Showing papers on "RAPD published in 2009"
TL;DR: It is proposed that this method could be used in conjunction with RAPD markers for applications such as genetic analysis, bulked segregant analysis, and quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.
Abstract: Random amplified polymorphic DNA (RAPD) markers have been used for numerous applications in plant molecular genetics research despite having disadvantages of poor reproducibility and not generally being associated with gene regions. A novel method for generating plant DNA markers was developed based on the short conserved region flanking the ATG start codon in plant genes. This method uses single 18-mer primers in single primer polymerase chain reaction (PCR) and an annealing temperature of 50°C. PCR amplicons are resolved using standard agarose gel electrophoresis. This method was validated in rice using a genetically diverse set of genotypes and a backcross population. Reproducibility was evaluated by using duplicate samples and conducting PCR on different days. Start codon targeted (SCoT) markers were generally reproducible but exceptions indicated that primer length and annealing temperature are not the sole factors determining reproducibility. SCoT marker PCR amplification profiles indicated dominant marker like RAPD markers. We propose that this method could be used in conjunction with these markers for applications such as genetic analysis, bulked segregant analysis, and quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.
589 citations
Journal Article•
TL;DR: This review will discuss about the biochemical and molecular markers their Advantages, disadvantages and the applications of the marker in comparison with other markers types.
Abstract: During the last few decades, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiates in two types first non PCR based (RFLP) and second is PCR based markers (RAPD, AFLP, SSR, SNP etc.), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about the biochemical and molecular markers their Advantages, disadvantages and the applications of the marker in comparison with other markers types.
308 citations
TL;DR: Narrow genetic variation among accessions from different regions of the world and rich diversity among Mexican genotypes in terms of phorbol ester content and distinct molecular profiles indicates the need for exploitation of germplasm from Mexico in J. curcas breeding programmes.
183 citations
TL;DR: This study characterized 95 enterococci isolated from 3 different goats' milk cheeses, belonging to the species Enterococcus devriesei,Enterococcus faecalis and E. malodoratus, among others, and found that the genotypes tended to be specific to particular cheeses; only two of the different cheeses contained two genotypes.
167 citations
TL;DR: These RAPD and AFLP identified markers will help in selective cultivation of specific variety and along with SSRs these markers can be exploited for further improvement of the species through breeding and Marker Ass Selection (MAS).
Abstract: Jatropha curcas L., a multipurpose shrub has acquired significant economic importance for its seed oil which can be converted to biodiesel, is emerging as an alternative to petro-diesel. The deoiled seed cake remains after oil extraction is toxic and cannot be used as a feed despite having best nutritional contents. No quantitative and qualitative differences were observed between toxic and non-toxic varieties of J. curcas except for phorbol esters content. Development of molecular marker will enable to differentiate non-toxic from toxic variety in a mixed population and also help in improvement of the species through marker assisted breeding programs. The present investigation was undertaken to characterize the toxic and non-toxic varieties at molecular level and to develop PCR based molecular markers for distinguishing non-toxic from toxic or vice versa. The polymorphic markers were successfully identified specific to non-toxic and toxic variety using RAPD and AFLP techniques. Totally 371 RAPD, 1,442 AFLP markers were analyzed and 56 (15.09%) RAPD, 238 (16.49%) AFLP markers were found specific to either of the varieties. Genetic similarity between non-toxic and toxic verity was found to be 0.92 by RAPD and 0.90 by AFLP fingerprinting. In the present study out of 12 microsatellite markers analyzed, seven markers were found polymorphic. Among these seven, jcms21 showed homozygous allele in the toxic variety. The study demonstrated that both RAPD and AFLP techniques were equally competitive in identifying polymorphic markers and differentiating both the varieties of J. curcas. Polymorphism of SSR markers prevailed between the varieties of J. curcas. These RAPD and AFLP identified markers will help in selective cultivation of specific variety and along with SSRs these markers can be exploited for further improvement of the species through breeding and Marker Assisted Selection (MAS).
131 citations
TL;DR: Results suggest that genomic template stability reflecting changes in RAPD profiles were significantly affected and it compared favourably with the traditional indices such as growth and soluble protein level at the above Cd concentrations.
117 citations
TL;DR: It is concluded that both RAPD and AFLP techniques are comparable in divergence studies of Jatropha species and can be employed efficiently for interspecific hybrids identification, marker assisted selection and genetic resource management.
Abstract: Genus Jatropha with 172 species having significant economic importance belongs to the family Euphorbiaceae. There are no reports on molecular characterization and phylogenetic relationship among the species of Jatropha. Hence, the present study was undertaken to assess the extent of genetic variability that exist and also to establish phylogenetic relationship among Jatropha curcas, J. glandulifera, J. gossypifolia, J. integerrima, J. multifida, J. podagrica and J. tanjorensis using RAPD and AFLP. The percentage of loci that are polymorphic among the species studied was found to be 97.74% by RAPD and 97.25% by AFLP. The mean percentage of polymorphism (PP) was found to be 68.48 by RAPD and 71.33 by AFLP. The phylogram generated with RAPD and AFLP data showed maximum similarity. With the generated data maximum relatedness was found between J. curcas and J. integerrima this may be the reason for the success of inter hybrid crosses between these two species. Neither RAPD nor AFLP data generated in this study supports the view of J. tanjorensis, a natural interspecific hybrid between J. curcas and J. gossypifolia. The present study concludes that both RAPD and AFLP techniques are comparable in divergence studies of Jatropha species. The markers generated by RAPD and AFLP can be employed efficiently for interspecific hybrids identification, marker assisted selection and genetic resource management.
105 citations
TL;DR: It is concluded that DNA alterations detected by RAPD analysis offered a useful biomarker assay for the evaluation of genotoxic effects of Hg, B, Cr and Zn pollutions on plants.
101 citations
TL;DR: The emergence of Escherichia coli that produce extended spectrum β-lactamases (ESBLs) and are multidrug resistant (MDR), and some of the antibiotic resistance genes were likely plasmid-encoded and transmissible were studied.
Abstract: The emergence of Escherichia coli that produce extended spectrum beta-lactamases (ESBLs) and are multidrug resistant (MDR) poses antibiotic management problems. Forty-seven E. coli isolates from various public hospitals in Malaysia were studied. All isolates were sensitive to imipenem whereas 36 were MDR (resistant to 2 or more classes of antibiotics). PCR detection using gene-specific primers showed that 87.5% of the ESBL-producing E. coli harbored the blaTEM gene. Other ESBL-encoding genes detected were blaOXA, blaSHV, and blaCTX-M. Integron-encoded integrases were detected in 55.3% of isolates, with class 1 integron-encoded intI1 integrase being the majority. Amplification and sequence analysis of the 5'CS region of the integrons showed known antibiotic resistance-encoding gene cassettes of various sizes that were inserted within the respective integrons. Conjugation and transformation experiments indicated that some of the antibiotic resistance genes were likely plasmid-encoded and transmissible. All 47 isolates were subtyped by PFGE and PCR-based fingerprinting using random amplified polymorphic DNA (RAPD), repetitive extragenic palindromes (REPs), and enterobacterial repetitive intergenic consensus (ERIC). These isolates were very diverse and heterogeneous. PFGE, ERIC, and REP-PCR methods were more discriminative than RAPD in subtyping the E. coli isolates.
98 citations
TL;DR: This study showed that information based on fruit characteristics and RAPD markers are complementary for genetic discrimination in soft-seed pomegranate accessions, and some accessions are hard or semi-hard seeded.
94 citations
TL;DR: It is concluded that RAPD polymorphisms are useful as genetic markers for cattle breed differentiation in pools of DNA representing three Zebu cattle breeds.
Abstract: A total of 141 short primers, of arbitrary nucleotide sequence, were used singly in polymerase chain reactions to amplify DNA fingerprints in pools of DNA representing three Zebu cattle breeds. Two primers, which discriminated between the breed-specific DNA pools were used further to amplify individual pool components in order to establish band frequencies of the amplified fingerprints. One of the primers (ILO 1127) amplified a RAPD fingerprint in 61% of TSZ animals but less than 6% in the other breeds, while another primer (ILO 1065) revealed a DNA sequence common to 89% of the Boran animals and less than 30% in the other two breeds. Bandsharing and mean average percentage difference calculated within and between the three breeds using RAPD fingerprint data showed a higher degree of homogeneity within than across the breeds and indicated measurable divergence between the three breeds. It is concluded that RAPD polymorphisms are useful as genetic markers for cattle breed differentiation.
TL;DR: Wide diversity in safflower germplasm indicates a considerable potential for improving this crop for both agronomic and quality traits and neither principal component analysis (PCA) nor marker analysis revealed a clear relationship between diversity pattern and geographical origin.
Abstract: Patterns of geographical diversity, and the relationship between agro-morphological traits and fatty acid composition were assessed for 193 safflower (Carthamus tinctorius) accessions representing forty countries. Accessions were assigned to eight groups based on geographical proximity. Cluster and Principal Component analyses were performed to assess patterns of diversity among the accessions and to select the most distant accessions from each of eight groups for analysis of randomly amplified polymorphic DNA (RAPD) markers. There was a large amount of diversity for agro-morphological traits, fatty acid composition, and RAPD markers. Most correlations among different traits were rather low. Plant height showed a positive correlation with days to flowering (r = 0.63**). Palmitic acid was positively correlated with stearic acid and oleic acid values, and negatively correlated with linoleic acid (P < 0.01). Oleic acid and linoleic acid showed a strong negative correlation (r = −0.89**). The first three principal components together explained 59% of the variation, however, neither principal component analysis (PCA) nor marker analysis revealed a clear relationship between diversity pattern and geographical origin. Accessions from some geographical regions tended to group together, such as accessions from South Western Asia, Central Western Europe, and the Mediterranean region. The correlation between the morphological matrix and the genetic matrix based on RAPD markers was not significant (r = 0.027). Wide diversity in safflower germplasm indicates a considerable potential for improving this crop for both agronomic and quality traits.
TL;DR: A simple and efficient plant DNA extraction procedure for isolation of high-quality DNA from plant tissues is presented in this paper, which requires maceration of plant tissue of about 1.0 cm(2) (e.g. of a leaf blade) in DNA extraction buffer (100 mM Tris-HCl, 100 mM EDTA, 250 mM NaCl) using 1.5-mL microfuge tubes, followed by cell lysis with 20% SDS, and DNA extraction with phenol: chloroform: iso-amyl alcohol (25:24:
Abstract: Polymerase chain reaction has found wide applications in modern research involving transformations and other genomic studies. For reproducible PCR results, however, the quantity and quality of template DNA is of considerable importance. A simple and efficient plant DNA extraction procedure for isolation of high-quality DNA from plant tissues is presented here. It requires maceration of plant tissue of about 1.0 cm(2) (e.g. of a leaf blade) in DNA extraction buffer (100 mM Tris-HCl, 100 mM EDTA, 250 mM NaCl) using 1.5-mL microfuge tubes, followed by cell lysis with 20% SDS, and DNA extraction with phenol: chloroform: iso-amyl alcohol (25:24:1). Hydrated ether is then used to remove polysaccharides and other contaminants from the DNA preparation. Average DNA yield is 20-30 microg cm(-2) for fresh tissues, and ratio of absorbance at 260 nm to absorbance at 280 nm is 1.5-1.8. The DNA is quite suitable for PCR using microsatellites, RAPD and specific markers for recombinant selection. Amplifications have been obtained for these markers by using template DNA extracted from fresh as well as frozen leaf tissues of various plants, including barley, oat, potato and tomato. DNA stored for more than 2 years has been successfully amplified with microsatellite markers, which shows suitability of this method after long-term storage of DNA. Besides, the ease of use and cost-effectiveness make the procedure attractive.
TL;DR: Evaluation of backcross interspecific derivatives of cross involving J. curcas and J. integerrima indicate scope for prebreeding and genetic enhancement of Jatropha curcas through interspecific hybridization.
Abstract: The present study aims at characterization of Jatropha species occurring in India using nuclear and organelle specific primers for supporting interspecific gene transfer. DNA from 34 accessions comprising eight agronomically important species (Jatropha curcas, J. gossypifolia, J. glandulifera, J. integerrima, J. podagrica, J. multifida, J. villosa, J. villosa. var. ramnadensis, J. maheshwarii) and a natural hybrid, J. tanjorensis were subjected to molecular analysis using 200 RAPD, 100 ISSR and 50 organelle specific microsatellite primers from other angiosperms. The nuclear marker systems revealed high interspecific genetic variation (98.5% polymorphism) corroborating with the morphological differentiation of the species used in the study. Ten organelle specific microsatellite primers resulted in single, discrete bands of which three were functional disclosing polymorphism among Jatropha species. The PCR products obtained with organelle specific primers were subjected to sequence analysis. PCR products from two consensus chloroplast microsatellite primer pairs (ccmp6 and 10) revealed variable number of T and A residues in the intergenic regions of ORF 77–ORF 82 and rp12–rps19 regions, respectively in Jatropha. Artificial hybrids were produced between J. curcas and all Jatropha species used in the study with the exception of J. podagrica. Characterization of F1 hybrids using polymorphic primers specific to the respective parental species confirmed the hybridity of the interspecific hybrids. Characterization of both natural and artificially produced hybrids using chloroplast specific markers revealed maternal inheritance of the markers. While the RAPD and ISSR markers confirmed J. tanjorensis as a natural hybrid between J. gossypifolia and J. curcas, the ccmp primers (ccmp6 and 10) unequivocally established J. gossypifolia as the maternal parent. Evaluation of backcross interspecific derivatives of cross involving J. curcas and J. integerrima indicate scope for prebreeding and genetic enhancement of Jatropha curcas through interspecific hybridization.
TL;DR: It was found that metabolites secreted by Erwinia/Pantoea and B. cepacia isolates had an inhibitory growth effect on some endophytic fungi, suggesting that these metabolites play a role in bacterial-fungal interactions inside the host plant.
Abstract: Endophytic bacteria were isolated from stems of Eucalyptus spp (Eucalyptus citriodora, E. grandis, E. urophylla, E. camaldulensis, E. torelliana, E. pellita, and a hybrid of E. grandis and E. urophylla) cultivated at two sites; they were characterized by RAPD and amplified rDNA restriction analysis (ARDRA). Endophytic bacteria were more frequently isolated from E. grandis and E. pellita. The 76 isolates were identified by 16S rDNA sequencing as Erwinia/Pantoea (45%), Agrobacterium sp (21%), Curtobacterium sp (9%), Brevibacillus sp (8%), Pseudomonas sp (8%), Acinetobacter sp (4%), Burkholderia cepacia (2.6%), and Lactococcus lactis (2.6%). Genetic characterization of these endophytic bacteria isolates showed at least eight ARDRA haplotypes. The genetic diversity of 32 Erwinia/Pantoea and 16 Agrobacterium sp isolates was assessed with the RAPD technique. There was a high level of genetic polymorphism among all the isolates and there was positive correlation between the clusters and the geographic origin of the strains. These endophytic bacteria were further analyzed for in vitro interaction with endophytic fungi from Eucalyptus spp. We found that metabolites secreted by Erwinia/Pantoea and B. cepacia isolates had an inhibitory growth effect on some endophytic fungi, suggesting that these metabolites play a role in bacterial-fungal interactions inside the host plant. Apparently, these bacteria could have an important role in plant development; in the future they may be useful for biological control of diseases and plant growth promotion, as well as for the production of new metabolites and enzymes.
TL;DR: The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated and showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazoles, itraconazole and voriconazole.
Abstract: The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated in this study. Randomly amplified polymorphic DNA (RAPD) analysis generated 5 unique profiles from 42 isolates. Based on the major DNA fragments of the RAPD profiles, the isolates were identified as RAPD type P1 (29 isolates), P2 (6 isolates), P3 (4 isolates), P4 (2 isolates) and P5 (1 isolate). Sequence analysis of the internal transcribed spacer (ITS) gene of the isolates identified RAPD type P1 as C. parapsilosis, P2 and P3 as Candida orthopsilosis, P4 as Candida metapsilosis, and P5 as Lodderomyces elongisporus. Nucleotide variations in ITS gene sequences of C. orthopsilosis and C. metapsilosis were detected. Antifungal susceptibility testing using Etests showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazole, itraconazole and voriconazole. C. parapsilosis isolates exhibited higher MIC(50) values than those of C. orthopsilosis for all of the drugs tested in this study; however, no significant difference in the MICs for these two Candida species was observed. The fact that C. orthopsilosis and C. metapsilosis were responsible for 23.8 and 4.8 % of the cases attributed to C. parapsilosis bloodstream infections, respectively, indicates the clinical relevance of these newly described yeasts. Further investigations of the ecological niche, mode of transmission and virulence of these species are thus essential.
TL;DR: Cluster analysis of the RAPD profiles revealed an average similarity coefficient of 0.944 thus confirming molecular stability of plants derived from encapsulated microshoots following 6 months of storage, and confirmed that Cineraria maritima can be transplanted to the greenhouse in three batches with 90% frequency of survival.
Abstract: Regrowth of encapsulated microshoots, using alginate encapsulation, of Cineraria maritima reached 82.35% following 6 months of storage. Amongst developing plantlets, 33.33% exhibited formation of multiple shoots at the onset of regrowth and 11.76% demonstrated simultaneous formation of shoots and roots. Healthy root formation was observed in plantlets following 2 weeks of their transfer to half-strength Murashige and Skoog medium containing 1.0 mg l−1 α-naphthalene acetic acid. Plants were transplanted to the greenhouse in three batches with 90% frequency of survival. Molecular analysis of randomly selected plants from each batch was conducted using 20 random amplified polymorphic DNA (RAPD) markers. Of 20 primers tested, 14 produced amplification products, and a total of 69 bands with an average of 4.93 bands per primer were observed. Of these 69 scorable bands, only 20% of bands were polymorphic. Cluster analysis of the RAPD profiles revealed an average similarity coefficient of 0.944 thus confirming molecular stability of plants derived from encapsulated microshoots following 6 months of storage.
TL;DR: Both types of methods complement each other and offer a more complete vision of the microbial diversity of these ecosystems, and the fingerprinting of Lactobacillus populations by length-heterogeneity PCR showed the predominance of the Lb.
TL;DR: The results suggest that the genetic diversity of this fig population is low and that multiple marker utilization is critical to estimate the relatedness of figs at the variety level.
Abstract: Nineteen fig varieties and lines from Europe and Asia have been fingerprinted by ISSR, RAPD, and SSR markers, respectively, using 13, 19, and 13 primer combinations. All primers produced 258 loci, with the highest number of loci (119) generated by RAPD (Rp: 48.42). Clustering analysis was applied to the three marker datasets to elucidate the genetic structure and relationships among these varieties. Mean genetic similarities were 0.787, 0.717, and 0.749, respectively, as determined using ISSR, RAPD, and SSR. Each marker system pro- duced incompletely separated clusters, although a weak binding group based on race type appeared in the combined dataset. Comparisons of coefficients revealed no correlation between different similarity matrices; congruence was observed between similar- ity matrices and co-phenetic matrices in all markers. Analysis of molecular variance (AMOVA) showed that most of the total polymorphism was attributable to within-group variance (ISSRs + RAPDs, 97.41%; SSRs, 90.18%). These results suggest that the genetic diversity of this fig population is low and that multiple marker utilization is critical to estimate the relatedness of figs at the variety level. Additionally, it was presumed that 'Houraihi', the oldest variety in Japan, was disseminated independently of other foreign varieties in the 17th century or before then.
TL;DR: The ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD-PCR, and the possible origin of line-specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.
Abstract: Summary
Thirteen highly inbred chicken lines were analysed at the DNA level by DNA fingerprinting (DFP) and by polymerase chain reaction (PCR) using random primers. In general, the DFP patterns of individuals within a line were identical. The DFP band-sharing (BS) values among lines from different breeds (Leghorn, Fayoumi, Spanish) ranged from 0.10 to 0.20. The DFP BS values among Leghorn lines from different genetic backgrounds ranged from 0.42 to 0.79. The DFP BS values among lines selected for different major histocompatibility complex serotypes from a common genetic background ranged from 0.70 to 0.95. Some randomly amplified polymorphic DNA (RAPD) PCR products were specific to a single line, some to all lines from the same genetic base, and some to all lines from the same breed. The RAPD-PCR band-sharing values ranged from 0.66 to 0.99 for all between-line comparisons. Thus, the ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD-PCR. The possible origin of line-specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.
TL;DR: Diversity and genetic relationship in 100 cashew germplasm accessions were analyzed by using RAPD and ISSR markers and high percentage of polymorphism observed with different markers indicated high level of genetic variation existing among the accessions.
TL;DR: The use of DAMD and RAPD methods that generate the profiles, to study genetic diversity in wild genotypes of the P. granatum in India show that these methods are sufficiently informative to unravel the genetic variations in wild pomegranates in Western Himalayas.
TL;DR: RAPD was efficient in demonstrating the high intraspecific genetic variation among isolates, and their ability to antagonize Sclerotium rolfsii using a dual culture assay was correlated with RAPD profiles.
Abstract: The random amplified polymorphic DNA (RAPD) procedure was used to examine the genetic variability among 8 isolates of Trichoderma harzianum, and their ability to antagonize Sclerotium rolfsii using a dual culture assay was correlated with RAPD profiles. Eight oligodeoxynucleotide primers were selected for the RAPD assays, which resulted in 86 bands for 8 isolates of T. harzianum. The data were entered into a binary matrix and a similarity matrix was constructed using the DICE similarity (SD) index. An unweighted pair grouping mathematical averaging (UPGMA) cluster based on SD values was generated using the NTSYS computer program. A mean coefficient of similarity obtained for pairwise comparisons was c. 30% and it showed that the variability among the isolates of T. harzianum was very high. Using the dual culture method in antagonism experiments, the T. harzianum isolates were classified in to antagonism classes. Further, T. harzianum isolates were screened for chitinase and β-1,3-glucanase activity. RAPD was efficient in demonstrating the high intraspecific genetic variation among isolates. The dendrogram did not show the grouping of isolates by their level of antagonism. Relationship among polymorphism existent, the aggressiveness and the origin of isolates were not found.
TL;DR: The RAPD method did not prove efficient for finding new polymorphisms in either species, because there is a greater presence of polymorphic RAPD markers in sheep, and according to the similarity indices the sheep populations showed a higher degree of homogeneity than the cattle breeds.
Abstract: The present study investigated the use of the random amplified polymorphic DNA (RAPD) method to detect genetic variation in cattle and sheep. The animals studied consisted of samples from five Finnish cattle breeds: native Eastern (18 animals), Northern (24), Western Finncattle (24), Finnish Ayrshire (24), and Finnish Friesian (18); as well as a white (6 animals) and a grey (9) colour type of Finnsheep. The cattle and sheep populations were analysed with 11 and 13 RAPD primers demonstrating the most repeatable amplification pattern. Two out of ten RAPD fragments tested by cross hybridization showed homology between the two species. The RAPD method did not prove efficient for finding new polymorphisms in either species, because we found only three polymorphic RAPD markers for cattle and seven markers for sheep with different allele frequencies between the breeds. Although there is a greater presence of polymorphic RAPD markers in sheep, according to the similarity indices the sheep populations showed a higher degree of homogeneity than the cattle breeds. However, the interbreed and intrabreed similarity indices for cattle did not suggest any significant differentiation of the Finnish breeds, contrary to earlier results based on blood group and protein polymorphism.
TL;DR: Result of cluster analysis based on RAPD data did not show any correlation with morphological characters based on Mantel’s test, and the mineral and fatty acid analysis for defining the nutrient composition of this plant revealed some differences among populations.
TL;DR: All accessions appear identical clones, not only because morphological characters but also at a molecular level, which strongly suggested that C. sativus is a monomorphic species.
Abstract: Background: Saffron (Crocus sativus) is considered the world's most expensive spice. Used mainly as a colorant for foodstuffs, it is highly appreciated for its aromatic and flavouring properties. Since no molecular markers for this species have been found in the literature, the objective of this study was to determine whether phenotypical differences found in C. sativus were supported by molecular analyses. Findings: Thirty primers from Operon Technologies were used in random amplified polymorphic DNA (RAPD) analysis, forty eight primers were screened using intersimple sequence repeats (ISSR) method and fifteen primers derived from a microsatellites library flanking sequences with repeat motifs were assayed in forty three isolates of C. sativus from eleven different countries and a C. kotschyanus isolate was used as outgroup. No polymorphic bands were detected in any of the accessions combining the different approaches used in this study. Conclusion: According to our findings, all accessions appear identical clones, not only because morphological characters but also at a molecular level. These data strongly suggested that C. sativus is a monomorphic species. Thus, genome sequencing is needed to find molecular markers for saffron.
TL;DR: The present comprehensive input, first of its own kind in safflower, will assist marker based improvement programmes in the crop and provide corroborating evidences for the present and previous studies that concluded fragmentation of saffer gene pool into many gene pools.
Abstract: Carthamus tinctorius (2n = 2x = 24), commonly known as safflower, is widely cultivated in agricultural production systems of Asia, Europe, Australia, and the Americas as a source of high quality vegetable and industrial oil. Twenty-two RAPD primers, 18 SSR primers, and 10 AFLP primer combinations were used to assess: (1) the genetic diversity of 85 accessions (originating from 24 countries) representing global germplasm variability of safflower and (2) the interrelationships among safflower ‘centers of similarity’ or ‘regional gene pools’ proposed earlier. The RAPD and SSR primers and AFLP primer combinations revealed 57.6, 68.0, and 71.2% polymorphism, respectively, among 111, 72, and 330 genetic loci amplified from the accessions. The sum of effective number of alleles (66.44), resolving power (59.16), and marker index (51.3) explicitly revealed the relative superiority of AFLP as a marker system in uncovering variation in safflower. Overall, AFLP markers could recognize ‘centers of similarity’ or ‘regional gene pools’. Analysis of molecular variance and Shannon’s information index provided corroborating evidences for the present and previous studies that concluded fragmentation of safflower gene pool into many gene pools. Divergent directional selection is likely to have played an important role in shaping the diversity. From the practical applications standpoint, the diversity of Iran–Afghanistan gene pool is very high, equivalent to the total diversity of the species. The Far East gene pool is the least diverse. The present comprehensive input, first of its own kind in safflower, will assist marker based improvement programmes in the crop.
TL;DR: Ploidy analysis of Cynodon accessions collected from Turkey was determined and SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems.
Abstract: Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.
TL;DR: Two DNA-based molecular marker techniques, intersimple sequence repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in Shisham, showing very good fit correlation in between ISSR- and RAPD-based similarities.
Abstract: Shisham (Dalbergia sissoo) is one of the most preferred timber tree species of South Asia. Two DNA-based molecular marker techniques, intersimple sequence repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in this species. A total of 30 polymorphic primers (15 ISSR and 15 random) were used. Amplification of genomic DNA of 22 genotypes, using ISSR analysis, yielded 117 fragments, of which 64 were polymorphic. Number of amplified fragments with ISSR primers ranged from five to ten and varied in size from 180 to 1,900 bp. Percentage polymorphism ranged from 0 to 87.5. The 15 RAPD primers produced 144 bands across 22 genotypes, of which 84 were polymorphic. The number of amplified bands varied from five to 13, with size range from 180 to 2,400 bp. Percentage polymorphism ranged from 0 to 100, with an average of 58.3 across. RAPD markers were relatively more efficient than the ISSR assay. The mental test between two Jaccard’s similarity matrices gave r ≥ 0.90, showing very good fit correlation in between ISSR- and RAPD-based similarities. Clustering of isolates remained more or less the same in RAPD and combined data of RAPD and ISSR. The similarity coefficient ranged from 0.734 to 0.939, 0.563 to 0.946, and 0.648 to 0.920 with ISSR, RAPD, and combined dendrogram, respectively.
TL;DR: The phylogenetic relationships of 36 locally grown Prunus armeniaca genotypes which are collected from nine sampling sites from two valleys of trans-Himalayan region were analyzed using 31 PCR markers, finding RAPD markers were found more efficient with regards to polymorphism detection.
Abstract: The phylogenetic relationships of 36 locally grown Prunus armeniaca genotypes which are collected from nine sampling sites from two valleys viz. Nubra (9,600 ft) and Leh (11,500 ft) of trans-Himalayan region were analyzed using 31 PCR markers (20 RAPDs and 11 ISSRs). This is the first report of molecular genetic diversity studies in apricot from this region of the world. RAPD analysis yielded 139 fragments, of which 136 were polymorphic, with an average of 6.8 polymorphic fragments per primer. ISSR analysis produced 58 bands, of which 56 were polymorphic, with an average of 5.09 polymorphic fragments per primer. The primers based on (CT)n produced maximum number of bands (nine) while, (AT)n and many other motifs gave no amplification. RAPD markers were found more efficient with regards to polymorphism detection, as they detected 97.84 % as compared to 96.5 % for ISSR markers. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in RAPD and combined data of RAPD + ISSR. The results of PCA analysis were comparable to the cluster analysis. These analyses, allowed us to identify the groups corresponding to the two apricot collection sites.