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1.
A total of 10 non-repetitive multi-drug-resistant Acinetobacter strains were collected. With reference to A. calcoaceticus (ATCC23055), A. baumannii (ATCC19606), A. lwoffii (ATCC17986), and A. junii (NCTC5866),DNA fingerprint technique, amplified ribosomal DNA restriction analysis (ARDRA), and random amplified polymorphism
DNA (RAPD) were carried out to identify the genomic species of Acinetobacter spp. The distances between them were calculated by the unweighted pair group method with arithmetic (UPGMA). Genotypes of
Acinetobacter spp. were effectively classified and an A. junii together with nine A. baumannii isolates was genomically identified. The combination of ARDRA and RAPD DNA-fingerprint technique shows high complementarity,
and could be a useful tool in Acinetobacter genomic species identification.
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Translated from Microbiology, 2007, 34(2): 303–306 [译自:微生物学通报] 相似文献
2.
Relationships among <Emphasis Type="Italic">Leymus</Emphasis> species assessed by RAPD markers 总被引:1,自引:0,他引:1
The DNA genetic diversity of 40 accessions of genus Leymus was analyzed by random amplified polymorphic DNA (RAPD) markers. A total of 352 products were amplified by 34 10-mer arbitrary
primers, among which 337 products (95.74 %) were found to be polymorphic. 5–14 polymorphic bands were amplified by each polymorphic
primer, with an average of 9.91 bands. The data of 352 RAPD bands were used to generate Jaccard’s similarity coefficients
and to construct a dendrogram by means of UPGMA. Great genetic diversity in genus Leymus was observed, the genetic diversity among the different species more abundant than that of the different accessions, and
the different accessions in a species or the species from the same areas were clustered together. 相似文献
3.
Naoya Shinzato Tomoyuki Namihira Yasutomo Tamaki Masatoshi Tsukahara Toru Matsui 《Applied microbiology and biotechnology》2009,82(6):1187-1193
Monascus fungi are commonly used for a variety of food products in Asia, and are also known to produce some biologically active compounds.
Since the use of Monascus is expected to increase in food industries, strain-level identification and management of Monascus will be needed in the near future. In the present study, random amplified polymorphic DNA (RAPD) analysis coupled with microchip
electrophoresis was applied for this purpose. Evaluations of the analysis stability revealed that reproducible results could
be obtained, although template DNA fragmentation could influence the resulting RAPD pattern. RAPD analysis using 15 Monascus strains consisting of four species, M. ruber, M. pilosus, M. purpureus, and M. kaoliang showed that each strain generated a unique RAPD pattern, which allows strain-level identification of Monascus. In addition, the phylogenetic tree constructed from RAPD patterns reflected M. ruber–M. pilosus and M. purpureus–M. kaoliang clusters inferred from both ITS and β-tubulin gene sequences, which indicated that the RAPD pattern could reflect their phylogenetic
traits to a certain extent. On the other hand, RAPD analysis did not support the monophyletic clustering of the four Monascus species used in this study, which suggests the necessity of reexamination of species boundaries in Monascus. 相似文献
4.
S. Fancelli M. Castaldini M. T. Ceccherini C. Di Serio R. Fani E. Gallori M. Marangolo N. Miclaus M. Bazzicalupo 《Applied microbiology and biotechnology》1998,49(2):221-225
Probes for the detection of Azospirillum strains were obtained from DNA fragments generated by random amplification of polymorphic DNA (RAPD) and tested to assess
their specificity towards DNA extracted from pure cultures. The most specific probe, referred to as α4, produced a hybridization
signal only with amplified DNA of A. lipoferum ATCC29731. This strain was inoculated, together with two other Azospirillum strains, in soil microcosms of different complexity and its presence tested with the probe α4. This probe confirmed its high
specificity with amplified DNA extracted from the soil microcosm and in the presence of other A. lipoferum strains, indicating that the strategy for bacterial detection, based on RAPD markers, is useful for monitoring the presence
of a particular strain under environment-like conditions. Other RAPD-derived probes, when tested on soil samples, did not
show the same level of specificity as that shown on DNA from pure cultures. This result suggests that some precautions are
necessary in the choice of a really specific RAPD marker. In a further development of this strategy, the α4 probe was sequenced
and two pairs of “nested” primers were designed, which enabled a diagnostic polymerase chain reaction from soil samples that
was specific for the A. lipoferum species.
Received: 7 July 1997 / Accepted: 14 October 1997 相似文献
5.
Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific
genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD),
19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic
fragments. ISSR confirmed maximum polymorphism of 98.55% whereas RAPD and AFLP showed 93.22 and 97.27%, respectively. Marker
index and polymorphic information content varied in the range of 8.64–48.1, 19.75–48.14, and 25–28 and 0.17–0.48, 0.19–0.48,
and 0.25–0.29 for RAPD, ISSR, and AFLP markers, respectively. The average value of number of observed alleles, number of effective
alleles, mean Nei’s gene diversity, and Shannon’s information index were 1.93–1.98, 1.37–1.62, 0.23–0.36, and 0.38–0.50, respectively,
for three DNA markers used. Dendrograms based on three molecular data using unweighted pair group method with arithmetic mean
(UPGMA) was congruent and classified the Curcuma species into two major clusters. Cophenetic correlation coefficient between dendrogram and original similarity matrix were
significant for RAPD (r = 0.96), ISSR (r = 0.94), and AFLP (r = 0.97). Clustering was further supported by principle coordinate analysis. High genetic polymorphism documented is significant
for conservation and further improvement of Curcuma species. 相似文献
6.
Cytological and molecular characterization of a novel monogenic dominant GMS in <Emphasis Type="Italic">Brassica napus</Emphasis> L. 总被引:1,自引:0,他引:1
A novel genic male sterile (GMS) line in Brassica napus L., which was identified in 1999, was found to be controlled by a monogenic dominant gene, which we have designated as MDGMS.
The microspores of the MDGMS abort before the degradation of the tapetal cell layer. The F1 fertility from any fertile lines
crossed with MDGMS segregated and the ratio was close to 1:1. Bulked segregation analysis (BSA) was employed to identify random
amplified polymorphic DNA (RAPD) markers linked to the Ms gene in MDGMS. Among 880 random 10-mer oligonucleotide primers screened against the bulk DNA of sterile and fertile, one
primer S243 (5′-CTATGCCGAC-3′) gave a repeatable 1500-bp DNA polymorphic segment S2431500 between the two bulks. Analysis of individual plants of each bulks and other types of GMS and cytoplasmic male sterility
(CMS) lines suggest that the RAPD marker S2431500 is closely linked to the MDGMS locus in rapeseed. This RAPD marker has been converted into sequence characterized amplified
region (SCAR) marker to aid identification of male-fertility genotypes in segregating progenies of MDGMS in marker-assisted
selection (MAS) breeding programs. 相似文献
7.
Ding Wei Zhang Zhengwang Chang Jiang Zhang Er Wu Xiushan Zhang Jinguo 《Frontiers of Biology in China》2006,1(4):394-397
The Tibetan Eared-pheasant Crossoptilon harmani is a rare species native to China. A captive population has been established in the Beijing Zoo since 1999. In order to determine
the kinship of the offsprings in 2001, randomly amplified polymorphic DNA (RAPD) was used to examine the parenthood of seven
Tibetan Eared-pheasants in the Beijing Zoo. To amplify the genomic DNA of each individual, 53 arbitrary primers were selected.
The results of amplifications showed that 14 primers had clear and distinct RAPD patterns. Totally, 226 amplified fragments
were generated by RAPD in this study. Cluster analysis of the seven Tibetan Eared-pheasants indicated that all the four young
birds had the same father (No.5 male). This study provides a practical method to determine the relationship of offsprings
whose parents are unknown in birds.
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Translated from Journal of Beijing Normal University (Natural Science), 2005, 41(5): 507–509 [译自: 北京师范大学学报 (自然科学版), 2005, 41(5): 507–509] 相似文献
8.
The averaged genomic similarities based on multilocus randomly amplified polymorphic DNA (RAPD) were calculated for eight
species representing three sections of the genus Vicia: faba, bithynica and narbonensis. The frequency of appearance of the sequences corresponding to 25 decamers selected at random
from genomes of different Fabace species was checked, and a high correlation with the frequency observed for Vicia allowed us to assume their similar weight in typing Vicia species. The RAPD-based similarity coefficients compared with those related to whole genome hybridization with barley rDNA
and those based on restriction fragment length polymorphism (RFLP) revealed similar interspecies relationships. The averaged
RAPD-based similarity coefficient (Pearson’s) was 0.68 for all the species, and was sectionspecific: 0.43 (bithynica), 0.50
(faba) and 0.73 (narbonensis). The averaged similarity coefficient for V. serratifolia (0.63) placed it apart from the rest (0.75) of its section. The results correspond to the interspecies relationships built
upon non-genetic data. The averaged similarity coefficient for particular RAPD was related to the presence and type of tandemly
repeated motif in a primer: 0.7–0.8 for heterodimers (GC, AG, CA, GT, CT), 0.5–0.6 for homodimers (CC, GG) and 0.6 for no
repeat, indicating the sensitivity of diversity range to the type of target sequences. 相似文献
9.
Mohd Arif N. W. Zaidi Y. P. Singh Qazi Mohd Rizwanul Haq U. S. Singh 《Plant Molecular Biology Reporter》2009,27(4):488-495
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. 相似文献
10.
Eleven type strains and 24 Lactobacillus isolates, preliminarily classified to the species due to phenotypic features, were investigated. Standard methods of identification
with species-specific PCRs and typing with PFGE (with ApaI, NotI and SmaI restriction enzymes) allowed us to distinguish 16 unique strains belonging to 5 species (L. acidophilus, L. delbrueckii ssp. bulgaricus, L. plantarum, L. rhamnosus, L. salivarius). Alternative approach with 16S–23S rDNA ARDRA identification (with merely two restrictases, BsuRI and TaqI) and PCR-based typing (RAPD with two random- and rep-PCR with (GTG)5 primers) showed to be more discriminative, i.e. 21 unique strains were classified in the same species as above. As a result, 7 out of 24 phenotypically species-assigned
isolates were reclassified. The alternative procedure of rapid identification and typing of Lactobacillus isolates appeared to be equally effective and shortened from 1 week to 2–3 d (in comparison to the standard methods). 相似文献
11.
S. Y. Park H. N. Murthy D. Chakrabarthy K. Y. Paek 《In vitro cellular & developmental biology. Plant》2009,45(1):104-108
Somaclones exhibiting variations with flower characteristics were recovered from the tissue-culture-derived plants of Doritaenopsis. Two molecular techniques, random amplified polymorphic DNA (RAPD) and methylation-sensitive amplification polymorphism (MSAP)
analyses, were used to characterize the somaclones. RAPD analysis, using 100 randomly selected primers, failed to differentiate
variants and normal plants, even though some primers (six out of 100 primers) exhibited 6–10 distinct banding patterns. However,
MSAP analysis revealed the differences in the DNA methylation patterns in the normal and variant plants which were correlated
with phenotypic variation. In all, 311, 337, 366, and 343 fragments were obtained with normal and V1, V2, and V3 variant plants,
respectively; each representing recognition site cleaved by either or both of the isoshizomers were amplified using 12 combination
of primers. A total of 36 (11.6%), 77 (22.9%), 73 (19.9%), and 47 (13.7%) sites were found to be methylated at cytosine in
the genomes of normal and V1, V2, and V3 variant Doritaenopsis plants. This study demonstrates usefulness of MSAP to detect DNA methylation events in tissue cultured Doritaenopsis plants. 相似文献
12.
Chin-Hong Ng Soon-Leong Lee Kevin Kit-Siong Ng Norwati Muhammad Wickneswari Ratnam 《Journal of genetics》2009,88(1):25-31
The mating system and seed variation of Acacia hybrid (A. mangium × A. auriculiformis) were studied using allozymes and random amplified polymorphic DNA (RAPD) markers, respectively. Multi-locus outcrossing
rate estimations indicated that the hybrid was predominantly outcrossed (mean±s.e. t
m = 0.86±0.01). Seed variation was investigated using 35 polymorphic RAPD fragments. An analysis of molecular variance (AMOVA)
revealed the highest genetic variation among seeds within a pod (66%–70%), followed by among pods within inflorescence (29%–37%),
and the least variation among inflorescences within tree (<1%). In addition, two to four RAPD profiles could be detected among
seeds within pod. Therefore, the results suggest that a maximum of four seeds per pod could be sampled for the establishment
of a mapping population for further studies. 相似文献
13.
J. O. Rasmussen S. Waara O. S. Rasmussen 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(1-2):41-49
Recipient protoplasts from three Solanum tuberosum genotypes, cv ‘Folva’ (2n=4x=48), cv ‘Matilda’ (4n) and ‘161 : 14’ (2n), were electrofused with X-ray-irradiated donor protoplasts
from two wild species S. spegazzinii (2n) or S. microdontum×S. vernei (2n). Prior to fusion, protoplasts were fluorescence-labelled with either fluorescein diacetate or scopoletin. Fusion products
were identified by dual fluorescence and selected by micromanipulation or fluorescence-activated cell sorting (FACS). All
putative hybrid plants were analysed by the random amplified polymorphic DNA (RAPD) technique. Our analysis demonstrates that
each asymmetric hybrid plant has an individual and stable profile of donor-specific RAPD bands. The irradiation of donor protoplasts
hampered the growth of selected heterofusion products in a dose-dependent way. Irradiation resulted in donor chromosome elimination,
but not in a dose dependent way, in the tested interval. In asymmetric hybrids with the S. spegazzinii donor 33–68% of the donor-specific RAPD bands were missing, indicating a similar level of chromosome elimination. In asymmetric
hybrid plants with the S. microdontum×S. vernei donor 74–95% of the donor RAPD bands were missing. Chromosome countings revealed that these hybrids had chromosome numbers
equal to or below the chromosome numbers found in the tetraploid recipients. This is the first time that highly asymmetric
hybrid plants between two tetraploid potato recipients and the donor S. microdontum×S. vernei have been obtained.
Received : 16 December 1996 / Accepted: 21 February 1997 相似文献
14.
RAPD fingerprints for identification and for taxonomic studies of elite poplar (Populus spp.) clones
S. Castiglione G. Wang G. Damiani C. Bandi S. Bisoffi F. Sala 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1993,87(1-2):54-59
RAPD (Random Amplified Polymorphic DNA) fingerprints have recently been used to estimate genetic and taxonomic relationships in plants. In this study RAPD analysis was performed on 32 clones belonging to different species of the genus Populus. Of these, 25 clones are registered in several countries for commercial use and, altogether, cover almost 50% of the worlds cultivated poplars. DNA was prepared from leaves and amplified by PCR using random oligonucleotide primers. Amplification products were separated by agarose-gel electrophoresis to reveal band polymorphisms. Four primers out of the 18 tested, were selected on the basis of the number and frequency of the polymorphisms produced. With these a total of 120 different DNA bands were reproducibly obtained, 92% of which were polymorphic. The polymorphisms were scored and used in band-sharing analyses to identify genetic relationships. With a few but interesting exceptions, these are consistent with the present taxonomy of the genus Populus and with the known predigrees of cultivated poplars. Moreover, the results show that RAPD analysis allows one to discriminate among all tested clones and can, therefore, be recommended as a convenient tool to defend plant breeders rights. 相似文献
15.
Fuli Liu Jianting Yao Xiuliang Wang Zimin Hu Delin Duan 《Journal of applied phycology》2011,23(4):709-713
To construct a molecular-marker-assisted selection (MAS) system, research was done on identifying molecular markers linking
to longer frond length, a crucial selection index in the breeding of the commercially important seaweed Saccharina japonica. An F2-segregant population of 92 individuals was obtained by crossing two prominent S. japonica strains. Genomic DNA from ten individuals with the longest frond and ten individuals with the shortest frond in the F2-segregant population were mixed to create two DNA pools for screening polymorphic markers. In bulked-segregant analysis (BSA),
out of 100 random amplified polymorphic DNA (RAPD) primers only two produced three polymorphic RAPD markers between the two
DNA pools. In conversion of the three RAPD markers into sequence-characterized amplified region (SCAR) markers, only one was
successfully converted into a SCAR marker FL-569 linking to the trait of longer frond. Test of the marker FL-569 showed that
80% of the individuals with longest fronds in a wild population and 87.5% of individuals with the longest fronds in an inbred
line “Zhongke No. 2” could be detected by FL-569. Additionally, genetic linkage analysis showed that the SCAR marker could
be integrated into the reported genetic map and QTL mapping showed that FL-569 linking to qL1-1. The obtained marker FL-569
will be beneficial to MAS in S. japonica breeding. 相似文献
16.
K. R. N. Reddy Ch. Surendhar Reddy P. Nataraj Kumar C. S. Reddy K. Muralidharan 《World journal of microbiology & biotechnology》2009,25(1):33-39
Twenty-two aflatoxin B1 (AFB1) producing Aspergillus flavus strains were isolated from 1,200 discolored rice grain samples collected from 20 states across India and tested their potential
to produce AFB1 on different agar media. Further these isolates were characterized through randomly amplified polymorphic
DNA method. All the strains of A. flavus were produced AFB1 on yeast extract sucrose agar media and none of the strains on A. flavus and A. parasiticus agar. Among the 22 strains, two strains from Tamil Nadu (DRAf 009) and Maharashtra (DRAf 015) produced high amount of AFB1
in all the media tested. To assess the genetic variability in A. flavus, the isolates were analyzed by using random amplified polymorphic DNA markers. Isolates showed 17–80% similarity with standard
culture of A. flavus (MTCC 2799). 相似文献
17.
Lake Averno sediment was used to isolate the facultative anaerobic bacteria having the potential for H2 production. Twenty-five out of 35 isolates recovered from the sediment sample produced hydrogen under anaerobic conditions
from glucose with yields ranging from 0.1 to 0.49 mol H2/mol glucose. Identification based on 16S rRNA gene sequence analysis revealed that most of them belong to the Firmicutes group, with a prevalence of the Paenibacillus polymyxa species. Seven distinct genomic fingerprints among the 11 P. polymyxa isolates were obtained using the random amplified polymorphic DNA (RAPD) technique. Glucose fermentation by P. polymyxa isolates was investigated. Glucose was totally consumed after 3 days of fermentation. The fermentation products were hydrogen
(0.18–0.47 mol H2/mol glucose), ethanol (0.1–0.5 mol ethanol/mol glucose), and 2,3-butanediol (0.1 mol 2,3-butanediol/mol glucose). Lower amounts
of acetic, butyric, formic, lactic, and propionic acids were detected. All metabolic data concerning P. polymyxa isolates were analyzed by cluster analysis to reveal similarities and/or differences with clustering based on RAPD profiles.
Despite the high metabolic similarity among almost all P. paenibacillus isolates, results of cluster analyses of metabolic and genetic data do not match completely. 相似文献
18.
The technique random amplified polymorphic DNA (RAPD)-PCR was evaluated as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii. Representative strains, including the type of each species, were selected from different clusters obtained by numerical analysis of total soluble cell protein patterns. Results obtained by RAPD-PCR corresponded well with results obtained by numerical analysis of total soluble cell protein patterns. The type strains of each species displayed different RAPD profiles. Strains with identical L(+)- nicotinamide adenine dinucleotide-dependent lactic dehydrogenase (nLDH) electrophoretic profiles could be distinguished on the basis of their RAPD profiles. 相似文献
19.
A collection of 32 lactococcal strains isolated from raw milk in the Camembert RDO (registered designation of origin) area
were phenotypically and genotypically characterized. As expected for environmental isolates, all strains had a Lactococcus lactis subsp. lactis phenotype. The strains were then genotypically identified by the randomly amplified polymorphic DNA (RAPD) technique, using
reference strains of lactococci. Two major clusters were identified containing the two subspecies lactis and cremoris. The subspecies lactis cluster could be divided into five subgroups whereas there was a high coefficient of similarity between all strains in the
subspecies cremoris cluster. This RAPD classification was then compared with that of a traditional PCR assay using L.lactis species-specific primers corresponding to part of the histidine biosynthesis operon. The two subspecies were differentiated
by the size of the fragment amplified (about 200 bp longer for subspecies cremoris). Unlike preliminary phenotypic assignments, the results of PCR experiments corroborated the genotypic identification of
the lactococcal strains by RAPD allowing the technique to be reconsidered on the basis of its taxonomic efficiency.
Received: 14 May 1998 / Accepted: 3 September 1998 相似文献
20.
Yamen A. S. Hamdan Leonardo Velasco Begoña Pérez-Vich 《Molecular breeding : new strategies in plant improvement》2008,22(3):385-393
Practically no molecular tools have been developed so far for safflower (Carthamus tinctorius L.) breeding. The objective of the present research was to develop molecular markers for the closely linked genes Li, controlling very high linoleic acid content, and Ms, controlling nuclear male sterility (NMS). A mapping population of 162 individuals was developed from the NMS line CL1 (64–79%
linoleic acid) and the line CR-142 (84–90%), and phenotyped in the F2 and F3 generations. Bulked segregant analysis with random amplified polymorphic (RAPD) markers revealed linkage of five RAPD bands
to the Li and Ms genes. RAPD fragments were converted into sequence-characterized amplified region (SCAR) markers. A linkage map including
the five SCAR markers and the Li and Ms genes was constructed. SCAR markers flanked both loci at minimum distances of 15.7 cM from the Li locus and 3.7 cM from the Ms locus. These are the first molecular markers developed for trait selection in safflower. 相似文献