Thirty decamer primers were used and 14 of them did not produce any polymorphism. The remaining 16 primers ranged in their amplification fragments between one (P-402, P-437, OPA 10, OPA 16, OPA 18 and OPA-19) and five (OPA-06 and OPA-07). The size of fragments varied from 100 to 1500 bp. Similarity values among the studied genotypes ranged between 0.483 and 0.925. The resulting dendrogram clustered into two groups (0.69 similarity value) based on evaluation of genetic similarities and differences. The results suggest that RAPD analysis could be used to distinguish and determine genetic variation among quince accessions. Also, the obtained clustering based on RAPD markers agreed to some extent with the geographical origin of the studied set of quince accessions.

Genetic diversity analysis using RAPD and ISSR markers revealed discrete genetic makeup in relation to fibre and oil content in Linum usitatissimum L. genotypes

Abstract: Flax is an important commercial crop yielding oil, fibre and medicinal products. Present study reports the genetic diversity analysis in a collection of 28 genotypes of flax, including 9 exotic lines. Randomly amplified polymorphic DNA and inter-simple sequence repeat markers were used to study the genetic diversity. The characterized genotypes showed high level of genetic variation with respect to oil and fibre contents of genotypes. Altogether, 27 markers amplified 130 fragments with an average of 4.8 fragments and mean polymorphism information content and marker index values of 0.385 and 1.90 respectively. Jaccards coefficient based dendrogram grouped all genotypes into three groups and separated genotypes based on their oil and fibre contents. STRUCTURE analysis showed two genetic stocks for all the analyzed genotypes and recorded higher admixture in indigenous germplasm. Overall, the results showed that the characterized genotypes were highly diverse genetically and can be used in future breeding and improvement programmes in this crop. Specifically, genotypes such as KL-257, KL-236, Surbhi, Bahgsu and Himani can be used as diverse parents in breeding programmes for generating improved lines in context to oil content.

Genetic structure of Galdieria populations from Iceland

Abstract: Galdieria is a photosynthetic unicellular protist, inhabiting thermoacidic environments around the world. The synchronicity of these thermoacidophilic algae with their extreme habitats makes them unable to thrive in different ecological conditions. The genetic structure of Galdieria populations has not yet been studied. In this report, the level of genetic diversity and structure of five Galdieria populations from Iceland were assessed through both random amplified polymorphic DNA (RAPD) markers, and a partial calmodulin gene fragment (previously used to assess the population structure of these extremophilic algae). The level of population differentiation from both the RAPD and CaM markers was estimated using PLP, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index, Ks, Kst. The migration ability of the Galdieria populations was suggested by the high level of genetic variations scored within each Galdieria population and by the small number of polymorphisms detected between the different Icelandic populations. The low genetic diversity between the two species was highlighted by RAPD and calmodulin markers, suggesting for the first time an interspecific genetic flow between species as strategy to evolve in stressful environments.

Molecular identification of clinical Candida isolates by simple and randomly amplified polymorphic DNA-PCR

Abstract: Thirty yeast isolates were obtained from specimens taken from different patients (sputum, vaginal and oral swabs). The isolates were identified by phenotyping and molecular methods. Six of the isolates were Candida albicans, identified by germ tube and CHROMagar. Three isolates were identified by CHROMagar as C. krusei. The remaining (21) clinical yeast isolates included C. sphaerica, C. guilliermondii C. kefyr, C. famata, C. glabrata, C. parapsilosis and C. norvegensis identified by Vitek2 and further confirmed by PCR. RAPD-PCR was also used in an attempt to identify DNA “fingerprints” for specific Candida spp. The DNA fingerprints of all Candida spp. except for C. sphaerica were determined.

Analysis of virulence and genetic variability of Alternaria alternata associated with leaf spot disease in potato plants in Iran

Abstract: Leaf spot disease in potato is caused by Alternaria alternata (Fr.) Keissler, an opportunistic pathogen that infests many agricultural crops worldwide in the field and during postharvest storage of vegetables and fruits. Alternaria alternata is associated with leaf spot disease in potato in Iran. Thus, there is a need to investigate the virulence and genetic variability of Iranian A. alternata isolates to facilitate the development of appropriate management strategies. In the present study, we analyzed a total of 28 isolates obtained from the main potato-growing regions of Iran, including the Ardebil, Hamedan, Isfahan, and Fars provinces. The pathogens were characterized based on sequence analysis of the genes encoding glyceraldehyde-3-phosphate dehydrogenase ( gpd ), plasma membrane ATPase, Alternaria allergen a 1 (Alt a1), calmodulin, and actin. In addition, random amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), and virulence studies were performed. Phylogenetic analysis of the combined dataset indicated that the five representative isolates were grouped with the subcluster comprising A. alternata . RAPD and ISSR analyses clustered the 28 A. alternata isolates into different groups with no correlation with their corresponding geographical origins. Results of the pathogenicity assay indicated that all A. alternata isolates were pathogenic against potato. However, the A. alternata isolates showed high variability in terms of virulence.

Genetic variability among seven cultivars of date palm (Phoenix dactylifera L.) based on embryonic DNA of old fruit

Abstract: One of the important factors in molecular biology analysis is DNA extraction process to obtain high quality DNA. Previously, all attempts to extract DNA from date palm involved either the use of fresh leaves or germinated seeds. The aim of this study was to extract genomic DNA from various parts of three years old date palm fruit and to evaluate the genetic diversity among seven cultivars of date palm. The fruit of each cultivar was dissected into perianth, seed without embryo, zygotic embryo, and endocarp-mescocarp-epicarp to extract the DNA. The results showed that genomic DNA could be easily extracted in sufficient quantity from zygotic embryo. Both RAPD and ISSR markers could effectively determine the genetic relationship among datepalm cultivars with polymorphism percentage ranging between 32.09% and 36.49% respectively. RAPD markers showed that cultivars with highest similarity value were Lbanah and Nabtat Ali (80.0%), followed by Khalas and Sukkary (73.81%), while the least were Ajwa and Safawi (59.56%). ISSR revealed that the highest similarity values were for Anbar and Khalas (88.0%), followed by Lbanah and Nabtat Ali (86.18%), while the least were Khalas and Safawi (73. 81%).

Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L.) Genotypes

Abstract: Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods The most efficient way of diversity estimation is application of molecular markers In this study, twenty random amplified polymorphic DNA (RAPD) primers were utilized to estimate the genetic diversity between ten sunflower genotypes Overall 227 bands were amplified by 20 primers with an average of 1135 bands per primer RAPD data showed 8634% polymorophic bands and 1365% of monomorophic bands Genetic similarity was ranged from 5022% to 8722% The lowest similarity (5022%) was observed between FH-352 and FH-359 and the maximum similarity 8722% was observed between A-23 and G-46 Polymorphic information content (PIC) values were varying from 005 to 012 with a mean of 009 Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2 Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes Ample diversity was found in all the genotypes Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement

Genetic Diversity between Pumpkin Accessions Growing in the Northern Border Region in Saudi Arabia Based on Biochemical and Molecular Parameters

Abstract: THE GENETIC variation and relationships among 16 pumpkin accessions of Cucurbita moschata & Cucurbita maxima were assessed based on variation in fruit shape, skin color, flesh and size of fruits. Polyacrylamide gel electrophoresis of seed protein and molecular markers revealed by SCoT and ISSR techniques. The SDS-PAGE electropherogram showed 12 bands; two (75 and 145 kDa) were found in accessions (1-8) and one (85 kDa) was found in accessions 9-16. Other three bands were unique to accessions 1, 2 & 11. Five ISSR primers produced 79 markers ranging in molecular size from 130 to 2140 bp. Six SCoT primers produced 173 markers ranging from 135 to 2660 bp. The ISSR polymorphism among the examined accessions was 100% in the case of primers 49A, 44 B and HB-12, and was 92% for primer HB-15. Similarly, 100% polymorphism was scored for the primers SCoT8, SCoT11, SCoT12 and SCoT14. The lowest polymorphism was 93.94% in case of primer SCoT1. Our data based on protein, RAPD and ISSR data using the SYSTAT version 7.0 program clearly distinguished accessions from each other.

Conversion of sequence-characterized amplified region (SCAR) bands into high-throughput DNA markers based on RAPD technique for detection of the stem nematode Ditylenchus dipsaci in crucial plant hosts

Abstract: Ditylenchus dipsaci, the stem nematode, is a migratory endoparasite of over 500 species of angiosperms. The main method of D. dipsaci control is crop rotation, but the presence of morphologically indistinguishable host races with different host preferences makes rotation generally ineffective. Therefore, a sensitive, rapid, reliable, as well as cost effective technique is needed for identification of D. dipsaci in biological samples. This study describes the development of species-specific pairs of PCR oligonucleotides for detection and identification of the D. dipsaci stem nematode in various plant hosts. Designed DIT-2 primer pair specifically amplified a fragment of 325 bp, while DIT-5 primer pair always produced a fragment of 245 bp in all D. dipsaci isolates. Two developed SCAR primer pairs were further tested using template DNA extracted from a collection of twelve healthy plant hosts; no amplification was however observed. The developed PCR protocol has proved to be quite sensitive and able to specifically detect D. dipsaci in artificially infested plant tissues.

Evaluation of Genetic Diversity in 19 Glycine max (L.) Merr. Accessions Included in the Czech National Collection of Soybean Genotypes

Abstract: The random amplified polymorphic DNA (RAPD) technique was used to evaluate both genetic diversity among 19 soybean accessions included in the Czech National Collection of Soybean Genotypes and their potential as a new source of genetic variations for soybean breeding programs. Only 22 of all the 40 random primers used in RAPD reactions showed poly- morphism acceptable for an effective characterisation of these accessions. Altogether 122 highly reproducible RAPD fragments were generated, 55 of them were polymorphic (46%). However, because of the previously observed low degree of RAPD poly- morphism in the case of Glycine max, fragments with low level of informativeness were evaluated, too. Presented results enable the selection of genetically distinct individuals. Such information may be useful to breeders willing to use genetically divers e introductions in soybean improvement process.

SCAR Marker for Gender Identification in Date Palm ( Phoenix dactylifera L.) at the Seedling Stage.

Abstract: Date palm (Phoenix dactylifera L.) is cultivated in arid and semiarid regions worldwide. Given the dioecious nature of this plant, gender identification is very important at the seedling stage. Molecular markers are very effective tools that help in gender identification at this stage. A sequence characterized amplified region (SCAR) marker linked to sex-specific regions in the genome of date palm was developed. Of the 300 tested randomly amplified polymorphic DNA (RAPD) primers, only one primer (OPC-06) produced reproducible band (294 bp) in male plants. The PCR product of this primer was cloned and sequenced. The specific primers were synthesized for amplification of a 186 bp fragment in male date palm plants. These primers were validated in male and female date palm plants, wherein the designed SCAR marker was reported only in male plants and no amplification was observed in female plants. The developed SCAR marker was used with seedlings of date palm and proved very effective in identification of gender.

Genetic variation in relation to adaptability of three mangrove species from the Indian Sundarbans assessed with RAPD and ISSR markers

Abstract: Rich genetic polymorphism is important for plants to adapt to changes because it enables the plant to make anatomical, physiological and biochemical changes in response to abiotic stress. Geomorphologic characteristics, demographic interference and a cumulative decrease in freshwater influx in the Indian Sundarbans region have proved detrimental to some economically important plants. In this study, genetic polymorphism of three mangrove species, Xylocarpus granatum, Excoecaria agallocha, and Phoenix paludosa, was assessed using RAPD and ISSR molecular markers. X. granatum, already in distress in the Sundarbans, had the least genetic polymorphism, 14.56% in the RAPD analysis and 12.92% in the ISSR. Relatively higher genetic polymorphism was recorded for the profusely growing E. agallocha and P. paludosa: 24.66 and 26.4% in RAPD; 24.87 and 20.32% in ISSR analysis respectively. A UPGMA dendrogram constructed using the similarity matrix from RAPD, ISSR and combined data showed that for X. granatum, the least and highest salinity zones clustered together, whereas for E. agallocha and P. paludosa, higher and lower salinity areas clustered in different clades. Nei’s genetic diversity, calculated from RAPD and ISSR data, was also in accordance with 0.0637 and 0.0583 for X. granatum, respectively, much lower than 0.0794 and 0.0818 for E. agallocha and 0.0799 and 0.0688 for P. paludosa. This opposing degree of polymorphism might be attributed to the profusely growing E. agallocha and P. paludosa and precarious status of X. granatum throughout the Indian Sundarbans.

Genetic and phenotypic variation among Turkish terrestrial orchid species as revealed by RAPD and morphological characteristics

Abstract: Terrestrial orchid species are natural sources of salep and a closely related group of plant species widely distributed throughout Turkey. The phylogenetic relationship among fourteen different tuber-producing orchid species was investigated after analyzing phenotypic and genetic variation within and among the natural population through fifteen morphometric traits and ten random amplified polymorphic DNA (RAPD) primer combinations. Statistical analyses (principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster analysis) using the generated data identified taxonomic and genetic distance within the studied plant samples. The results of PCA from morphological traits show that there are no major groupings within and among different species instead somehow overlapping with few distinctly characterized species. In addition, the UPGMA-based phenogram with Euclidean distance (0-1) produces five major clusters among the studied orchid species according to their taxonomic status with few exceptions. On the other hand, PCoA and the phylogenetic dendrogram with the coefficient (0.56-0.79) from RAPD band profiles determine the true genetic diversity of those species. Although both combinations of genetic and phenotypic characteristics reveal the phylogenetic relationship of some those studied species very effectively, they are not clear for others. These results suggest that in the natural population of terrestrial orchid species significant amounts of gene flow are ongoing at intra/interspecies level. Therefore, it is recommended that conservation studies of these groups of orchid species should be done as a geographical unit rather than according to taxonomic status.