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  • RAPD  (64)
  • Springer  (64)
  • American Meteorological Society
  • Nature Publishing Group (NPG)
  • 2000-2004  (64)
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  • Springer  (64)
  • American Meteorological Society
  • Nature Publishing Group (NPG)
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  • 1
    ISSN: 1572-9702
    Keywords: Panonychus citri ; spider mite ; microsatellite ; RAPD ; PCR ; DNA polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genetic markers were searched using PCR with 40 kinds of decanucleotide primers to investigate DNA polymorphism in Panonychuscitri. A region consisting of a variable number of CT tandem repeats (microsatellite) was found in a fragment amplified with the OPB10 primer. The microsatellite differed in size by ca. 100 bp among several P. citri populations screened and was derived from at least seven alleles. This region was characteristic of P. mori and P. osmanthi, but was lacking in P. ulmi. The flanking regions were highly conserved among these species.
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  • 2
    ISSN: 1572-9737
    Keywords: allozyme ; microgeographic divergence ; microsatellite ; natural selection ; RAPD ; Triticum dicoccoides ; wild emmer wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The levels of genetic diversity were compared by means of 35 allozyme, 60 RAPD, and 25 microsatellite (SSR) markers for 75–175 individuals of tetraploid wild emmer wheat (Triticum dicoccoides) collected in 1993 from a microgeographic microsite, Ammiad, north of the Sea of Galilee, Israel. This microsite included four major habitats, which showed highly significant differentiation in ecological factors, in particular with respect to rock cover, proximity and height, and surface soil moisture in the early growing season of T. dicoccoides. Higher within-subpopulation genetic diversity was found in the primarily non-coding DNA regions (RAPD and SSR) rather than in the protein-coding (allozymes) regions. However, much larger gene differentiation (G ST) among the subpopulations was observed in the protein-coding allozymes than in the RAPDs and SSRs. Larger genetic distance was found at SSR loci, followed by allozyme and RAPD loci. The subpopulations in drier habitats tend to have higher allozyme, RAPD and SSR diversities (He), the relatively wet Karst subpopulation showed only about half He of the other relatively drier habitats. The subpopulations with larger difference of soil moisture between habitats tend to show larger genetic distances at allozyme, RAPD and SSR loci. These results suggest that climatic selection through aridity stress may be an important factor acting on both structural protein-coding and presumably partly regulatory non-coding DNA regions, resulting in microscale adaptive patterns, although hitchhiking and random drift may also intervene. These results have profound implications for genetic conservation both in situ and ex situ.
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  • 3
    ISSN: 1572-9737
    Keywords: Australia ; conservation strategy ; cpDNA ; Euphorbiaceae ; Fontainea ; nrDNA ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Four new eastern Australian Fontainea species have beenrecently described and all have a limited distribution. F.oraria is the rarest, being restricted to 10 adult individualswithin a single site in regrowth littoral rainforest. In order todevelop adequate management strategies, this study was aimed atsurveying the genetic variability remaining within the species by usingRAPD analysis. To assist with the correct interpretation of the results,a matching study was conducted on four populations of the closelyrelated F. australis. Similar amounts of within-populationgenetic diversity were recorded for both species. The RAPD-based studysuggested that adult plants are contributing unevenly to successivegenerations. RAPD analysis also recognised a close evolutionaryrelationship between F. oraria and F. australis.Sequencing of cpDNA (trnL-F) and nrDNA (ITS2) regions,confirmed recent divergence and possibly some historical reticulationbetween these two species and two other members of the genus. Ofparticular interest was the recognition that one of the F.australis populations (Limpinwood) represented a novel genotypiccombination in need of conservation attention. The implications of theRAPD and sequencing results are discussed in reference to theirinfluence upon the development of adequate conservation strategies forall important conservation units.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 12 (2000), S. 353-359 
    ISSN: 1432-2145
    Keywords: Key words Rosa sect Caninae ; Heterogamy ; Apomixis ; RAPD ; Pollen viability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  All members of Rosa section Caninae, dogroses are polyploid and characterized by their unbalanced meiosis, which in most cases leads to a pronounced morphological influence from the maternal parent. In a previous investigation on a pair of reciprocal crosses between two species in this section, Rosa dumalis and R. rubiginosa (2n=35), nine offspring plants (approximately 10%) did not receive any of the 21 RAPD markers present in the respective pollen parent. This was interpreted as a possible occurrence of apomixis. These nine plants have now been subjected to a further study with additional markers. Thirteen new RAPD markers showed the same result as in the previous investigation: none of the nine plants inherited any of the pollen donor markers. The reproducibility of the RAPD markers was checked by mixing DNA samples to obtain a series of artificial hybrids between the two parent plants. Twelve RAPD markers gave the expected result, whereas one marker appeared only 50% of the time. In addition, pollen viability, mean number of seeds per hip, mean seed weight, and mean weight of fruit flesh per hip have been studied on the four progeny groups: R. dumalis×R. rubiginosa plants which received pollen donor markers (PM plants), R. dumalis×R. rubiginosa plants which did not receive any pollen donor markers (NPM plants), R. rubiginosa×R. dumalis PM plants and R. rubiginosa×R. dumalis NPM plants. A canonical discriminant analysis based on these four reproductive characters separated the four progeny groups. There were significant differences between the two PM groups in all investigated characters, and also between the PM and the NPM groups in pollen viability. The result from the RAPD markers together with the differences in pollen viability between the PM and NPM progeny groups is taken as an indication that apomixis occurs within the Caninae section.
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  • 5
    ISSN: 1432-2242
    Keywords: Key words Citrus ; RAPD ; SCAR ; cpDNA ; Phylogeny ; Origin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes analyzed included 36 accessions belonging to Citrus together with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus and from each other. Within Citrus, the separation into two subgenera, Citrus and Papeda, designated by Swingle, was clearly observed except for C. celebica and C. indica. Almost all the accessions belonging to subgenus Citrus fell into three clusters, each including 1 genotype that was considered to be a true species. Different phylogenetic relationships were revealed with cpDNA data. Citrus genotypes were separated into subgenera Archicitrus and Metacitrus, as proposed by Tanaka, while the division of subgenera Citrus and Papeda disappeared. C. medica and C. indica were quite distant from other citrus as well from related genera. C. ichangensis appeared to be the ancestor of the mandarin cluster, including C. tachibana. Lemon and Palestine sweet lime were clustered into the Pummelo cluster led by C. latipes. C. aurantifolia was located in the Micrantha cluster. Furthermore, genetic origin was studied on 17 cultivated citrus genotypes by the same molecular markers, and a hybrid origin was hypothesized for all the tested genotypes. The assumptions are discussed with respect to previous studies; similar results were obtained for the origin of orange and grapefruit. Hybrids of citron and sour orange were assumed for lemon, Palestine sweet lime, bergamot and Volkamer lemon, while a citron × mandarin hybrid was assumed for Rangpur lime and Rough lemon. For Mexican lime our molecular data indicated C. micrantha to be the female parent and C. medica as the male one.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 100 (2000), S. 1209-1216 
    ISSN: 1432-2242
    Keywords: Key words Digitalis spp. ; AMOVA ; Genetic relationships ; RAPD ; Scrophulariaceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  RAPD markers were used to study inter-specific variation among six species of the genus Digitalis: D. obscura, D. lanata, D. grandiflora, D. purpurea, D. thapsi and D. dubia, and the hybrid D. excelsior (D. purpurea×D. grandiflora). A total of 91 highly reproducible bands amplified with four arbitrarily chosen decamer primers were obtained. Homology of the co-emigrating RAPD markers was tested by blot hybridisation and sequencing of selected bands. The application of a range of statistical approaches for RAPD data analysis, including distance and parsimony methods, family clustering and the analysis of molecular variance (AMOVA), indicated that these molecular markers were taxonomically informative in Digitalis. The species relationships revealed were fully consistent with those previously obtained using morphological affinities. The hybrid D. excelsior seems to have stronger affinity to the section Digitalis than to Grandiflorae. This is the first known report of the application of RAPD markers for the study of genetic relationships among species of the genus Digitalis.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 101 (2000), S. 70-79 
    ISSN: 1432-2242
    Keywords: Key words Poa annua L. ; Genetic diversity ; RAPD ; Turfgrass weeds ; Selection pressure ; Analysis of molecular variance ; AMOVA ; POPGENE
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The genetic diversity of Poa annua L.populations collected from western Oregon grass-seed fields was surveyed using 18 randomly amplified polymorphic DNA (RAPD) markers. Markers from 1357 individual plants from 47 populations collected at three sampling dates (fall, winter, and spring) for 16 sites were used to measure genetic diversity within and among populations. Site histories varied from low to high herbicide selection pressure, and some sites were subdivided by 3 years of differing post-harvest residue management. Gene diversity statistics, simple frequency of haplotype occurrence, and analysis of molecular variance (AMOVA) revealed the presence of significant variability in P. annua among sites, among collection dates within sites, and within collection dates. Nei gene-diversity statistics and population-differentiation parameters indicated that P. annua populations were highly diverse. Mean Nei gene diversity (h) for all 47 populations was 0.241 and total diversity (HT) was 0.245. A greater proportion of this diversity, however, was within (HS=0.209) rather than among (GST=0.146) populations. When populations were grouped by season of collection, within-group diversity was HS=0.241, while among-group diversity was GST=0.017. When populations were grouped by site, within-group diversity was HS=0.224, while among-group diversity was GST=0.087. The diversity among populations within season for fall, winter, and spring collections was GST=0.121, 0.142, and 0.133, respectively. Populations collected from fields with histories of high herbicide selection pressure showed low differentiation among collection dates, with GST as low as 0.016, whereas those collected from fields with low herbicide selection pressure showed greater differentiation among collection dates, with GST as high as 0.125. At high selection-pressure sites, populations were also lower in gene diversity (as low as h=0.155), while at low selection-pressure sites there was higher gene diversity (as high as h=0.286). The site to site variability was greater for the high selection-pressure sites (GST=0.107 or 69% of the total among-population variance), while the season of germination variability was greater at sites of low herbicide-selection pressure (GST=0.067, or 70% of the total among-population variance). High initial diversity coupled with a long-term re-supply of genotypes from the seed bank must have been factors in maintaining the genetic diversity of this weed despite the intensive use of herbicides. Knowledge of the genetic diversity of Willamette Valley P. annua should help in formulating more effective strategies for managing this weed.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 101 (2000), S. 90-94 
    ISSN: 1432-2242
    Keywords: Key words Molecular map ; AFLP ; RAPD ; Optimisation algorithm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A computer algorithm is presented which allows selection of a subset of multiplex markers based on the minimisation of an optimality criterion for a genetic linkage map. It could be applied for choosing a subset of primers (e.g. RAPD, IMA or AFLP), each of which provides several unevenly spaced genetic markers. The goal is to achieve a saturated map of evenly spaced markers, using as few primers as possible to minimise cost and labour. Minimising the average map distance between markers is trivial, but simply leads to selection of those primers which provide the greatest number of markers. However, minimising the standard deviation of interval length ensures that weight is given both to the number of markers and to the evenness of their distribution on the linkage map. This criterion was found empirically to give a result fairly close to the optimum. A stepwise-like selection procedure is therefore implemented, which stops when the optimality criterion does not decrease any more. An example is given of a molecular map of perennial ryegrass with 463 markers obtained from 17 AFLP primers. It is demonstrated that this can be safely reduced to a 175 marker map with only 6 primers. Genetic diversity studies may also benefit from using such a subset of less-redundant markers in genetic distance estimation.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 101 (2000), S. 292-300 
    ISSN: 1432-2242
    Keywords: Key words AFLP ; DNA markers ; Early germination ; ISSR ; ISTR ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Different DNA marker types were used to construct linkage maps in coconut (Cocos nucifera L.; 2n = 32) for the two parents of the cross Malayan Yellow Dwarf (MYD) × Laguna Tall (LAGT). A total of 382 markers was sufficient to generate 16 linkage groups for each parent. The total genome length corresponded to 2226 cM for the LAGT map and 1266 cM for the MYD map with 4–32 markers per linkage group. Common markers allowed the association of 9 linkage groups for the two parents MYD and LAGT. QTL analysis for the trait early germination identified six loci. These QTLs correlate with early flowering and yield, representing characters which are important in coconut breeding. The co-segregation of markers with these QTLs provides the first opportunity for marker-assisted selection in coconut breeding programmes.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 100 (2000), S. 614-620 
    ISSN: 1432-2242
    Keywords: Key words Aigeiros ; Leuce ; Marssonina brunnea ; Poplar ; RAPD ; Tacamahaca
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A broad collection was made for 42 isolates of Marssonina brunnea affecting poplar trees from three different sections (Leuce, Aigeiros and Tacamahaca) within the same Populus genus in China. Genetic diversity among these isolates was analyzed for morphological traits, cultural features, pathogenicity, hyphal anastomosis and randomly amplified polymorphic DNA markers (RAPDs). No significant difference was found in conidial morphological features, such as size, shape and septum location. Yet, considerable differences occur in other characteristics, which leads to the classification of the 42 isolates into two distinct groups, M. brunnea f.sp. monogermtubi and M. brunnea f.sp. multigermtubi. Isolates of M. brunnea f.sp. monogermtubi, derived from section Leuce, germinate only one germ tube, grow fast, produce dark-reddish conidiosorus clusters on the PDA medium, and are highly pathogenic to Populus tomentosa of section Leuce. By contrast, isolates of M. brunnea f.sp. multigermtubi, derived from sections Aigeiros and Tacamahaca, germinate 1–5 germ tubes, grow slowly, produce yellow-greenish conidiosorus clusters on PDA medium, and are pathogenic to Populus ×euramericana cv I-45 and Populus canadensis of section Aigeiros. DNA amplification using 11 RAPD primers generate 78 polymorphic bands among isolates. Cluster analyses based on RAPD markers broadly support such a classification by phenotypes, but provide a new insight into the possible origins of M. brunnea. It is proposed that the pathogen co-evolves with the poplars of section Leuce and has been subsequently distributed to the poplars of sections Aigeiros and Tacamahaca. An isolate from Populus adenopoda of section Leuce is placed in the third group, which is most likely a transmission type from M. brunnea f.sp. monogermtubi to M. brunnea f.sp. multigermtubi.
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