Showing papers on "RAPD published in 2013"
TL;DR: Extrolite analysis of strains of A. luchuensis showed that they do not produce mycotoxins and therefore can be considered safe for food and beverage fermentations, and the species is probably common in the fermentation environment of East Asia.
Abstract: Aspergilli known as black- and white-koji molds which are used for awamori, shochu, makgeolli and other food and beverage fermentations, are reported in the literature as A. luchuensis, A. awamori, A. kawachii, or A. acidus. In order to elucidate the taxonomic position of these species, available ex-type cultures were compared based on morphology and molecular characters. A. luchuensis, A. kawachii and A. acidus showed the same banding patterns in RAPD, and the three species had the same rDNA-ITS, b-tubulin and calmodulin sequences and these differed from those of the closely related A. niger and A. tubingensis. Morphologically, the three species are not significantly different from each other or from A. niger and A. tubingensis. It is concluded that A. luchuensis, A. kawachii and A. acidus are the same species, and A. luchuensis is selected as the correct name based on priority. Strains of A. awamori which are stored in National Research Institute of Brewing in Japan, represent A. niger (n=14) and A. luchuensis (n=6). The neotype of A. awamori (CBS 557.65= NRRL 4948) does not originate from awamori fermentation and it is shown to be identical with the unknown taxon Aspergillus welwitschiae. Extrolite analysis of strains of A. luchuensis showed that they do not produce mycotoxins and therefore can be considered safe for food and beverage fermentations. A. luchuensis is also frequently isolated from meju and nuruk in Korea and Puerh tea in China and the species is probably common in the fermentation environment of East Asia. A re-description of A. luchuensis is provided because the incomplete data in the original literature.
161 citations
TL;DR: Amplification of monomorphic bands with all primer combinations authenticated the true to type nature of the in vitro raised plants of D. asper which underwent up to 30 subculture passages over a period of approximately 2 years thereby supporting the commercial utilization of the developed micropropagation protocol.
Abstract: Dendrocalamus asper, an edible bamboo is valued for its tender edible shoots in the food industry. However, overexploitation of natural stands of D. asper coupled with minimal conservation and reforestation efforts has led to its rapid depletion in nature. Therefore protocol for rapid multiplication of D. asper via direct regeneration using nodal segments from mature clumps was standardized and more than 25,000 plants were transferred to the field (Singh et al. 2012a). However, genetic fidelity of these in vitro raised plants needs to be authenticated for commercial scale application of the developed micropropagation protocol. PCR-based molecular markers have emerged as simple, fast, reliable and labor-effective tools for testing the genetic fidelity of in vitro raised plants. This study report the genetic fidelity analysis of in vitro raised plants of D. asper for the first time using arbitrary (Random Amplified Polymorphic DNA, RAPD), semi-arbitrary (Inter-Simple Sequence Repeat, ISSR; Amplified Fragment Length Polymorphism, AFLP), and sequence-based (Simple Sequence Repeat, SSR) markers. Bulked DNA samples of 20 in vitro raised shoots (collected after every three subculture cycles starting from 3rd to 30th passage) and field transferred plantlets were compared with the mother plant DNA using 90 primer combinations (25 each of RAPD, ISSR, SSR, and 15 AFLP) and scorable bands were produced by 78 (22 RAPD, 24 ISSR, 21 SSR, and 11 AFLP) primers. A total of 146 distinct and scorable bands were produced by 22 RAPD primers with an average of 6.6 bands per primer while the number of bands for ISSR primers varied from 3 (ISSR-4 and 9) to 13 (ISSR-17), with an average of 7.1 bands per primer. Similarly, SSR markers also showed wide variation in number of bands, ranging from 2 (RM 261) to 12 (RM 44, 140, and 224) with an average of 7.8 bands. AFLP primer combinations could generate 35–72 bands with an average of 48.7 bands per primer pair. Amplification of monomorphic bands with all primer combinations authenticated the true to type nature of the in vitro raised plants of D. asper which underwent up to 30 subculture passages over a period of approximately 2 years thereby supporting the commercial utilization of the developed micropropagation protocol.
67 citations
TL;DR: A huge genetic diversity among the cultivars is revealed and this can be utilised for conservation and cultivar development in breeding programmes to produce high yielding, nutritionally superior cultivars.
Abstract: Moringa oleifera is a less used, drought-tolerant tropical plant, rich in nutritionally and nutraceutically important bioactive compounds. It is native to India and now under cultivation in many countries, but no data is available on genetic variability. Three DNA marker techniques, i.e., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and cytochrome P450 gene-based markers were used for the detection of genetic variability in eight Indian cultivars of M. oleifera, collected from various states of India. A total of 17 RAPD, 6 ISSR and 7 pairs of cytochrome P450-based markers generated 48.68, 48.57 and 40.00 % polymorphisms, respectively. The marker index (MI) for each of these marker systems (3.25 for RAPD, 4.73 ISSR and 2.95 for Cyt P450-based markers) suggest that ISSR markers are the most effective for assessment of genetic diversity. Based on the three types of marker data, the eight cultivars of M. oleifera were grouped into four sub-clusters in a dendrogram, but without any distinct geographical pattern. This suggests spread of planting material and high rates of gene flow through cross pollination. High bootstrap values (94.4 and 82.3) were obtained at major nodes of the dendrogram using the winboot software. The dendrogram and PCA plots generated from the binary data matrices of the three marker systems were found highly concordant to each other. This study reveals a huge genetic diversity among the cultivars and this can be utilised for conservation and cultivar development in breeding programmes to produce high yielding, nutritionally superior cultivars.
57 citations
TL;DR: This study cloned fragments from improved randomly amplified polymorphic DNA (RAPD), developed stably diagnostic sequence-characterized amplified region (SCAR) markers, and provided an effective and precise PCR-based diagnostic method and markers to identify D. longan species.
Abstract: As an edible fruit and source of traditional medicine, D. longan is grown in most areas of Southern China. Identification of D. longan cultivars by using molecular markers is important genetically. In this study, we cloned fragments from improved randomly amplified polymorphic DNA (RAPD), and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific RAPD bands of D. longan cultivars from Guangxi, with size ranging from 500 bp to 900 bp were gel-purified, cloned and sequenced. Four clones named LY2-1, LY4-7, LY4-8 and LY5-2 were identified. In order to investigate whether the fragments were specific for the species, four pairs of SCAR primers were then designed. PCR amplifications were conducted to analyze 18 samples including different D. longan cultivars and other species. The specific bands with expected sizes were amplified in five D. longan samples but not in others. To identify and characterize the difference between D. longan and D. confinis, PCR amplifications were performed again. The specific bands with expected sizes were found in D. longan but not in D. confinis by SCAR markers LY2-1, LY4-7 and LY5-2, respectively. These results showed that our developed SCAR markers could be very useful as a specific D. longan variety authentication. Therefore, our study provides an effective and precise PCR-based diagnostic method and markers to identify D. longan species.
54 citations
TL;DR: In the present investigation, a RAPD marker for tall-type palm trait was identified using a pooled DNA approach and the SCAR marker was utilized in assessing the purity of hybrid seedlings of D × T (Dwarf ×-Tall) cross.
51 citations
TL;DR: It is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers and the in vitro conservation medium (T2) is a safe method for conservation of potato micro Tubers to produce true-to-type plans.
Abstract: The genetic stability of in vitro propagated potato microtubers was assessed using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Microtubers were developed through in vitro from potato microplants using standardized protocols. The microtubers were conserved for 1 year under three different culture media and consequently microplants were regenerated for the DNA analyses. During the study, a total of 38 (10 RAPD, 11 ISSR, 12 SSR and 5 AFLP) primers produced a total of 407 (58 RAPD, 56 ISSR, 96 SSR and 197 AFLP) clear, distinct and reproducible amplicons. Cluster analysis revealed 100 % genetic similarity among the mother plant and its derivatives within the clusters by SSR, ISSR and RAPD analyses, whereas AFLP analysis revealed from 85 to 100 % genetic similarity. Dendrogram analysis based on the Jaccard’s coefficient classified the genotypes into five clusters (I–V), each cluster consisting of mother plant and its derivatives. Principal component analysis (PCA) also plotted mother plant and its genotypes of each cluster together. Based on our results, it is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers. The in vitro conservation medium (T2) is a safe method for conservation of potato microtubers to produce true-to-type plans.
Electronic supplementary material
The online version of this article (doi:10.1007/s12298-013-0190-6) contains supplementary material, which is available to authorized users.
50 citations
TL;DR: This is the first report of genetic characterization of L. japonica using improved RAPD analysis which has been validated by ISSR analysis, and this characterization may be useful for the preservation of genetic diversity and Lonicera population identification.
Abstract: In traditional medicine, Lonicera japonica (Thunb.) has a notable place, and it has been used for thousands of years in China, Japan, Korea and other East-Asian countries for treating cancer, inflammation, hepatic complications, influenza and wounds. However, the molecular or genetic characteristic of this plant is not well defined. In this study, improved random amplified polymorphic DNA (RAPD) has been employed for the genetic characterization of five varieties of L. japonica collected from different geographic locations of Southern China. A total of 147 bands of DNA fragments were obtained in RAPD-PCR by using 18 primers, and the band sizes ranged from approximately 300–2,000 bp, with 3–11 amplified bands for each primer. Based on the RAPD amplification profiles, cluster dendrogram was obtained, which showed that the similarity coefficients among five varieties of L. japonica ranged from 0.59 to 0.77. To our knowledge, this is the first report of genetic characterization of L. japonica using improved RAPD analysis which has been validated by ISSR analysis, and this characterization may be useful for the preservation of genetic diversity and Lonicera population identification. Moreover, as an option, the improved method could be employed for a variety of applications in genetic diversity and fingerprinting analyses.
48 citations
TL;DR: A rapid, efficient and universal protocol for isolating total DNA from the members of Zingiberales which harbor a high amount of polysaccharides and secondary metabolites is described.
Abstract: Different protocols are usually used for extracting total deoxyribonucleic acid (DNA) from different plant species of same order and DNA of the associated viruses. Here, we describe a rapid, efficient and universal protocol for isolating total DNA from the members of Zingiberales which harbor a high amount of polysaccharides and secondary metabolites. DNA isolated with this protocol was successfully used for PCR based downstream applications viz. random amplified polymorphic DNA (RAPD), Inter-simple sequence repeats (ISSR), DNA barcoding gene (Internal transcribed spacer and trnl-f) amplification and detection of the viruses.
47 citations
TL;DR: It is proposed that, since the information provided by morphological and SSR marker systems in walnut is similar, they should serve for cultivar characterization and assessment in genebanks and more advisable to investigate genetic relationships.
46 citations
TL;DR: An efficient in vitro protocol has been established for clonal propagation of elite plant of Spilanthes calva DC, an important source of spilanthol, an antimalarial larvicidal compound, and the genetic fidelity of the in vitro clones was confirmed.
Abstract: An efficient in vitro protocol has been established for clonal propagation of elite plant of Spilanthes calva DC., an important source of spilanthol, an antimalarial larvicidal compound. Nodal explants excised from field grown plant of S. calva DC. when reared on Murashige and Skoog’s medium augmented with different cytokinins, viz. N6-Benzyladenine (BA), N6-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn), differentiated multiple shoots from the axils. BA at 10 μM proved optimum for elicitation of multiple shoots in 91.6 % cultures with an average of 7.12 shoots per explant within 6 weeks. The excised shoots rooted on half strength Murashige and Skoog’s medium supplemented with 0.1 μM IBA. Micropropagated plants were hardened and transferred to field for acclimatization, where 95 % plants survived and were phenotypically similar to the donor plant. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to evaluate the genetic fidelity amongst the regenerants. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 71 scorable bands, ranging in size from 100 bp to 1,100 bp were generated by a combination of the two markers in the aforesaid plants. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant. The similarity values amongst the aforesaid plants varied from 0.967 to 1.000. The dendrogram generated through UPGMA (Unweighted Pair Group Method with arithmetic mean) analysis revealed 98 % similarity amongst them, thus confirming the genetic fidelity of the in vitro clones.
43 citations
TL;DR: The propagation protocol developed in this study provides a basis for germplasm conservation and harnessing the medicinally active compounds of A. violaceum.
Abstract: Aconitum violaceum Jacq. is an important medicinal species used for various health ailments including renal pain, rheumatism and high fever. In the present report, a reproducible in vitro regeneration system for Aconitum violaceum Jacq. has developed from the nodal segment of the plant. Induction of shoot buds was achieved on basal Murashige and Skoog (MS) medium. The shoots were elongated on MS medium supplemented with 0.5 μM 6-benzylaminopurine (BAP) and 0.1 μM α-napthaleneacetic acid (NAA) and subsequently transferred to rooting medium. In vitro grown microshoots of A. violaceum were encapsulated in the alginate beads. The success rate of their re-growth was found to be approximately 85.43 %. Of the encapsulated microshoots, 39.86 % exhibited formation of multiple shoots following re-growth on plant growth regulator free MS medium. Healthy root formation was observed in all microshoots following 2 weeks of transfer on half-strength MS medium containing 0.1 μM indole-3-acetic acid (IAA) and 1.0 μM α-naphthalene acetic acid (NAA). These plants were subsequently transferred to pots containing a mixture of soil, sand and compost (1:1:1 v/v), and same were then shifted in the greenhouse with 87 % survival rate. The molecular analysis was carried out using 35 random amplified polymorphic DNAs (RAPD) primers and 25 inter simple sequence repeats (ISSR) primers. Cluster analysis of the RAPD and ISSR profile revealed an average similarity coefficient of 0.966 and 0.974, respectively, confirming genetic stability of tissue culture-raised (TR) plants and synthetic seed-derived plants (SR). The phytochemical analysis of tissue culture-raised and synthetic seeds-derived plants showed higher aconitine content than control plant. The propagation protocol developed in this study provides a basis for germplasm conservation and harnessing the medicinally active compounds of A. violaceum.
TL;DR: This study showed that rapid and cost-effective markers like RAPD and ISSR coupled with appropriate statistical tools can be successfully applied to study phylogenetic relationships at the interspecific and intraspecific level in Allium.
Abstract: RAPD and ISSR markers have been used to reveal the genetic diversity and phylogenetic analysis of some economically important species of Allium. Two plants related to Allium were also included for better understanding of the phylogeny. ISSR showed more polymorphism within A. cepa and A. sativum, while RAPD showed more polymorphism within A. porrum. Overall, RAPD revealed more intraspecific diversity than ISSR, while ISSR showed more interspecific diversity than RAPD. This showed the usefulness of using both markers for the study of Allium. UPGMA-based dendrograms showed a close relationship between Allium sativum and Allium porrum. A. porrum showed less genetic variability than A. cepa and A. sativum. Several unique bands were identified with RAPD and ISSR, which can be converted into cultivar-specific markers. Principal coordinated analysis, however, showed some minor differences with UPGMA-based dendrograms. This study showed that rapid and cost-effective markers like RAPD and ISSR coupled with appropriate statistical tools can be successfully applied to study phylogenetic relationships at the interspecific and intraspecific level in Allium. These markers proved to be suitable for both phylogenetic studies among different species as well as for characterisation of different cultivars of Allium.
TL;DR: Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies; among the molecular markers, ISSR revealed more genetic variation among the genotypes, however, using all three typesof molecular markers provided a better overall view of cotton genome polymorphism.
Abstract: Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F(2) progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism. The OPB12/OPH08 primer gave the highest effective number of alleles (N(E)), and the largest Shannon index (I), Nei's genetic diversity (H), and polymorphism information content (PIC) values. Some RAPD bands were present in the parental genotypes but were absent in their hybrids. Ten ISSR primers produced 206 reproducible bands, with 49.4% polymorphism. The UBC807 locus gave the highest N(E), I, H, and PIC values. Some ISSR bands occurred only in the parental genotype, while others were only present in the hybrid genotypes. Four microsatellite loci produced 12 alleles, ranging from 181 to 236 bp, with 54% polymorphism. The TMB1421 locus, with a monomorphic allele, was digested with three restriction enzymes (CAP-microsatellite) to evaluate sequence variations among samples. Association analysis between molecular markers and agronomic data revealed a significant correlation between ISSR-UBC807-1500 and yield. The Mantel test performed among the genetic distance matrices obtained from RAPD, ISSR and SSR showed a non-significant regression between RAPD versus ISSR and ISSR versus SSR, while RAPD versus SSR showed a significant regression; regression for ISSR and RAPD+ISSR+SSR combined data was also significant. Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies. Among the molecular markers, ISSR revealed more genetic variation among the genotypes. However, using all three types of molecular markers provided a better overall view of cotton genome polymorphism.
TL;DR: These molecular techniques can be utilized to more definitively screen GF and selectively colonized animals for bacterial contamination when Gram stain and/or culture results are un-interpretable or inconsistent.
Abstract: Gnotobiotic rodents provide an important technique to study the functional roles of commensal bacteria in host physiology and pathophysiology. To ensure sterility, these animals must be screened frequently for contamination. The traditional screening approaches of culturing and Gram staining feces have inherent limitations, as many bacteria are uncultivable and fecal Gram stains are difficult to interpret. Thus, we developed and validated molecular methods to definitively detect and identify contamination in germ-free (GF) and selectively colonized animals. Fresh fecal pellets were collected from rodents housed in GF isolators, spontaneously contaminated ex-GF isolators, selectively colonized isolators and specific pathogen-free (SPF) conditions. DNA isolated from mouse and rat fecal samples was amplified by polymerase chain reaction (PCR) and subjected to quantitative PCR (qPCR) using universal primers that amplify the 16S rRNA gene from all bacterial groups. PCR products were sequenced to identify conta...
TL;DR: The results of the present study highlighted the health-promoting compound content of strawberry fruits, and provided a good prospect for discriminating strawberries by phenolic content and genetic analysis.
TL;DR: To develop such an assay, genomic DNA from 45 individual plants belonging to different varieties of date palm was subjected to PCR amplification using 100 random amplified polymorphic DNA (RAPD) and 104 intersimple sequence repeat (ISSR) primers.
Abstract: Genetics of control mechanisms that underlies sex differentiation in date palm is not known. Sex of the plants becomes known only at the time of first flowering, which takes around 5 years. In comparison, molecular diagnosis (if available/feasible) promises quick and reliable identification of sex types very early when plantlets are growing in seedbeds. To develop such an assay, genomic DNA from 45 individual plants (25 female and 20 male) belonging to different varieties of date palm was subjected to PCR amplification using 100 random amplified polymorphic DNA (RAPD) and 104 intersimple sequence repeat (ISSR) primers. Initially, two bulk genomic DNA samples (each made by pooling DNA from ten male and female plants, separately) were used. A primer showing sex-specific band in bulked samples was further used for amplification of the genomic DNA of the individual samples of that bulk. Only one RAPD primer, OPA-02, amplified a fragment of ~1.0 kb in all the individual samples of male genotypes, whereas this fragment was absent in all the female genotypes. This male-specific fragment was cloned and sequenced (GenBank accession no. JN123357), and a sequence-characterized amplified region (SCAR) primer pair was designed that amplified a 406-bp fragment in both female and male genotypes and a unique fragment of 354 bp in only male genotypes. The SCAR marker was further validated using 25 female and ten male date palm plants belonging to different varieties collected from different locations.
Journal Article•
TL;DR: The salt tolerant landraces identified in this study could be used as parents to incorporate salt tolerance in future wheat cultivars and should be further investigated in segregating populations to determine their usefulness in marker assisted selection for saltolerance in wheat.
Abstract: Salinity is one of the major constraints to wheat production. Salt affected soils can be better utilized by developing and growing salt tolerant wheat varieties. Genetic diversity for salt tolerance is a prerequisite for developing salt tolerant wheat varieties. Therefore, the present study was conducted to evaluate the level of genetic diversity among 172 (123 Pakistani and 49 exotic) wheat genotypes for salinity tolerance at germination and early seedling stage. All the genotypes were first tested at 200 mM NaCl stress. Based on the results, 34 genotypes were selected and subsequently tested at 250 mM and 300 mM NaCl stress. Genetic variation for salt tolerance existed in the studied wheat genotypes. Plumule growth was affected more than radicle growth at higher salinity levels. Based on salt tolerance index, 18 accessions were identified as salt tolerant at 200 mM NaCl stress. Egyptian accession 11466 was the most salt tolerant at 250 mM NaCl stress, whereas Pakistani accession 11299 and Egyptian accession 11466 were the most salt tolerant at 300 mM NaCl stress. Genetic similarity coefficients based on RAPD marker data ranged from 0.38 to 0.95. RAPD primer OPA 2 produced a unique fragment of 1000 bp, whereas OPF 13 generated two fragments of 1200 bp and 1400 bp only in some tolerant genotypes. Genetic similarity coefficients for SSR markers ranged from 0.45 to 0.95. Both RAPD and SSR markers revealed genetic variation in the studied genotypes. The salt tolerant landraces identified in this study could be used as parents to incorporate salt tolerance in future wheat cultivars. The unique DNA fragments observed in this study should be further investigated in segregating populations to determine their usefulness in Marker assisted selection for salt tolerance in wheat.
TL;DR: Present investigation suggests the efficiency of SPAR methods to estimate the genetic diversity of V. coerulea and can be seen as a starting point for future research on the population and evolutionary genetics of this species.
Journal Article•
TL;DR: The SRAP dendrogram was correlated most with the combined data set indicating that SRAP makers could be a better tool for genetic diversity analysis in basil than RAPD and ISSR markers.
Abstract: Genetic diversity among 37 basil accessions representing four species (Ocimum basilicum, O. americanum. O. gratissimum and O. tenuiflorum) was evaluated individually using different maker systems. The applied marker systems potentiallty targeted different regions of the genome and included 36 inter-simple sequence repeat (ISSR). 20 random amplified polymorphic DNA (RAPD), and ten sequence-related amplified polymorphism (SRAP) markers. Among these three marker systems, SRAP showed the highest mean value of polymorphic information content (PIC, 0.29) and resolving power (Rp, 30.19) which were much higher than those of RAPD (0.23, 5.13) and ISSR (0.19, 1.39). Basil accessions were clustered into three groups using data from SRAP or the combined data set, indicating that the genetic diversity in different target regions of the tested basil genomes was not the same. All showed very good fit of cophenetic matrices between similarity matrix and dendrogram and the results were highly correlated between marker types. In addition, the SRAP dendrogram was correlated most with the combined data set indicating that SRAP makers could be a better tool for genetic diversity analysis in basil than RAPD and ISSR markers.
TL;DR: This study showed that DNA stability is highly affected by metal pollution which was identified by RAPD markers and suggested that heavy metal stress influences antioxidant status and also induces DNA damages in U. dioica which may help to understand the mechanisms of metals genotoxicity.
Abstract: Heavy metals have the potential to interact and induce several stress responses in the plants; thus, effects of heavy metal stress on DNA damages and total antioxidants level in Urtica dioica leaves and stems were investigated. The samples are sampled from areas with different metal exposition. Metal content was analyzed by Inductively Coupled Plasma-Atomic Emission Spectrometer (ICP-AES), for total antioxidants level assessment the Ferric-Reducing Antioxidant Power (FRAP) assay was used, and genomic DNA isolation from frozen plant samples was performed to obtain DNA fingerprints of investigated plant. It was found that heavy metal contents in stems generally changed synchronously with those in leaves of the plant, and extraneous metals led to imbalance of mineral nutrient elements. DNA damages were investigated by Random Amplified Polymorphic DNA (RAPD) technique, and the results demonstrated that the samples exposed to metals yielded a large number of new fragments (total 12) in comparison with the control sample. This study showed that DNA stability is highly affected by metal pollution which was identified by RAPD markers. Results suggested that heavy metal stress influences antioxidant status and also induces DNA damages in U. dioica which may help to understand the mechanisms of metals genotoxicity.
TL;DR: Interspecific hybrids between cultivars of eggplant and its wild relative S. torvum, which has disease resistance and desirable traits for crop improvement, were obtained by cross-hybridization and embryo rescue and had low pollen viability.
Abstract: Interspecific hybrids between cultivars of eggplant (Solanum melongena L.) and its wild relative S. torvum, which has disease resistance and desirable traits for crop improvement, were obtained by cross-hybridization and embryo rescue. Twenty-one hybrid progenies were obtained and examined based on morphological traits, RAPD and ISSR markers. Five of them were confirmed to be true interspecific hybrids. Eighteen and 14 bands from 7 RAPD and 14 ISSR primers, respectively, were polymorphic and present in all five hybrid seedlings and their parents. The morphological characteristics of leaf margin, inflorescence type and spine positions of the five seedlings were intermediate to the parents. These interspecific hybrids had low pollen viability, probably due to abnormal meiosis.
TL;DR: RAPD-PCR technique is found as a useful tool for investigation of the genetic variation among P. aeruginosa strains, and could assist to screen for the original of infection caused by this organism with subsequent control of colonization and transmission.
TL;DR: Groups exclusive to RS or PR support the hypothesis that divergence between groups is possible owing to the fixation of regional adaptation alleles and to spatial barriers hindering genetic flow between locations.
Abstract: Maize landraces derived from tropical germplasm represent an important source of genetic variability, which is currently poorly understood and under-exploited by Brazilian crop breeding programs. The aims of our study were to a) estimate the genetic diversity across 48 varieties of maize landraces cultivated at different locations in the States of Rio Grande do Sul (RS) and Parana (PR) by means of random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP) markers; b) cluster these varieties based on their genetic similarity estimates, and c) establish possible correlations between genetic similarity and germplasm collection sites. Maize landrace accessions were genotyped through the 30 RAPD, 47 SSR, and 25 combinations of AFLP primers. The results revealed high levels of variability across landraces within and between collection sites. AFLP analysis resulted in amplification of 762 polymorphic fragments and a polymorphic index of 40.3%, followed by RAPD with 335 fragments (81.9%) and SSR with 105 fragments (78.3%). The genetic similarity estimates of the investigated landraces ranged from 41 (SSR) to 74% (AFLP), and the amplitudes of these indices were notably similar between RAPD and SSR, as well as between AFLP and joint analysis. Regarding the RAPD and AFLP dendrograms, groups comprising accessions from RS prevailed, whereas SSR comprised varieties from both collection sites. Groups exclusive to RS or PR support the hypothesis that divergence between groups is possible owing to the fixation of regional adaptation alleles and to spatial barriers hindering genetic flow between locations.
TL;DR: The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linking maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.
Abstract: Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.
TL;DR: The present investigation was carried out to study the inheritance and identify molecular markers linked with MYMV resistance gene by using F1, F2 and 167 F2 : 8 recombinant inbred lines (RILs) developed from the cross ‘TM-99-37’ (resistant) × Mulmarada (susceptible).
Abstract: Yellow mosaic disease (YMD) caused by mungbean yellow mosaic virus (MYMV) is the most important disease of mungbean, causing great yield loss. The present investigation was carried out to study the inheritance and identify molecular markers linked with MYMV resistance gene by using F1, F2 and 167 F2 : 8 recombinant inbred lines (RILs) developed from the cross ‘TM-99-37’ (resistant) × Mulmarada (susceptible). The F1 was susceptible, F2 segregated in 3S:1R phenotypic ratio and RILs segregated in 1S:1R ratio in the field screening indicating that the MYMV resistance gene is governed by a single recessive gene. Of the 140 RAPD primers, 45 primers showing polymorphism in parents were screened using bulked segregant analysis. Three primers amplified specific polymorphic fragments viz. OPB-07600, OPC-061750 and OPB-12820. The marker OPB-07600 was more closely linked (6.8 cM) with a MYMV resistance gene as compared to OPC-061750 (22.8 cM) and OPB-12820 (25.2 cM). The resistance-specific fragment OPB-07600 was cloned, sequenced and converted into a sequence-characterized amplified region (SCAR) marker and validated in twenty genotypes with different genetic backgrounds.
TL;DR: Two preliminary genetic linkage maps were constructed using 90 F1 progeny individuals derived from an interspecific cross between D. nobile and D. moniliforme, providing an important basis for genetic studies and further medicinal and horticultural traits mapping and marker-assisted selection in Dendrobium breeding programmes.
Abstract: Dendrobium is an endangered genus in the orchid family with medicinal and horticultural value. Two preliminary genetic linkage maps were constructed using 90 F1 progeny individuals derived from an interspecific cross between D. nobile and D. moniliforme (both, 2n = 38), using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR). A total of 286 RAPD loci and 68 ISSR loci were identified and used for genetic linkage analysis. Maps were constructed by double pseudo-testcross mapping strategy using the software Mapmaker/EXP ver. 3.0, and Kosambi map distances were constructed using a LOD score ≥ 4 and a recombination threshold of 0.4. The resulting frame map of D. nobile was 1474 cM in total length with 116 loci distributed in 15 linkage groups; and the D. moniliforme linkage map had 117 loci placed in 16 linkage groups spanning 1326.5 cM. Both maps showed 76.91% and 73.59% genome coverage for D. nobile and D. moniliforme, respectively. These primary maps provide an important basis for genetic studies and further medicinal and horticultural traits mapping and marker-assisted selection in Dendrobium breeding programmes.
TL;DR: Analysis of the genotypes from dairy samples revealed that dairy B. licheniformis isolates are more heterogeneous than previously thought and that this new method can potentially allow for more discriminatory tracking and monitoring of specific genotypes.
TL;DR: The present study has established the rapid micropropagation protocol for the first time and will be of great use in conservation of C. panchganiensis with low risk of genetic instability and the rapid amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers.
TL;DR: Two types of DNA based marker RAPD and ISSR were used to characterize 8 date palm genotypes grown in the Kutch region and it was found that RAPD markers were more efficient than ISSR assay with regard to polymorphic detection.
Abstract: First line in abstract should be Date palm is an important fruit crop of the arid and semiarid region. In thepresent investigation two types of DNA based marker RAPD and ISSR were used to characterize 8 date palmgenotypes grown in the Kutch region. Amplification of genomic DNA of 8 genotypes using 13 RAPD analysesyielded 88 fragments, of which 35 were polymorphic, with an average of 2.69 polymorphic fragments perprimer. Two ISSR primers produced 13 bands of which 3 were polymorphic. RAPD markers were moreefficient than ISSR assay with regard to polymorphic detection; RAPD markers detected 39.77% as comparedto 23.07% of ISSR markers. Cluster analysis by UPGMA showed that the dendrogram obtained by RAPD andRAPD + ISSR were similar. Cluster A consisted of Early maturing, Ghanshyam and Late maturing femalegenotypes with 0.81 to 0.88 Jaccard's similarity range. Cluster B consisted of Seasonal female, Male-1, Male-2,Male-3 and Male-4 genotypes with 0.82 to 0.91 similarity range. Genotypes Male-1 and Male-2 were mostclosely related with the highest value in similarity for Jaccard's coefficient (0.91). Principal coordinate analysisdifferentiated one group of genotype Male-1 and Male-4 while other genotypes were randomly distributed.
TL;DR: AFLP and SSR, allies to the intrinsic characteristics of each technique, are the most suitable molecular markers for genetic studies of C. canephora, but the choice of AFLP or SSR in the species characterization should be made in agreement with some characteristics that are discussed in this work.
Abstract: The genetic variability characterization of the accessions of the germplasm collection, using molecular markers, is being applied as a complementary strategy to the traditional approaches to redefine the plant genetic resources. In this study, we compared the informativeness and efficiency of the molecular markers RAPD, AFLP and SSR in the analysis of 94 accessions of Coffea canephora germplasm held by the breeding program of the Brazilian Agricultural Research Corporation (Embrapa), Rondonia State, Brazil. For this, we considered the marker’s discriminatory power and level of polymorphism detected and also the genetic relationships and clustering (dendrogram) analysis. The RAPD marker yielded low-quality data and problems in the discrimination of some accessions, being less recommended for genetic studies of C. canephora. The SSRs had a higher level of information content and yielded high-quality data, while AFLP was the most efficient marker system because of the simultaneous detection of abundant polymorphism markers per few reactions. Our results indicate that AFLP and SSR, allies to the intrinsic characteristics of each technique, are the most suitable molecular markers for genetic studies of C. canephora. However, the choice of AFLP or SSR in the species characterization should be made in agreement with some characteristics that are discussed in this work.