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  • RAPD  (93)
  • Springer  (93)
  • American Association for the Advancement of Science
  • American Meteorological Society
  • 1995-1999  (93)
  • 1990-1994
  • 1999  (55)
  • 1995  (38)
Collection
Keywords
Publisher
  • Springer  (93)
  • American Association for the Advancement of Science
  • American Meteorological Society
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  • 1995-1999  (93)
  • 1990-1994
Year
  • 1
    Electronic Resource
    Electronic Resource
    Molecular markers to differentiate two morphologically-close species of the genus Sitobion (1999)
    Springer
    Entomologia experimentalis et applicata 92 (1999), S. 217-225 
    Details
    ISSN: 1570-7458
    Keywords: Sitobion avenae ; Sitobion fragariae ; RAPD ; PCR ; microsatellites ; mtDNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A set of molecular markers to differentiate the aphid (Hemiptera: Aphidoidea) species Sitobion avenae (Fabricius) from Sitobion fragariae (Walker), is presented. These markers correspond to (1) a region of the mitochondrial DNA, (2) five species-specific RAPD banding patterns and (3) four microsatellite loci. Each of the markers was able to clearly distinguish between the species. The utility of each molecular marker is discussed. Mitochondrial DNA is best applicable to species determination and relative abundance, RAPDs to the evaluation of genetic diversity, and microsatellites to the assessment of the population genetic structure; the combined use of mtDNA with the other techniques can be of importance when the presence of hybrids is suspected, and RAPDs with microsatellites are best used together in population genetics and host preference studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003855919065
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  • 2
    Electronic Resource
    Electronic Resource
    Strain typing of ectomycorrhizal basidiomycetes from subalpine Tyrolean forest areas by random amplified polymorphic DNA analysis (1995)
    Springer
    Mycorrhiza 6 (1995), S. 35-41 
    Details
    ISSN: 1432-1890
    Keywords: Key words Ectomycorrhiza ; Boletus ; Amanita ; Lactarius ; Russula ; Picea abies ; RAPD ; Intra- and infraspecific variability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The application of random amplified polymorphic DNA (RAPD) analysis for the identifcation of ectomycorrhizal symbionts of spruce (Picea abies) belonging to the genera Boletus, Amanita and Lactarius at and below the species level was investigated. Using both fingerprinting [M13, (GTG)5, (GACA)4] as well as random oligonucleotide primers (V1 and V5), a high degree of variability of amplified DNA fragments (band-sharing index 65–80%) was detected between different strains of the same species, hence enabling the identification of individual strains within the same species. The band-sharing index between different species of the same genus (Boletus, Russula and Amanita) was in the range of 20–30%, and similar values were obtained when strains from different taxa were compared. Thus RAPD is too sensitive at this level of relatonship and cannot be used to align an unknown symbiont to a given taxon. We therefore conclude that RAPD is a promising tool for the identification of individual strains, and could thus be used to distinguish indigenous and introduced mycorrhizal strains from the same species in natural ecosystems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050103
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  • 3
    Electronic Resource
    Electronic Resource
    Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 440-448 
    Details
    ISSN: 1432-1432
    Keywords: Escherichia coli ; RAPD ; RFLP ; Clonal theory ; Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of the Escherichia coli population by multilocus enzyme electrophoresis (MLEE) has established its clonal organization, but there is increasing evidence that horizontal DNA transfer occurs in E. coli. We have assessed the genetic structure of the species E. coli and determined the extent to which recombination can affect the clonal structure of bacteria. A panel of 72 E. coli strains from the ECOR collection was characterized by random amplified polymorphic DNA (RAPD) and restriction-fragment-length polymorphism (RFLP) of the ribosomal RNA gene (rrn) regions. These strains have been characterized by MLEE and are assumed to reflect the range of genotypic variation in the species as a whole. Statistical analysis, including factorial analysis of correspondence (FAC) and hierarchical classifications, established that the data obtained with the three genetic markers are mutually corroborative, thus providing compelling evidence that horizontal transfer does not disrupt the clonal organization of the population. However, there is a gradient of correlation between the different classifications which ranges from the highly clonal structure of 132 group strains causing extraintestinal infections in humans to the less-stringent structure of B1 group strains that came mainly from nonprimate mammals. This group (B1) appears to be the framework from which the remaining non-A group strains have emerged. These results indicate that RAPD analysis is well suited to intraspecies characterization of E. coli. Lastly, treating the RAPD data by FAC allowed description of subgroup-specific DNA fragments which can be used, in a strategy comparable to positional cloning, to isolate virulence genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160315
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  • 4
    Electronic Resource
    Electronic Resource
    The genetic heterogeneity of deer mouse populations (Peromyscus maniculatus) in an insular landscape (1999)
    Springer
    Population ecology 41 (1999), S. 263-268 
    Details
    ISSN: 1437-5613
    Keywords: Key words AMOVA ; Dispersion ; Gene flow ; Genetic distance ; HOMOVA ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A survey of the genetic variability in deer mouse populations was performed using specimens collected from six different islands on a lake covering approximately 50 km2. Random amplified polymorphic DNA (RAPD) was used to measure the extent of the genetic differences in this insular system. An analysis of molecular variance (AMOVA) revealed that populations are clearly separated at this microgeographic scale (F st = 0.13863; P 〈 0.001). The homogeneity of molecular variance test (HOMOVA) indicated that within-population levels vary greatly (B p = 0.76831; P 〈 0.001). The within-population molecular variance was found to be mainly correlated with the accessibility of the islands, computed as the inverse of the geographic distance separating an island from the lakeshore (r = 0.916; P 〈 0.003).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s101440050030
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  • 5
    Electronic Resource
    Electronic Resource
    Rapid Construction of a Random Genomic Library from Date-Palm (Phoenix Dactylifera L.) (1999)
    Springer
    Plant molecular biology reporter 17 (1999), S. 409-409 
    Details
    ISSN: 1572-9818
    Keywords: Date-palm ; DNA library ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A random genomic library of Tunisian date-palm varieties has been built from total cellular DNA, previously amplified according to an RAPD procedure. The resultant recombinant DNA is characterised by a size ranging from 200 to 1600 bp inserts. This DNA would constitute a large number of anonymous probes useful in Southern hybridisation experiments. It would also provide potential markers aimed at the molecular characterisation of date-palm varieties, aid the search of those associated with bayoud disease and suggest a sex determination of trees.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007631420875
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  • 6
    Electronic Resource
    Electronic Resource
    Isolation and PCR Amplification of Genomic DNA from Market Samples of Dry Tea (1999)
    Springer
    Plant molecular biology reporter 17 (1999), S. 171-178 
    Details
    ISSN: 1572-9818
    Keywords: Camellia sinensis ; DNA isolation ; PCR ; RAPD ; Tea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A simple procedure for DNA isolation from processed dried commercial samples of tea is described. The method involves a modified CTAB procedure employing extensive washing, use of 1% PVP to remove polyphenolics and a single phenol:chloroform extraction step. The average yield ranges from 164–494 μg/g tea sample for various market samples. The DNA obtained from 11 different brands of tea using this procedure were consistently amplifiable (using both RAPD primers as well as defined sequences as primers) and digestible with restriction endonucleases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007562802361
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  • 7
    Electronic Resource
    Electronic Resource
    Parental analysis using RAPD markers in the antColobopsis nipponicus: A test of RAPD markers for estimating reproductive structure within social insect colonies (1995)
    Springer
    Insectes sociaux 42 (1995), S. 337-346 
    Details
    ISSN: 1420-9098
    Keywords: RAPD ; DNA polymorphism ; parental analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Previously known parent-offspring relationship for queens and her daughters of the antColobopsis nipponicus was examined using RAPD markers in order to test the reliability of this molecular technique for estimating the reproductive structure within colonies of social insects. RAPD markers from 20 oligomers successfully clustered the queen with her daughters among an artificially generated polygynous society, even when paternal information was unavailable. When information from both the queen and her sperm was included in the analysis, 20 polymorphic bands seem to be sufficient to cluster correctly the true parents to their offspring. Lack of father's information considerably decreased accuracy of the analysis. Thus, if RAPD markers are to be used to demonstrate parent-offspring relationship between individuals in the field, sperm from the queen's spermatheca should be incorporated in analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01242162
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  • 8
    Electronic Resource
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    Somaclonal variation in cryopreserved embryogenic clones of white spruce [Picea glauca (Moench) Voss.] (1999)
    Springer
    Plant cell reports 18 (1999), S. 948-953 
    Details
    ISSN: 1432-203X
    Keywords: Key words Somaclonal variation ; Picea glauca ; RAPD ; Somatic embryogenesis ; Cryopreservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Trees were regenerated from six white spruce embryogenic clones after cryopreservation for 3 and 4 years, respectively. Genetic stability was evaluated using randomly amplified polymorphic DNA (RAPD) fingerprints. Somaclonal variation was detected in some in vitro embryogenic cultures 2 and 12 months after they were re-established following cryopreservation but not in the corresponding regenerated trees. These results suggest that trees regenerated from cryopreserved cultures in subsequent years are primarily genetically stable in the genomic regions tested and that variation observed due to the in vitro culture process infrequently affects trees regenerated from normally maturing and germinating somatic embryos. However, trees regenerated from somatic embryos that matured or germinated abnormally in in vitro culture exhibited altered RAPD fragment patterns.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002990050689
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  • 9
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    Detection of somaclonal variation in garlic (Allium sativum L.) using RAPD and cytological analysis (1999)
    Springer
    Plant cell reports 18 (1999), S. 473-477 
    Details
    ISSN: 1432-203X
    Keywords: Key wordsAllium sativum ; Garlic ; Genetic instability ; RAPD ; Somaclonal variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Plants were regenerated by somatic embryogenesis from long-term callus cultures derived from five garlic (Allium sativum L.) cultivars. Thirty-five of these plants were subjected to RAPD analysis. The frequency of variation was found to be cultivar dependent: approximately 1% in the two clones Solent White and California Late and around 0.35% in another three clones, Chinese, Long Keeper and Madena. Certain band changes were found in regenerants of different cultivars, suggesting the existence of a mutation-sensitive part of the garlic genome. The karyotypes of another 75 regenerants derived from the same callus cultures of three parental garlic clones were examined. Of these plants, 9.3% were found to be tetraploids, 4% aneuploid and 2.6% showed a change in the position of the secondary constriction. No association could be shown between the rate of variation for molecular and cytological characters either by comparing cultivars or examining individual regenerants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002990050606
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  • 10
    Electronic Resource
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    Construction of near-isogenic lines to investigate the efficiency of different resistance genes to anthracnose (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 859-864 
    Details
    ISSN: 1432-2242
    Keywords: Phaseolus vulgaris ; Colletotrichum lindemuthianum ; PAL mRNA ; Cytology ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A suitable experimental model was designed with the aim of investigating the specific effect of different resistance genes in the Phaseolus vulgaris — Colletotrichum lindemuthianum interaction. The four resistance genes examined were chosen because they confer a different phenotype (resistance or susceptibility) to the lines carrying them when challenged by a range of C. lindemuthianum races. These different resistance genes were introgressed independently into the same susceptible recipient line. The isogenicity of the five near-isogenic lines (NILs) thus obtained (four resistant lines, one susceptible line = recipient line) was assessed by a RAPD analysis. The hypersensitive reaction occurred at the same time after infection, whatever the resistance gene present, when the NILs were challenged by the avirulent race 9 of the pathogen. In contrast, the pathogen development was arrested more or less rapidly in the different NILs. At the first stages of the infection process, the transcripts encoding phenylalanine ammonia-lyase were accumulated to a different extent in the different resistant NILs but always to a higher level than in the susceptible recipient line. These results suggest that the different resistance genes operate through more than one way in the production of defense factors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222023
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  • 11
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    The identification of duplicate accessions within a rice germplasm collection using RAPD analysis (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 1049-1055 
    Details
    ISSN: 1432-2242
    Keywords: Oryza sativa ; Rice ; Genetic resources ; RAPD ; Molecular markers ; Cluster analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A set of accessions of Oryza sativa from the International Rice Research Institute (Philippines) that included known and suspected duplicates as well as closely related germplasm has been subjected to RAPD analysis. The number of primers, the number of polymorphic bands and the total number of bands were determined that will allow the accurate discrimination of these categories of accessions, including the identification of true and suspected duplicates. Two procedures have been described that could be employed on a more general basis for identifying duplicates in genetic resources collections, and further discussion on the values of such activities is presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222920
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  • 12
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    Sensitivity of random amplified polymorphic DNA analysis to detect genetic change in sugarcane during tissue culture (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 1169-1173 
    Details
    ISSN: 1432-2242
    Keywords: RAPD ; Sugarcane ; Embryogenic callus ; Genetic transformation ; Somaclonal variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Random amplified polymorphic DNA (RAPD) analysis using 10-mer oligonucleotide primers efficiently differentiated sugarcane cultivars and proved suitable for detecting gross genetic change such as that which can occur in sugarcane subjected to prolonged tissue culture, for example in protoplast-derived callus. However, RAPD analysis was not sufficiently sensitive to detect smaller genetic changes that occur during sugarcane genetic transformation. The length of DNA scored for polymorphism per primer averaged 13.2 kb, or 0.0001% of the typical sugarcane genome size of 1.2 × 107 kb (2C). RAPD analysis of sugarcane plants regenerated from embryogenic callus revealed very few polymorphisms, indicating that gross genetic change is infrequent during this tissue culture procedure, although epigenetic effects result in transient morphological changes in regenerated plants. More sensitive variations on the RAPD technique may increase the practicality of DNA-based screening of regenerated plant lines to reveal somaclonal variants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222939
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  • 13
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    Identification of a RAPD marker for palmitic-acid concentration in the seed oil of spring turnip rape (Brassica rapa ssp. oleifera) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 477-480 
    Details
    ISSN: 1432-2242
    Keywords: Brassica rapa ; RFLP ; RAPD ; QTL ; Palmitic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract F2 progeny (105 individuals) from the cross Jo4002 x Sv3402 were used to identify DNA markers associated with palmitic-acid content in spring turnip rape (Brassica rapa ssp. oleifera). QTL mapping and ANOVA analysis of 140 markers exposed one linkage group with a locus controlling palmitic-acid content (LOD score 27), and one RAPD (random amplified polymorphic DNA) marker, OPB-11a, closely linked (1.4 cM) to this locus. Palmitic-acid content in the 62 F2 plants with the visible allele of marker OPB-11a was 8.45 ±3.15%, while that in the 24 plants without it was 4.59 ±0.97%. As oleic-acid concentration is affected by a locus on the same linkage group as the palmitic-acid locus, this locus probably controls the chain elongation from palmitic acid to oleic acid (through stearic acid). Marker OPB-11a may be used in future breeding programs of spring turnip rape to simplify and hasten the selection for palmitic-acid content.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222976
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  • 14
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    Relationships among cultivated and wild lentils revealed by RAPD analysis (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 647-654 
    Details
    ISSN: 1432-2242
    Keywords: Lens ; RAPD ; Cluster analysis ; Diversity ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPD markers were used to distinguish between six different Lens taxa, representing cultivated lentil and its wild relatives. Twenty-four arbitrary sequence 10-mer primers were identified which revealed robust and easily interpretable amplification-product profiles. These generated a total of 88 polymorphic bands in 54 accessions and were used to partition variation within and among Lens taxa. The data showed that, of the taxa examined, ssp. orientalis is most similar to cultivated lentil. L. ervoides was the most divergent wild taxon followed by L. nigricans. The genetic similarity between the latter two species was of the same magnitude as between ssp. orientalis and cultivated lentil. In addition, species-diagnostic amplification products specific to L. odemensis, L. ervoides and L. nigricans were identified. These results correspond well with previous isozyme and RFLP studies. RAPDs, however, appear to provide a greater degree of resolution at a sub-species level. The level of variation detected within cultivated lentils suggests that RAPD markers may be an appropriate technology for the construction of genetic linkage maps between closely related Lens accessions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223292
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  • 15
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    Genetic diversity in European and Mediterranean faba bean germ plasm revealed by RAPD markers (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 27-32 
    Details
    ISSN: 1432-2242
    Keywords: RAPD ; Genetic diversity ; Vicia faba L ; Germ plasm ; Gene pools
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Broadening of the genetic base and systematic exploitation of heterosis in faba bean requires reliable information on the genetic diversity in the germ plasm. Three groups of faba bean inbred lines were examined by means of RAPDs (random amplified polymorphic DNAs) assays: 13 European small-seeded lines, 6 European large-seeded lines, and 9 Mediterranean lines. Out of 59 primers, 35 were informative and yielded 365 bands, 289 of which were polymorphic with a mean of 8.3 bands per primer. Monomorphic bands were omitted from the analyses and genetic distances (GD) were estimated via the coefficient of Jaccard. The mean GD among the European small-seeded lines was significantly greater than those among the lines of the other two groups. Repeatability of GD estimates was high. Cluster (UPGMA) and principal coordinate analyses identified European small-seeded lines and Mediterranean lines as distinct groups with European large-seeded lines located in between. The results are in harmony with published archaeobotanical findings. We conclude that RAPDs are useful for classification of germ plasm and identification of divergent heterotic groups in faba bean.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220992
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  • 16
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    Identification of molecular markers linked to the Agropyron elongatum-derived leaf rust resistance gene Lr24 in wheat (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 982-990 
    Details
    ISSN: 1432-2242
    Keywords: Leaf rust ; RFLP ; RAPD ; Wheat ; Agropyron elongatum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The objective of this study was to identify molecular markers linked to the wheat leaf rust resistance gene Lr24 derived from Agropyron elongatum (3DL/3Ag translocation). Two near isogenic lines (NILs), ‘Arina’ and Lr24/7 * “Arina”, were screened for polymorphism at the DNA level with 115 RFLP probes. Twenty-one of these probes map to the homoeologous group 3. In addition, 360 RAPD primers were tested on the NILs. Six RFLP probes showed polymorphism between the NILs, and 11 RAPD primers detected one additional band in the resistant NIL. The genetic linkage of the polymorphic markers with Lr24 was tested on a segregating F2 population (150 plants) derived from a cross between the leaf rust resistant Lr24/7 * “Arina” and the susceptible spelt (Triticum spelta) variety ‘Oberkulmer’. All 6 RFLP markers were completely linked to Lr24: one was inherited as a codominant marker (PSR1205), one was in coupling phase (PSR1203) and 4 were in repulsion phase (PSR388, PSR904, PSR931, PSR1067) with Lr24. The localization of these probes on chromosome 3D was confirmed by nulli-tetrasomic analysis. Distorted genotypic segregation was found for the Codominant RFLP marker PSR1205. This distortion can be explained by the occurrence of hemizygous plants. One of the 11 RAPD markers (OPJ-09) also showed complete linkage to theLr24 resistance gene. The polymorphic RAPD fragment was cloned and sequenced. Specific primers were synthesized, and they produced an amplification product only in the resistant plants. This specific marker allows a reliable and rapid screening of a large number of genotypes in practical breeding. Analysis of 6 additional lines containing Lr24 revealed that 3 lines have a smaller chromosomal segment of A. elongatum than lines derived from ‘Agent’, a commonly used gene donor for the Lr24 resistance gene.
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    URL: http://dx.doi.org/10.1007/BF00222911
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  • 17
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    Genetics of resistance to ascochyta blight (Ascochyta lentis) of lentil and the identification of closely linked RAPD markers (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 93-98 
    Details
    ISSN: 1432-2242
    Keywords: Key words Ascochyta lentis ; Lens culinaris ssp. culinaris ; Bulked segregant analysis ; Resistance genes ; RAPD ; QTL analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Foliar resistance to Ascochyta lentis is controlled at a single major locus by a dominant gene (AbR 1 ) in the lentil accession ILL5588 (cv ‘Northfield’). Flanking RAPD markers that are closely linked to the resistance locus in coupling phase were identified by bulked segregant analysis. Out of 261 decanucleotide primers screened 7 produced a polymorphic marker that segregated with the resistance locus, and all markers were found to exist within a single linkage group. Five of the seven RAPD markers were within 30 cM of the resistance locus. Log likelihood analysis for detecting QTL associated with the foliar resistance revealed that a single narrow peak accounted for almost 90% of the variance of resistance between the bulks. Preliminary mapping in an F3 population revealed that the closest flanking markers were approximately 6 and 14 centiMorgans (cM) away from the resistance locus. These markers should be useful for the discrimination of resistant germplasm through marker-assisted selection in future breeding programmes and represent the first essential step towards the map-based cloning of this resistance gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051044
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  • 18
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    Linkage relationships among molecular markers and storage root traits of carrot (Daucus carota L. ssp. sativus) (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 58-64 
    Details
    ISSN: 1432-2242
    Keywords: Key words Genetic map ; RFLP ; AFLP ; RAPD ; SAMPL ; Daucus carota L. ssp. sativus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A 109-point linkage map consisting of three phenotypic loci (P 1, Y 2, and Rs), six restriction fragment length polymorphisms (RFLPs), two random amplified polymorphic DNAs (RAPDs), 96 amplified fragment length polymorphisms (AFLPs), and two selective amplification of microsatellite polymorphic loci (SAMPL) was constructed for carrot (Daucus carota L. ssp. sativus; 2n=2x=18). The incidence of polymorphism was 36% for RFLP probes, 20% for RAPD primers, and 42% for AFLP primers. The overall incidence of disturbed segregation was 18%. Linkage relationships at a LOD score of 4.0 and θ=0.25 indicated 11 linkage groups. The total map length was 534.4 cM and the map was clearly unsaturated with markers spaced at 4.9 cM. AFLP P6B15 was 1.7 cM from P 1, AFLP P1B34 was 2.2 cM from Y 2, and AFLP P3B30XA was 8.1 cM from Rs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051208
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  • 19
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    An integrated genetic linkage map for eucalypts using RFLP, RAPD and isozyme markers (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 869-875 
    Details
    ISSN: 1432-2242
    Keywords: Genetic map ; Linkage ; Eucalypts ; RFLP ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An integrated genetic linkage map for E. nitens was constructed in an outbred three-generation pedigree. Analysis of 210 RFLP, 125 RAPD and 4 isozyme loci resulted in 330 markers linked in 12 linkage groups covering 1462 cM (n=11 in eucalypts). The 12th linkage group is comprised of only 5 markers and will probably coalesce with another linkage group when further linked loci are located. Co-dominant RFLP loci segregating in both parents were used to integrate linkages identified in the male and female parents. Differences in recombination frequencies in the two parents were observed for a number of pairs of loci, and duplication of sequences was identified both within and between linkage groups. The markers were distributed randomly across the genome except for the RFLPs in linkage group 10 and for some loci showing segregation distortion, which were clustered into three regions of the map. The use of a large number of co-dominant RFLP loci in this map enables it to be used in other pedigrees of E. nitens and forms a basis for the detection and location of QTL in E. nitens and other eucalypt species.
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    URL: http://dx.doi.org/10.1007/BF00223894
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  • 20
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    RAPD mapping of three QTLs determining trichome formation in Microseris hybrid H27 (Asteraceae:Lactuceae) (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 853-858 
    Details
    ISSN: 1432-2242
    Keywords: Microseris ; RAPD ; QTL ; Trichomes Gene regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Segregation for 289 random amplified polymorphic DNA markers (RAPDs) has been determined in 106 F2 plants of an interspecific hybrid (H27) between Microseris douglasii (strain B14) and M. bigelovii (C94). Multicelluar trichomes (“type D”, specific for Microseris) occur on the leaf teeth of early vegetative rosettes of the B14 parent and on the leaf blades of later rosettes in both parents. Trichomes on the leaf blades appear earlier and eventually more densely in B14. Segregation for trichome appearance is quantitative and strongly transgressive in the F2 hybrid. Cosegregation between RAPDs and trichome phenotypes combined with linkage data have revealed a main gene (“quantitative trait locus A”, QTL-A) with a pleiotropic effect on all trichome characters and two unlinked additive modifiers (QTL-B, QTL-C). Alleles of both modifiers reduce the main gene effect in each parent. Their recombination explains the occurrence of plants with transgressive phenotypes in the hybrid offspring. Additional QTLs affecting trichomes are at and below the level of statistical significance.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222022
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    Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 933-947 
    Details
    ISSN: 1432-2242
    Keywords: RAPD ; Pseudo-testcross ; Eucalyptus ; QTL ; Vegetative propagation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have extended the combined use of the “pseudo-testcross” mapping strategy and RAPD markers to map quantitative trait loci (QTLs) controlling traits related to vegetative propagation in Eucalyptus. QTL analyses were performed using two different interval mapping approaches, MAPMAKER-QTL (maximum likelihood) and QTL-STAT (non-linear least squares). A total of ten QTLs were detected for micropropagation response (measured as fresh weight of shoots, FWS), six for stump sprouting ability (measured as # stump sprout cuttings, #Cutt) and four for rooting ability (measured as % rooting of cuttings, %Root). With the exception of three QTLs, both interval-mapping methods yielded similar results in terms of QTL detection. Discrepancies in the most likely QTL location were observed between the two methods. In 75% of the cases the most likely position was in the same, or in an adjacent, interval. Standardized gene substitution effects for the QTLs detected were typically between 0.46 and 2.1 phenotypic standard deviations (σp), while differences between the family mean and the favorable QTL genotype were between 0.25 and 1.07 (σp). Multipoint estimates of the total genetic variation explained by the QTLs (89.0% for FWS, 67.1 % for#Cutt, 62.7% for %Root) indicate that a large proportion of the variation in these traits is controlled by a relatively small number of major-effect QTLs. In this cross, E. grandis is responsible for most of the inherited variation in the ability to form shoots, while E. urophylla contributes most of the ability in rooting. QTL mapping in the pseudo-testcross configuration relies on withinfamily linkage disequilibrium to establish marker/trait associations. With this approach QTL analysis is possible in any available full-sib family generated from undomesticated and highly heterozygous organisms such as forest trees. QTL mapping on two-generation pedigrees opens the possibility of using already existing families in retrospective QTL analyses to gather the quantitative data necessary for marker-assisted tree breeding.
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    URL: http://dx.doi.org/10.1007/BF00222906
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    Random amplified polymorphic DNA (RAPD) analysis reveals genetic relationships among the annual Cicer species (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 657-663 
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    ISSN: 1432-2242
    Keywords: Key words Cicer ; Species relationships ; DNA fingerprinting ; RAPD ; Chickpea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Random amplified polymorphic DNA markers were used to distinguish between nine different Cicer taxa representing the cultivated chickpea and eight other related annual wild species. Of the 75 random10-mer primers tested, only 8 amplified genomic DNA across all the species. A total of 115 reproducibly scorable RAPD markers were generated, all except 1 polymorphic, and these were utilized to deduce genetic relationships among the annual Cicer species. Four distinct clusters were observed and represented C. arietinum, C. reticulatum and C. echinospermum in first cluster followed by C. chorassanicum and C. yamashitae in the second cluster, while C. pinnatifidum, C. judaicum and C. bijugum formed the third cluster. Cicer cuneatum did not cluster with any of the species and was most distantly placed from the cultivated species. Except for the placement of C. chorassanicum and C. yamashitae, deduced species’ relationships agreed with previous studies. In addition, species-diagnostic amplification products specific to all the nine species were identified. The results clearly demonstrate a methodology based on random-primed DNA amplification that can be used for studying Cicer phylogeny and chickpea improvement.
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    URL: http://dx.doi.org/10.1007/s001220051117
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    Development of a genetic composite map of Vicia faba using F2 populations derived from trisomic plants (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 736-743 
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    ISSN: 1432-2242
    Keywords: Key words Vicia faba ; Genetic map ; Trisomics ; RAPD ; Seed-protein genes ; QTLs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Seven F2 families of faba bean descendent from plants trisomic for chromosomes 3, 4, 5 and 6 were analyzed for isozyme markers and two of these were also studied for morphological and RAPD markers and seed-protein genes. Linkage analysis revealed 14 linkage groups, 8 of which were unambiguously assigned to specific chromosomes. Several QTLs for seed weight were identified, the most important of which, located on chromosome 6, explained approximately 30% of the total phenotypic variation. Comparison of results from Vicia faba with the maps of the related species Pisum sativum L. and Cicer arietinum L. revealed one possible new case of linkage conservation. A composite linkage analysis based on 42 markers analyzed in this and previous studies, where line Vf 6 was also used as the female parental, allowed the new assignment of previously independent linkage groups and/or markers to specific chromosomes. Thus, the number of linkage groups was reduced to 13, each comprising an increased number of markers. No contradictory results were detected, indicating the suitability of the statistical procedure and methodology used so far in the development of the map of this species.
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    URL: http://dx.doi.org/10.1007/s001220051129
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    Variation among and within Capsicum species revealed by RAPD markers (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 147-156 
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    ISSN: 1432-2242
    Keywords: Key words Capsicum ; Diagnostic markers ; Genetic diversity ; Germplasm ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Germplasm characterization is an important link between the conservation and utilization of plant genetic resources. A total of 134 accessions from six Capsicumspecies maintained at the Asian Vegetable Research and Development Center were characterized using 110 randomly amplified polymorphic DNA (RAPD) markers. Ten pairs of potentially duplicated accessions were identified. Multidimensional scaling analysis of the genetic distances among accessions resulted in clustering corresponding to a previous species assignment except for six accessions. Diagnostic RAPDs were identified which discriminate among the Capsicumspecies. The diagnostic markers were employed for improved taxonomic identification of accessions since many morphological traits used in the identification of Capsicumare difficult to score. Three Capsicumaccessions, misclassified based on morphological traits, were reassigned species status based on diagnostic RAPDs. Three accessions, not previously classified, were assigned to a species based on diagnostic RAPDs. Definitive conclusions about the species assignment of three other accessions were not possible. The level of diversity between Capsicum annuumaccessions from the genebank and the breeding program were compared and no differences were observed either for RAPD variation or diversity. The utilization of genetic resources as a source of variance for useful traits in the breeding program may be the reason for the similarity of these two groups.
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    URL: http://dx.doi.org/10.1007/s001220051219
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    Genetic relationships among Native American maize accessions of the Great Plains assessed by RAPDs (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 1061-1067 
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    ISSN: 1432-2242
    Keywords: Key words Native American maize ; RAPD ; Genetic relationships ; Reproducibility ; Geography and evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Genetic variation among 15 accessions of Native American maize from the Great Plains was investigated using random amplified polymorphic DNA (RAPD). RAPDs revealed very high levels of polymorphism among accessions. Banding patterns ranged in percentage polymorphism from 46.7% to 86.2% with an overall mean of 70.7% for the primers analyzed. The construction of genetic relationships using cluster analysis and principal coordinates analysis revealed that RAPDs are successful in confirming hypothesized relationships and in identifying misclassified specimens. Furthermore, the phenogram fails to reveal a strong correspondence between genetic relationships and the geographical position of Native Americans prior to contact. This provides support for the hypothesis that multiple introductions of maize into the Great Plains via trade may have resulted in the great morphological variation found among accessions in the region. Based on these data, it is unlikely that a separate Great Plains race of maize can be distinguished. In general, we conclude that RAPDs are potentially very useful in organizing seed collections and understanding intraspecific genetic differentiation.
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    URL: http://dx.doi.org/10.1007/s001220051415
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    High-resolution genetic and physical mapping of the region containing the Bs2 resistance gene of pepper (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 1201-1206 
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    ISSN: 1432-2242
    Keywords: Key words Bs2 resistance gene ; Pepper ; RAPD ; AFLP ; Positional cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The Bs2 resistance gene of pepper confers resistance against the bacterial pathogen Xanthomonas campestris pv. vesicatoria. As a first step toward isolation of the Bs2 gene, molecular markers tightly linked to the gene were identified by randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analysis of near-isogenic lines. Markers flanking the locus were identified and a high-resolution linkage map of the region was developed. One AFLP marker, A2, was found to cosegregate with the locus, while two others, F1 and B3, flank the locus and are within 0.6 cM. Physical mapping of the A2 and F1 markers indicates that these markers may be within 150 kb of each other. Together, these results indicate that the Bs2 region may be cloned either by chromosome walker or landing. The linked markers were also used to characterize gamma-irradiation-induced mutants at the Bs2 locus.
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    URL: http://dx.doi.org/10.1007/s001220051325
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    RAPD fingerprinting of blackcurrant (Ribes nigrum L.) cultivars (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 166-172 
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    ISSN: 1432-2242
    Keywords: Ribes nigrum ; RAPD ; Genetic variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ribes nigrum germplasm was screened for random amplified polymorphic DNA (RAPD) markers. Fiftyfour markers were identified which generated individual fingerprints for each of 21 cultivars. Genetic variation within R. nigrum germplasm, as detected by RAPDs, demonstrated that the genetic basis for improvement of blackcurrant is narrower than would be expected by the analysis of parentage.
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    URL: http://dx.doi.org/10.1007/BF00222198
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    Conversion of a RAPD-generated PCR product, containing a novel dispersed repetitive element, into a fast and robust assay for the presence of rye chromatin in wheat (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 636-642 
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    ISSN: 1432-2242
    Keywords: Wheat ; Rye ; RAPD ; PCR ; In situ hybridization ; Dispersed repeat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bulk segregant analysis was used to obtain a random amplified polymorphic DNA (RAPD) marker specific for the rye chromosome arm of the 1BL.1RS translocation, which is common in many high-yielding bread wheat varieties. The RAPD-generated band was cloned and end-sequenced to allow the construction of a pair of oligonucleotide primers that PCR-amplify a DNA sequence only in the presence of rye chromatin. The amplified sequence shares a low level of homology to wheat and barley, as judged by the low strength of hybridization of the sequence to restriction digests of genomic DNA. Genetic analysis showed that the amplified sequence was present on every rye chromosome and not restricted to either the proximal or distal part of the 1RS arm. In situ hybridization studies using the amplified product as probe also showed that the sequence was dispersed throughout the rye genome, but that the copy number was greatly reduced, or the sequence was absent at both the centromere and the major sites of heterochromatin (telomere and nucleolar organizing region). The probe, using both Southern blot and in situ hybridization analyses, hybridized at a low level to wheat chromosomes, and no hybridizing restriction fragments could be located to individual wheat chromosomes from the restriction fragment length polymorphism (RFLP) profiles of wheat aneuploids. The disomic addition lines of rye chromosomes to wheat shared a similar RFLP profile to one another. The amplified sequence does not contain the RIS 1 sequence and therefore represents an as yet undescribed dispersed repetitive sequence. The specificity of the amplification primers is such that they will provide a useful tool for the rapid detection of rye chromatin in a wheat background. Additionally, the relatively low level of cross-hybridization to wheat chromatin should allow the sequence to be used to analyse the organization of rye euchromatin in interphase nuclei of wheat lines carrying chromosomes, chromosome segments or whole genomes derived from rye.
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    URL: http://dx.doi.org/10.1007/BF00222127
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    Random amplified polymorphic DNA variation in the eggplant, Solanum melongena L. (Solanaceae) (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 767-770 
    Details
    ISSN: 1432-2242
    Keywords: Solanum melongena ; Insanum ; RAPD ; Interrelationships
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPD analysis was carried out on 52 accessions of Solanum melongena (eggplant) and related weedy forms known as “insanum”. Twenty-two primers amplified 130 fragments. Solanum melongena exhibited 117 of the fragments, all of which were also present in insanum. Insanum displayed an additional 13 fragments not found in S. melongena. Overall, the insanum accessions were more diverse than those of S. melongena. The calculated similarity between them was 0.947. The RAPD results were closely concordant with the results of an electrophoretic isozyme survey performed on the same accessions. The concordance of the results shows that even though S. melongena and insanum are highly diverse morphologically, it is no longer appropriate to distinguish them taxonomically.
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    URL: http://dx.doi.org/10.1007/BF00222010
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    Allozyme, chloroplast DNA and RAPD markers for determining genetic relationships between Abies alba and the relic population of Abies nebrodensis (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 1012-1018 
    Details
    ISSN: 1432-2242
    Keywords: Allozymes ; Chloroplast DNA ; RAPD ; Genetic variation ; Abies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Allozyme, chloroplast (cpDNA) and random amplified polymorphic DNA (RAPD) markers have been used to estimate genetic and taxonomic relationships among different populations of Abies alba and the relic population of A. nebrodensis. Twelve isozyme gene loci, as well as restriction fragment length polymorphism (RFLP) at cpDNA spacer regions between t-RNA genes were analysed. Moreover, a set of 60 random sequence 10-mer primers were tested. Over all isozyme loci, evident differences in allele frequencies among A. nebrodensis and A. alba populations were found, particularly at 2 loci, phosphoglucose isomerase (Pgi-a) and shikimate dehydrogenase (Skd-a). More than 10% of the total genetic diversity was due to differences among populations. High values of genetic distances among populations were also found. Out of the 60 primers tested, 12 resulted in a polymorphic banding pattern both within and among populations. A total of 84 RAPD fragments were produced by the 12 selected primers. A phenogram of relationships among populations was constructed based on RAPD band sharing: the differentiation of the A. nebrodensis population was evident. The analysis of molecular variance (AMOVA) was used to apportion the variation among individuals within populations and among populations. There was considerable variation within each population: even so, genetic divergence was found among populations. This pattern of genetic variation was very different from that reported for inbred species. Identical cpDNA amplification and restriction patterns were observed among all the individuals sampled from the populations. Taken together, the results of allozyme and RAPDs show a clear differentiation among A. nebrodensis and A. alba populations and provide support for their classification into two different taxonomic groups.
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    URL: http://dx.doi.org/10.1007/BF00222915
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    Species-specific RAPD fingerprints for the closely related Picea mariana and P. rubens (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 142-149 
    Details
    ISSN: 1432-2242
    Keywords: DNA fingerprint ; Molecular markers ; Picea mariana ; Picea rubens ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Species-specific molecular markers were designed to assist in the identification of closely related black spruce (Picea mariana [B.S.P.] Mill.) and red spruce (P. rubens Sarg.) in northeastern North America. Trees from six provenances of black spruce and three provenances of red spruce were sampled from outside the sympatric zone. They were first classified using a composite index of five qualitative morphological traits. The species-specific genetic markers were developed using random amplified polymorphic DNAs (RAPD) and a combination of bulk sample and individual tree analyses. Each species bulk sample was constructed from DNAs obtained from 12 trees that were from outside the sympatric zone and showed a morphological composite index specific of each species. A total of 161 primers were screened with the bulk samples. From these, 52 primers showing segregating fingerprints were further screened with the individual trees. Most of the markers observed were shared by the two species, and there was less diversity in P. rubens. A small number of markers were found to be monomorphic or nearly monomorphic and specific to either P. mariana or P. rubens. These markers remained species-specific when F1 progenies derived from independent intraspecific crosses were screened, and they were subsequently found to co-segregate in hybrids derived from independent interspecific crosses here used as controls.
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    URL: http://dx.doi.org/10.1007/BF00220871
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    Irregular meiosis in a somatic hybrid between S. bulbocastanum and S. tuberosum detected by species-specific PCR markers and cytological analysis (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 401-408 
    Details
    ISSN: 1432-2242
    Keywords: Solanum ; Potato ; RAPD ; Interspecific hybrids ; SCAR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A system of randomly amplified polymorphic DNA (RAPD) markers was developed to facilitate the transfer of S. bulbocastanum (blb) genes into the S. tuberosum (tbr) genome by hybridization and backcrossing. DNA from tbr, blb and the hexaploid hybrid was used as a template for polymerase chain reaction (PCR) amplification. Polymorphic RAPD products, originating from 10-mer primers, specific for blb were cloned and sequenced at their ends to allow the synthesis of 18-mer primers. The 18-mer primers allowed a more reproducible assay than the corresponding RAPDs. Of eight 18-mer primer pairs, four amplified the expected products specific for blb. However, the stringency of the primer annealing conditions needed to be carefully optimized to avoid amplification of the homeologous tbr product, suggesting that the original RAPD polymorphisms were due to single base-pair changes rather than deletions or insertions. Two primers used for amplification of backcross 2 progeny segregated in a 1∶1 (presence:absence) ratio; the other two were unexpectedly absent. The most likely explanation for the loss of these markers is irregular meiosis in the original hexaploid hybrid and subsequent elimination of chromosomes. Cytological analysis of the meiosis in the hybrid demonstrated widespread irregular pairing and the presence of lagging univalents. In addition, the first backcross individual used as the parent for the second backcross had 54 chromosomes instead of the predicted 60. In conclusion, our results demonstrate that PCR technology can be used for the efficient isolation of taxon-specific markers in Solanum. Furthermore, by the use of these markers we detected the loss of chromosomes that was subsequently shown by cytological analysis to be caused by irregular meiosis of the somatic hybrid.
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    URL: http://dx.doi.org/10.1007/BF00222966
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    Gynogenic lines of onion (Allium cepa L.): evidence of their homozygosity (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 598-602 
    Details
    ISSN: 1432-2242
    Keywords: Gynogenesis ; Isozyme ; RAPD ; Agronomic evaluation ; Gametoclonal variation ; Genetic homogeneity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Haploid induction via gynogenesis offers the possibility of using doubled haploid (DH) inbred lines in onion breeding. A first DH line that originated from the open-pollinated (OP) cultivar ‘Dorata di Parma’ was obtained after overcoming difficulties associated with the haploidy of the regenerants. Spontaneous chromosome doubling occurs seldom in onion. The first DH line obtained was cloned and selfed to produce sufficient seeds for genetic studies. The homozygosity of the DH gynogenic line was revealed on the basis of the low standard deviations of the bulb traits polar diameter, shape index and weight with respect to those of the S1 line or the OP cultivar. In the DH line, moreover, segregation of RAPD and alpha esterase markers was not noted. Out of four primers revealing polymorphism at 16 ge-netic loci in the OP cultivar ‘Dorata di Parma’, none produced polymorphism in the DH gynogenic line. The Est-1 locus, homozygous in 22 plants (Est-1 1/1 in 3 and Est-1 2/2 in 19) and heterozygous (Est-1 1/2) in 11 plants of the OP cultivar, always carried the same alleles in the DH line. We also tested genetic stability during micropropagation of a second halpoid line obtained via gynogenesis from var. ‘Senshyu Yellow’. Seventeen plants of this line were tested to detect changes occurring during the tissue culture process. Again no polymorphism was observed. The high genetic homogeneity observed in the two gynogenic lines of onion could be related to the absence of the callus phase during the gynogenic process.
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    Tagging and mapping the thermo-sensitive genic male-sterile gene in rice (Oryza sativa L.) with molecular markers (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 1111-1114 
    Details
    ISSN: 1432-2242
    Keywords: Rice TGMS gene ; RAPD ; RFLP ; Molecular markers ; Gene tagging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The thermo-sensititve genic male-sterile (TGMS) gene in rice can alter fertility in response to temperature and is useful in the two-line system of hybrid rice production. However, little is known about the TGMS gene at the molecular level. The objective of this study was to identify molecular markers tightly linked with the TGMS gene and to map the gene onto a specific rice chromosome. Bulked segregant analysis of an F2 population from 5460s (a TGMS mutant line) x ‘Hong Wan 52’ was used to identify RAPD markers linked to the rice TGMS gene. Four hundred RAPD primers were screened for polymorphisms between the parents and between two bulks representing fertile and sterile plants; of these, 4 primers produced polymorphic products. Most of the polymorphic fragments contained repetitive sequences. Only one singlecopy sequence fragment was found, a 1.2-kb fragment amplified by primer OPB-19 and subsequently named TGMS1.2. TGMS1.2 was mapped on chromosome 8 with a RIL population and confirmed by remapping with a DHL population. Segregation analysis using TGMS1.2 as a probe indicated that TGMS1.2 both consegregated and was lined with the TGMS gene in this population. It is located about 6.7 cM from the TGMS gene. As TGMS1.2 is linked to the TGMS gene, the TGMS gene must be located on chromosome 8.
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    URL: http://dx.doi.org/10.1007/BF00223928
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    Identification of two RAPD markers tightly linked with the Nicotiana debneyi gene for resistance to black root rot of tobacco (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 1184-1189 
    Details
    ISSN: 1432-2242
    Keywords: Nicotiana tabacum ; Chalara elegans ; Black root rot ; Resistance gene ; RAPD ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Linkage of randomly amplified polymorphic DNA (RAPD) markers with a single dominant gene for resistance to black root rot (Chalara elegans Nag Raj and Kendrick; Syn. Thielaviopsis basicola [Berk. and Broome] Ferraris) of tobacco (Nicotiana tabacum L.), which was transferred from N. debneyi Domin, was investigated in this study. There were 2594 repeatable RAPD fragments generated by 441 primers on DNAs of ‘Delgold’ tobacco, a BC5F8 near isogenic line (NIL) carrying the resistance gene in a ‘Delgold’ background, and ‘PB19’, the donor parent of the resistance gene. Only 7 of these primers produced eight RAPD markers polymorphic between ‘Delgold’ and ‘PB19’, indicating there are few RAPD polymorphisms between them despite relatively dissimilar pedigrees. Five of the eight RAPD markers were not polymorphic between ‘Delgold’ and the NIL. All of these markers proved to be unlinked with the resistance gene in F2 linkage tests. Of the remaining three RAPD markers polymorphic between ‘Delgold’ and the NIL, two were shown to be strongly linked with the resistance gene; one in coupling and the other in repulsion. Application of the two RAPDs in the elimination of linkage drag associated with the N. debneyi resistance gene and marker-assisted selection for the breeding of new tobacco cultivars with the resistance gene is discussed.
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    URL: http://dx.doi.org/10.1007/BF00220927
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    Genetic diversity in populations of Cronartium ribicola in plantations and natural stands of Pinus strobus (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 1214-1221 
    Details
    ISSN: 1432-2242
    Keywords: Population genetics ; White pine blister rust ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genetic diversity was studied in 22 populations of the white pine blister rust fungus Cronartium ribicola from natural stands and plantations of eastern white pine, Pinus strobus. Pseudo-allelic frequencies were estimated at each of 7 putative RAPD loci by scoring for presence or absence of amplified fragments in dikaryotic aecidiospores. Analysis of genetic distance between all pairs of populations did not reveal any trend with regard to geographic origin or type of white pine stand. In addition, when hierarchical population structure was analysed, total genetic diversity (H s =0.214) was mostly attributable to diversity within populations (H s =0.199; AMOVA φ st =0.121, P〈0.01). Genetic diversity of populations relative to region of origin (east, centre, and west) or type of stand (natural stands vs plantations) was not significantly different from zero (P〉0.10) Nevertheless, a significant proportion of genetic differentiation was found between populations within region or stand type (F st =0.114; φ sc =0.132, P〈0.001). This result indicates that some population structure exists but that it appears to be independent of region of origin or type of stand. At least for 2 populations from white pine plantations, it appears possible that a recent introduction of a limited number of propagules was responsible for low levels of genetic diversity. We interpret these results as meaning that either long-distance dispersal is taking place between populations more than 1000 km apart or that these populations share a common recent ancestor. In addition, we suggest that C. ribicola may still be expanding its distribution by colonizing new plantations.
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    URL: http://dx.doi.org/10.1007/BF00220932
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    Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 171-177 
    Details
    ISSN: 1432-2242
    Keywords: Key words Varietal identification ; RAPD ; Microsatellite ; Vitis vinifera L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The aim of this study was to develop a cultivar identification tool based on molecular analysis and a statistical approach. From the PIC parameter we defined the D parameter, which evaluates the efficiency of a primer for the purpose of identification of varieties; i.e. the probability that two randomly chosen individuals have different patterns. D can be used to compare different types of markers even if only the allelic frequencies are known. We used this parameter to develop an algorithm for selecting the optimal combination of primers necessary to identify a set of varieties. The optimal combination of primers determined for a small elite group of varieties applied on a larger set induces a risk of confusion involving 1 of the elite varieties. We estimated the risk of confusion using the D value of each primer of the combination. We applied this methodology on a set of 224 varieties of Vitis vinifera screened with 21 RAPD primers and two microsatellite loci. The discriminating power of the primers did not only depend on the number of patterns it generates but also on the frequencies of the different patterns. A combination of 8 primers (6 RAPD and two microsatellite) was found to be optimum for the discrimination of these 224 varieties. A subset of 38 elite varieties was also investigated. The determined optimal combination of 4 primers (3 RAPD and one microsatellite) applied on the 224 varieties gave 9 risks of confusion involving 1 of the elite varieties. Confusion can happen between varieties with the same origin as well as between varieties of very diverse geographical origins.
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    URL: http://dx.doi.org/10.1007/s001220051054
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    Intertribal hexaploid somatic hybrid plants regeneration from electrofusion between diploids of Citrus sinensis and its sexually incompatible relative, Clausena lansium (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 581-585 
    Details
    ISSN: 1432-2242
    Keywords: Key words Somatic hybridization ; Hexaploid ; RAPD ; Chromosome number variation ; Genetic improvement ; Aurantioideae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Chinese wampee [Clausena lansium (Lour.) Skeels], a sexually incompatible relative of citrus, is commercially cultivated in South China. In this study, embryogenic protoplasts of ‘Bonanza’ navel orange [Citrus sinensis (L.) Osbeck] were electrically fused with leaf protoplasts isolated from ‘Chicken Heart’ Chinese wampee. After 8 months of culture, fusion products regenerated into shoots. More than 70% of the shoots unexpectedly rooted well. Chromosome counting of several shoot- and root-tips revealed that their chromosome numbers were not 2n=4x=36 as expected, but 2n=6x=54, suggesting that chromosome doubling occurred rather than chromosome elimination in this intertribal fusion combination. RAPD analysis of embryoids and the leaves of unrooted and rooted shoots verified their hybridity. This is the first report of hexaploid somatic hybrid plant regeneration from fusion between diploids in Aurantioideae.
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    URL: http://dx.doi.org/10.1007/s001220051107
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    Mean, genetic variance, and usefulness of selfing progenies from intra- and inter-pool crosses in faba beans (Vicia faba L.) and their prediction from parental parameters (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 569-580 
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    ISSN: 1432-2242
    Keywords: Key words Vicia faba L. ; RAPD ; Mahalanobis genetic distance ; Usefulness ; Genetic variance ; Mid-parent heterosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Determining the genetic potential of a base population from the properties of their parental lines would improve the efficiency of a breeding program. In the present study, we investigated whether the means of the parents and the genetic distance determined from RAPD data (GD) or multivariate analysis (Mahalanobis D2), mid-parent heterosis (MPH), and the absolute difference between means of the parents (∣P1−P2∣) can be used for predicting the means and genetic variances (σ^2 g ) of F3:4 lines derived from different crosses in faba beans. The material comprised 18 intra- and 18 inter-pool crosses among lines from the Minor, Major, and Mediterranean germplasm pools. Fifty F3:4 lines from each cross were evaluated for days to anthesis, plant height, seeds per plant, and seed yield in German (GE) and Mediterranean (ME) environments. GD estimates between parent lines ranged from 0.38 to 0.58, while D2 ranged from 45.5 to 134.7. Correlations between means of the parents and F3:4 lines were highly significant for most traits. Estimates of σ2 g for all traits showed non-significant correlations with MPH, GD, D2. In one ME, ∣P1−P2∣ had significant associations with σ^2 g for seed yield and days to anthesis. The predicted usefulness of crosses, defined as the sum of the population mean and selection responses, was most closely associated with the means of F3:4 lines. We conclude from this study that the means of F3:4 lines can be predicted from the means of the parents, whereas the prediction of genetic variance is still an unsolved problem
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    URL: http://dx.doi.org/10.1007/s001220051106
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    Development and characterization of Hordeum chilense chromosome-specific STS markers suitable for wheat introgression and marker-assisted selection (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 721-727 
    Details
    ISSN: 1432-2242
    Keywords: Key words Addition lines ; Multiplexed PCR ; RAPD ; Sequence tagged site ; Tritordeum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  RAPD markers were developed for octoploid×Tritordeum (amphiploid Hordeum chilense×Triticum aestivum) and its parents. Addition lines were used to identify specific RAPD markers for the Hordeum chilense chromosomes detectable in a wheat background. Twelve RAPD fragments have been cloned, sequenced and converted into STS markers. Eleven of these STSs have maintained both the chromosome specificity and the possibility of detection in a wheat background. The use of these markers in multiplexed PCRs facilitates both the efficient and reliable screening of new addition lines as well as the monitoring of introgression of H. chilense in bread and durum wheat.
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    URL: http://dx.doi.org/10.1007/s001220051126
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    Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 793-801 
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    ISSN: 1432-2242
    Keywords: Key words Pinus contorta ; Silviculture ; Reforestation ; Gene conservation ; RAPD ; SSR ; DNA analyses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  We examined the effects of different methods of forest regeneration on the genetic diversity of lodgepole pine (Pinus contorta var ‘latifolia’) using two different DNA-based molecular markers [randomly amplified polymorphic DNA (RAPDs) and microsatellites or simple sequence repeats (SSRs)]. Genetic diversity was estimated for 30 individuals in each of four populations for the following three stand types: (1) mature lodgepole pine (〉100 years); (2) 20- to 30-year-old harvested stands left for natural regeneration; (3) 20- to 30-year-old planted stands (4 stands of each type); and one group of 30 operationally produced seedlings. There was no significant effect of stand type on expected heterozygosity, although allelic richness and diversity were much higher for SSRs than for RAPDs. Expected heterozygosity ranged from 0.39 to 0.47 based on RAPDs and from 0.67 to 0.77 based on SSRs. The number of alleles per locus for SSRs ranged from 3 to 34 (mean 21.0), and there was a significant relationship between sequence repeat length and the number of alleles at a locus. Both marker types showed that over 94% of the variation was contained within the populations and that the naturally regenerated stands sampled had lower (not significant) expected heterozygosity than the planted or unharvested stands. The group of seedlings (assessed by RAPDs only) had expected heterozygosity and allele frequencies similar to those of the unharvested stands. Genetic distance measures were higher than obtained previously in the species using isozyme markers. There was no correlation between the two marker types for pair-wise genetic distances based on populations analyzed by both methods. Pair-wise genetic distance measures and an ordination of allele frequencies for both marker types showed little effect of geographic location or stand type on genetic similarity.
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    Development and polymorphism of microsatellite markers for Fagus crenata and the closely related species, F. japonica (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 11-15 
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    ISSN: 1432-2242
    Keywords: Key words Fagus crenata ; Fagus japonica ; Microsatellite ; RAPD ; RAHM ; SSR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  We have developed microsatellite markers (SSRs) applicable to Fagus crenata using the RAHM method and investigated their polymorphisms. We also applied the SSRs in an analysis of a closely related species, F. japonica. Here we describe the isolation and characterization of nine polymorphic microsatellite markers, of which eight are applicable to both species. Among 30 individuals of each of F. crenata and F. japonica we detected a total of 79 and 77 alleles, respectively, with an average of 9.9 and 8.6 alleles per locus. The mean expected heterozygosity (He) was 0.615 (range: 0.216–0.925) in F. crenata and 0.660 in F. japonica (range: 0.259–0.827). The He values were considerably higher than those previously found for isozymes. Paternity exclusion probabilities for multiple loci, calculated over all loci, were extremely high (0.999 and 0.998 in F. crenata and F. japonica, respectively): sufficiently high to study pollen flow in both species.
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    URL: http://dx.doi.org/10.1007/s001220051203
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    Genetic variation of petaloid male-sterile cytoplasm of carrots revealed by sequence-tagged sites (STSs) (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 837-843 
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    ISSN: 1432-2242
    Keywords: Key words Daucus carota spp. sativus ; RAPD ; Cytoplasmic male sterility (CMS) ; Asymmetric cell fusion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The mitochondrial DNA of various carrot lines was characterized by random amplified polymorphic DNA (RAPD) analysis, and six sequence-tagged sites (STSs) led to identification of the petaloid type of cytoplasmic male sterility (CMS). Using six STS primer combinations, we were able to classify five CMS lines into two groups and eight fertile carrots into six groups. Both the STS1 and the STS4 primer combinations differentiated CMS cytoplasms from the fertile cytoplasms, and the STS2 primer combination revealed two different types of CMS cytoplasms – of Wisconsin Wild and Cornell origins. Cybrid carrot lines with petaloid flowers which had been obtained by asymmetric cell fusion could also be separated from fertile cybrids by the STS1 primer combination. The STS1 fragment contained a homologous sequence with the orfB gene. DNA gel blot analysis indicated that homologous regions to the STS1 fragment existed in fertile types as well as the CMS types, although the restriction fragment size patterns differed. These observations demonstrate that rearrangements involving this region occurred in the mitochondrial genome. The STS4 fragment had a more complicated gene structure, including retrotransposon-like sequences and small segments of chloroplast genome.
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    An extended map of the sugar beet genome containing RFLP and RAPD loci (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 189-193 
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    ISSN: 1432-2242
    Keywords: Sugar beet ; Beta vulgaris ; RFLP ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An updated map of sugar beet (Beta vulgaris L. ssp. vulgaris var ‘altissima Doell’) is presented. In this genetic map we have combined 248 RFLP and 50 RAPD loci. Including the loci for rhizomania resistance Rr1, hypocotyl colour R and the locus controlling the monogerm character M, 301 loci have now been mapped to the nine linkage groups covering 815 cM. In addition, the karyotype of some of the Beta vulgaris chromosomes has been correlated with existing RFLP and RAPD linkage maps.
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    URL: http://dx.doi.org/10.1007/BF00222201
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    Mapping the Sw-5 locus for tomato spotted wilt virus resistance in tomatoes using RAPD and RFLP analyses (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 451-456 
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    ISSN: 1432-2242
    Keywords: Lycopersicon esculentum ; Lycopersicon peruvianum ; RAPD ; RFLP ; Tomato spotted wiltvirus (TSWV)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Sw-5 locus confers dominant resistance to tomato spotted wilt virus (TSWV). To map the location and facilitate the identification of markers linked to Sw-5 we developed a pair of near-isogenic lines (NILs) and an F2 Lycopersicon esculentum x L. pennellii population segregating for resistance to TSWV. DNA from the NILs was analyzed using 748 random 10-mer oligonucleotides to discern linked molecular markers using a random amplified polymorphic DNA (RAPD) approach. One random primer (GAGCACGGGA) was found to produce a RAPD band of about 2200 bp that demonstrates linkage to Sw-5. Data from co-segregation of resistance and restriction fragment length polymorphisms (RFLPs) in a F2 interspecific population position Sw-5 between the markers CT71 and CT220 near the telomere of the long arm of chromosome 9.
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    A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 835-840 
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    ISSN: 1432-2242
    Keywords: RFLP ; RAPD ; Linkage map ; Sugi (Cryptomeria japonica) ; Three-generation pedigree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A linkage map for sugi was constructed on the basis of restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and isozyme loci using a three-generation pedigree prepared for genetic analysis of heartwood color. A total of 128 RFLP (123 cDNA and 5 genomic probes), 33 RAPD, 2 isozyme, and 1 morphological (dwarf) loci segregated in 73 progeny. Of the 164 segregating loci, 145 loci were distributed in 20 linkage groups. Of these loci, 91 with confirmed map positions were assigned to 13 linkage groups, covering a total of 887.3 cM. A clustering of markers with distorted segregation was observed in 6 linkage groups. In the four clusters, distortions with a reduction in the number of homozygotes from one parent only were found.
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    Infraspecific differentiation of garlic (Allium sativum L.) by isozyme and RAPD markers (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 89-97 
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    ISSN: 1432-2242
    Keywords: Garlic ; Isozyme ; RAPD ; Crop evolution ; Domestication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Garlic (Allium sativum L.) is a sterile species of considerable variability with respect to morphological and physiological features. The crop presumably originated in West to Middle Asia from its progenitor A. longicuspis Regel and was transported from there to the Mediterranean and other areas of cultivation. In order to clarify older classification schemes, often based on small or biased collections, we used isozyme and RAPD markers to analyze and structure a collection of 300 accessions, many of which were gathered in Middle Asia close to the assumed center of origin. All of the accessions were first investigated with isozymes, and 48 were selected for a RAPD analysis. The resulting molecular markers were used to construct neighbor-joining dendrograms to group the accessions and to indicate the genetic distances between them. Based on the dendrograms and in conjunction with some morphological features, we propose an infraspecific classification of garlic with four major groups. In agreement with the results of other workers, A. longicuspis lies within the range of the species A. sativum. Numerous forms with varying degrees of domestication are part of our longicuspis group, from which presumably the more derived cultivar groups originated. The origin and spreading of the crop are discussed with respect to the geographical distribution and the genetic distances of the accessions.
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    Identification of chrysanthemum cultivars and stability of DNA fingerprint patterns (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 439-447 
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    ISSN: 1432-2242
    Keywords: Chrysanthemum ; RAPD ; DNA fingerprint ; RFLP ; Stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several techniques of DNA analysis were applied to identify chrysanthemum cultivars. Unrelated cultivars could be distinguished by using RAPDs (random amplified polymorphic DNAs), inter-SSR (simple sequence repeat) PCR (polymerase chain reaction), hybridization-based DNA fingerprinting, as well as RFLPs (restriction fragment length polymorphisms). Cultivars with different flower colours and belonging to one family, i.e. vegetatively derived from 1 cultivar, appeared to have the same DNA fragment patterns, whichever technique was applied. The absence of polymorphisms between different accessions of the same cultivar indicated a high stability of the observed patterns.
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    Identification of molecular markers associated with leptine production in a population of Solanum chacoense Bitter (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 39-46 
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    ISSN: 1432-2242
    Keywords: Key words Glycoalkaloids ; Potato ; Metabolic pathways ; RAPD ; Leptine ; Insect resistance ; Solanum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract   Solanum chacoense Bitter, a wild relative of the cultivated potato, produces several glycoalkaloids, including solanine, chaconine, and the leptines. The foliar-specific leptine glycoalkaloids are believed to confer resistance to the Colorado Potato Beetle (CPB). Using two bulked DNA samples composed of high- and low-percent leptine individuals from a segregating F1 population of S. chacoense, we have identified two molecular markers that are closely linked to high percent solanine+chaconine and, conversely, to nil/low percent leptine. One of these, a 1,500-bp RAPD product (UBC370-1500), had a recombination value of 3% in the F1 progeny, indicating tight linkage. UBC370-1500 mapped to the end of the short arm of potato chromosome 1, in the region of a previously mapped major QTL for solanidine, from a S. tuberosum (solanidine)×S. berthaultii (solasodine) cross. Taken together, these results suggest that either (1) a major locus determining solanidine accumulation in Solanum spp. is on chromosome 1 in the region defined by the RFLP markers TG24, CT197, and CT233, or (2) this region of chromosome 1 may harbor two or more important genes which determine accumulation of steroidal aglycones. These findings are important for the genetics of leptine (as well as other glycoalkaloid) accumulation and for the development of CPB-resistant potato varieties.
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    Identification of DNA markers linked to the male sex in dioecious hemp (Cannabis sativa L.) (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 86-92 
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    ISSN: 1432-2242
    Keywords: Key words Cannabis sativa ; Dioecy ; Sex ; RAPD ; SCAR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A 400-bp RAPD marker generated by a primer of random decamer sequence has been found associated with the male sex phenotype in 14 dioecious cultivars and accessions of hemp (Cannabis sativa L.). The primer OPA8 generates a set of bands, most of which polymorphic among all the individual plants tested, and 1 of which, named OPA8400, present in all male plants and absent in female plants. A screening of 167 plants belonging to different genotypes for the association of the OPA8400 marker with the sex phenotype revealed that only in 3 cases was the 400-bp band was present in plants phenotypically female; on the contrary, in male plants the band was never missing, while in monoecious plants it was never present. Despite this sex-specific association, the sequences corresponding to OPA8400 were present in both staminate and carpellate plants, as revealed by Southern blotting and hybridization with the cloned RAPD band. The RAPD marker was sequenced, and specific primers were constructed. These primers generated, on the same genotypes used for RAPD analysis, a SCAR marker 390 bp in length and male-specific. This SCAR is suitable for a precise, early and rapid identification of male plants during breeding programs of dioecious and monoecious hemp.
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    URL: http://dx.doi.org/10.1007/s001220051043
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    Morphological and RAPD markers show a highly skewed distribution in a pair of reciprocal crosses between hemisexual dogrose species, Rosa sect. Caninae (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 557-563 
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    ISSN: 1432-2242
    Keywords: Key words Rosa sect. Caninae ; Biometrics ; Heterogamy ; RAPD ; Segregation distortion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The dogroses, Rosa sect. Caninae, are polyploid and characterized by their unique meiosis with an unequal number of chromosomes in the male and female gametes. The pollen cells have 7 chromosomes and the egg cells 21, 28 or 35 depending on the ploidy level of the species. The resulting matroclinal inheritance was studied with both morphological and molecular markers in a pair of reciprocal crosses between R. dumalis and R. rubiginosa (2n=35). A canonical discriminant analysis based on seven morphological characters showed only a minor overlapping between the two progeny groups. In addition, the R. dumalis×R. rubiginosa offspring were more heterogeneous than the offspring from the reciprocal cross in each of the characters analysed. Eleven RAPD markers specific for the R. dumalis parent and 10 RAPD markers specific for the R. rubiginosa parent were scored in the offspring. Each of the offspring exhibited either all, or all-but-one, of the seed parent markers. The average number of pollen donor markers found in the offspring was 3.2 (R. dumalis×R. rubiginosa) and 2.7 (R. rubiginosa×R. dumalis). About half of the pollen donor markers were never transmitted to the progeny. This is, to our knowledge, the first time the highly skewed chromosome distribution in Rosa sect. Caninae has been demonstrated with statistically evaluated morphological data and with molecular markers.
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    The use of RAPD analysis to classify Triticum accessions (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 602-607 
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    ISSN: 1432-2242
    Keywords: Key words Triticum ; Germplasm ; RAPD ; Misclassification ; Duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Crop germplasm collections contain a considerable percentage of misclassified accessions which may affect the use of germplasm for agricultural crop improvement. The objective of this study was to determine if random amplified polymorphic DNA (RAPD) analysis could be used to reclassify misclassified Triticum accessions. Twelve accessions suspected to be misclassified, based on morphological characters, as either macha or vavilovii wheat were studied using RAPD and cytological analyses. In the RAPD analysis, a dendrogram, based on Jaccard genetic similarity coefficients, grouped 5 dicoccum-like, 1 timopheevii-like, and 6 monococcum-like accessions with Triticum dicoccum, T. timopheevii, and T. monococcum accessions, respectively. These results were confirmed by the cytological analysis. A RAPD marker specific to the D genome was also detected. This study suggests that RAPD analysis can be used to classify germplasm and to distinguish some species in Triticum.
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    URL: http://dx.doi.org/10.1007/s001220051110
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    RAPD markers on seed bulks efficiently assess the genetic diversity of a Brassica oleracea L. collection (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 1029-1035 
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    ISSN: 1432-2242
    Keywords: Key words Brassica oleracea L. ; RAPD ; Seed bulk ; Genetic resources ; Genetic variability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The concept of a core collection was elaborated to fit the necessity of optimizing the management, for both conservation and use, of genetic resources in sizeable collections. This approach requires an analysis of how the genetic variability is structured among the accessions. The large number of heterogeneous populations in our collection of Brassica oleracea makes genetic diversity studies based on plant-to-plant analysis impracticable. To overcome this limitation, the variability analysis by RAPD on seed bulks was investigated for its efficiency in assessing the structure of the genetic diversity of this collection. The optimal bulk size and the bulking or sampling variation were evaluated with bulks of different size and with replicated samples. A mixture of known genotypes was also used to characterise the band detection in bulks, and to compare the plant-to-plant and the bulk methods. Forty seeds were chosen to represent each population. In such a bulk, the detection of bands depended on the proportion of the genotype they were derived from in the mixture. Intense and frequent bands were detected in the bulk with a 15% detection limit. The observed bulking or sampling variation within populations was smaller than the variation between populations, leading to an efficient separation of populations with a clustering of all samples of the same population. The distances calculated from bulk data were highly correlated with the distances based on the plant-to-plant analysis. We demonstrated that RAPD on seed bulks can be used to describe the genetic diversity between populations.
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    RAPD variation within and among natural populations of outcrossing willow-leaved foxglove (Digitalis obscura L.) (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 985-994 
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    ISSN: 1432-2242
    Keywords: Key words Digitalis obscura ; AMOVA ; HOMOVA ; Population genetics ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Random amplified polymorphic DNA (RAPD) markers were used to assess levels and patterns of genetic diversity in Digitalis obscura L. (Scrophulariaceae), an outcrossing cardenolide-producing medicinal plant species. A total of 50 plants from six natural populations on the Iberian Peninsula were analysed by six arbitrarily chosen decamer primers resulting in 96 highly reproducible RAPD bands. To avoid bias in parameter estimation, analyses of population genetic structure were restricted to bands (35 of 96) whose observed frequencies were less than 1–3/n in each population. The analysis of molecular variance (AMOVA) with distances among individuals corrected for the dominant nature of RAPDs (genotypic analysis) showed that most of the variation (84.8%) occurred among individuals within populations, which is expected for an outcrossing organism. Of the remaining variance, 9.7% was attributed to differences between regions, and 5.5% for differences among populations within regions. Estimates of the Wright, Weir and Cockerham and Lynch and Milligan FST from null-allele frequencies corroborated AMOVA partitioning and provided significant evidence for population differentiation in D. obscura. A non-parametric test for the homogeneity of molecular variance (HOMOVA) also showed significant differences in the amount of genetic variability present in the six populations. UPGMA cluster analyses, based on Apostol genetic distance, revealed grouping of some geographically proximate populations. Nevertheless, a Mantel test did not give a significant correlation between geographic and genetic distances. This is the first report of the partitioning of genetic variability within and between populations of D. obscura and provides important baseline data for optimising sampling strategies and for conserving the genetic resources of this medicinal species.
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    URL: http://dx.doi.org/10.1007/s001220051159
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    Development and utility of cleaved amplified polymorphic sequences (CAPS) and restriction fragment length polymorphisms (RFLPs) linked to the Fom-2 fusarium wilt resistance gene in melon (Cucumis melo L.) (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 453-463 
    Details
    ISSN: 1432-2242
    Keywords: Key words Cucumis melo ; Molecular markers ; RAPD ; CAPS ; RFLP ; Fusarium oxysporum ; Fusarium resistance ; Marker-assisted selection (MAS)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Fusarium wilt, caused by Fusarium oxysporum Schlecht f. sp. melonis Snyder & Hans, is a worldwide soil-borne disease of melon (Cucumis melo L.). Resistance to races 0 and 1 of Fusarium wilt is conditioned by the dominant gene Fom-2. To facilitate marker-assisted backcrossing with selection for Fusarium wilt resistance, we developed cleaved amplified polymorphic sequences (CAPS) and restriction fragment length polymorphisms (RFLP) markers by converting RAPD markers E07 (a 1.25-kb band) and G17 (a 1.05-kb band), respectively. The RAPD-PCR polymorphic fragments from the susceptible line ’Vedrantais’ were cloned and sequenced in order to construct primers that would amplify only the target fragment. The derived primers, E07SCAR-1/E07SCAR-2 from E07 and G17SCAR-1/G17SCAR-2 from G17, yielded a single 1.25-kb fragment (designated SCE07) and a 1.05-kb fragment (designated SCG17) (the same as RAPD markers E07 and G17), respectively, from both resistant and susceptible melon lines, thus demonstrating locus-specific associated primers. Potential CAPS markers were first revealed by comparing sequence data between fragments amplified from resistant (PI 161375) and susceptible (’Vedrantais’) lines and were then confirmed by electrophoresis of restriction endonuclease digestion products. Twelve restriction endonucleases were evaluated for their potential use as CAPS markers within the SCE07 fragment. Three (BclI, MspI, and BssSI) yielded ideal CAPS markers and were subsequently subjected to extensive testing using an additional 88 diverse melon cultigens, 93 and 119 F2 individuals from crosses of ’Vedrantais’ x PI 161375 and ’Ananas Yokneam’×MR-1 respectively, and 17 families from a backcross BC1S1 population derived from the breeding line ’MD8654’ as a resistance source. BclI- and MspI-CAPS are susceptible-linked markers, whereas the BssSI-CAPS is a resistant-linked marker. The CAPS markers that resulted from double digestion by BclI and BssSI are co-dominant. Results from BclI- and MspI-CAPS showed over 90% accuracy in the melon cultigens, and nearly 100% accuracy in the F2 individuals and BC1S1 families tested. This is the first report of PCR-based CAPS markers linked to resistance/susceptibility for Fusarium wilt in melon. The RFLP markers resulting from probing with a clone-derived 1.05-kb SCG17 PCR fragment showed 85% correct matches to the disease phenotype. Both the CAPS and RFLP markers were co-dominant, easier to score, and more accurate and consistent in predicting the melon phenotype than the RAPD markers from which they were derived.
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    URL: http://dx.doi.org/10.1007/s001220051257
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    Rapid preparation of PCR-amplifiable fungal DNA by benzyl bromide extraction (1995)
    Springer
    Mycoscience 36 (1995), S. 465-467 
    Details
    ISSN: 1618-2545
    Keywords: benzyl bromide ; DNA preparation ; fungal DNA ; PCR ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract For isolation of fungal DNA for PCR amplification, we compared three DNA isolation methods: enzymatic cleavage and the use of benzyl chloride or benzyl bromide. Since benzyl bromide is more reactive, its use enabled us to readily isolate the total nucleic acids as a DNA template source from various fungi, including dematiaceous hyphomycetes, for RAPD analysis.
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    URL: http://dx.doi.org/10.1007/BF02268634
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    Genetic relationships between peanut and wild species ofArachis sect.Arachis (Fabaceae): Evidence from RAPDs (1995)
    Springer
    Plant systematics and evolution 198 (1995), S. 167-178 
    Details
    ISSN: 1615-6110
    Keywords: Fabaceae ; Arachis ; Arachis hypogaea ; RAPD ; systematics ; evolution ; germplasm resources
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Twenty-six accessions of wildArachis species and domesticated peanuts,A. hypogaea, introduced from South America were analyzed for random amplified polymorphic DNA (RAPD). The objective of the study was to investigate inter- and intraspecific variation and affinities among species of sect.Arachis which have been proposed as possible progenitors for the domesticated peanut. Ten primers resolved 132 DNA bands which were useful for separating species and accessions. The most variation was observed among accessions ofA. cardenasii andA. glandulifera whereas the least amount of variation was observed inA. hypogaea andA. monticola. The two tetraploid species could not be separated by using RAPDs.Arachis duranensis was most closely related to the domesticated peanut and is believed to be the donor of the A genome. The data indicated thatA. batizocoi, a species previously hypothesized to contribute the B genome toA. hypogaea, was not involved in its evolution. The investigation showed that RAPDs can be used to analyze both inter- and intraspecific variation in peanut species. Southern hybridization of RAPD probes to blots containing RAPD of theArachis species provided information on genomic relationships and revealed the repetitive nature of the amplified DNA.
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    URL: http://dx.doi.org/10.1007/BF00984735
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    RAPD variations among pure and hybrid populations ofPicea mariana, P. rubens, andP. glauca (Pinaceae), and cytogenetic stability ofPicea hybrids: Identification of species-specific RAPD markers (1999)
    Springer
    Plant systematics and evolution 215 (1999), S. 229-239 
    Details
    ISSN: 1615-6110
    Keywords: Pinaceae ; Picea mariana ; P. rubens ; P. glauca ; RAPD ; genetic relationship ; interspecific hybrids ; mitotic stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Random amplified polymorphic DNA (RAPD) analysis was used to determine genetic relationships amongP. mariana (black spruce),P. rubens (red spruce), andP. glauca (white spruce) and to assess the degree of polymorphism within populations from different provenances and among spruce hybrids. Eleven arbitrary decamer primers were used to amplify genomic DNAs extracted from embryogenic cultures and seedlings. Species-specific RAPD markers were identified.Picea mariana andP. rubens showed similar RAPD profiles confirming their close genetic relationship. Species-specific RAPD markers were identified and were useful in distinguishing white spruce from black and red spruces. RAPD differentiation between populations within each species was small. The level of polymorphism was much higher in spruce hybrid populations than in the pure species. Cytological analysis ofP. mariana ×P. rubens hybrids showed normal mitotic behaviour at prophase, metaphase, anaphase, and telophase. All the hybrids analyzed from different cross combinations were euploids.
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    URL: http://dx.doi.org/10.1007/BF00984657
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    Identification of hybrids betweenQuercus petraea andQ. robur (Fagaceae): Results obtained with RAPD markers confirm allozyme studies based on theGot-2 locus (1999)
    Springer
    Plant systematics and evolution 217 (1999), S. 137-146 
    Details
    ISSN: 1615-6110
    Keywords: Fagaceae ; Quercus ; Hybridization ; RAPD ; allozymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPDs were employed as genetic markers to detect interspecific hybridization between the closely related oak speciesQuercus robur andQ. petraea. Fourteen primers were used in order to check the genetic status (“pure” or hybrid) of individuals classified morphologically. Among the 147 PCR fragments obtained 11 appear to be species-specific. In the phenotypically intermediate individuals different combinations of these species-specific bands were obtained. The patterns in these putative hybrids were not additive, which may be either the result of repeated backcrossing and introgression between the two species or of heterozygosity within the parental species. The results of the RAPD study are consistent with morphological analyses and allozyme data obtained for theGot-2 locus. Thus the RAPD markers used in this study may provide a powerful genetic tool for the identification of hybrids and the discrimination between the two “pure” species.
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    URL: http://dx.doi.org/10.1007/BF00984926
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    Clonal structure of Rubus chamaemorus populations: comparison of different molecular methods (1999)
    Springer
    Plant ecology 143 (1999), S. 123-128 
    Details
    ISSN: 1573-5052
    Keywords: Clonal structure ; Cloudberry ; Genetic variation ; DNA fingerprinting ; RAPD ; Rubus chamaemorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The clonal structure of Rubus chamaemorus populations was investigated using DNA fingerprinting. The PCR-based methods included the use of 10-base RAPD primers and 16-base simple sequence repeat primers. In the hybridization method variation was studied using hypervariable multilocus probes, one derived from the M13 bacteriophage and the other a synthetic (AC)/(TG) polynucleotide. Although R. chamaemorus expresses clear variation in morphology, the level of genetic differentiation appears to be fairly low. The observed numbers of clones in the three populations examined in Finland varied from 2 to 4. The total number of genotypes across populations was 5, of which one was unique. The results obtained using the two fingerprinting methods were comparable but lead to a slightly different grouping of clones.
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    URL: http://dx.doi.org/10.1023/A:1009898209220
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    Comparison of PCR-based molecular marker analyses of Musa breeding populations (1999)
    Springer
    Molecular breeding 5 (1999), S. 233-244 
    Details
    ISSN: 1572-9788
    Keywords: Musa ; plantain ; RAPD ; VNTR ; AFLP ; breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Progress in the breeding of plantain and banana has been restricted by the complex genetic structure and behaviour of cultivated polyploid Musa. Genetic improvement has been hindered due to the large amount of space required for growth and maintenance of plant populations, in addition to the long growth cycle and the low levels of fertility and seed viability characteristic of cultivated genotypes. Molecular marker assisted breeding has the potential to dramatically enhance the pace and efficiency of genetic improvement in Musa. This study was conducted to compare different PCR-based marker systems (RAPD, VNTR and AFLP) for the analysis of breeding populations generated from two diverse Musa breeding schemes. All three assays detected a high level of polymorphism between parental genotypes and within progeny populations. As expected, AFLP assays had by far the highest multiplex ratio while VNTR analysis detected the highest levels of polymorphism. AFLP analysis of a full-sib tetraploid hybrid population confirmed previous reports based on VNTR analysis, of a high frequency of recombination during 2n (3x) gamete formation by a triploid plantain landrace. In addition, both VNTR and RAPD analyses of a full-sib triploid hybrid population suggested a high frequency of homoeologous recombination during n (2x) gamete formation by tetraploid hybrids. In general, there was a poor correlation between estimates of genetic similarity based on different types of marker. The implications of these findings for the molecular breeding of Musa crops are discussed.
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    URL: http://dx.doi.org/10.1023/A:1009649521009
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    Evaluation of AFLP for genetic mapping in Pinus radiata D. Don (1999)
    Springer
    Molecular breeding 5 (1999), S. 275-281 
    Details
    ISSN: 1572-9788
    Keywords: AFLP ; DNA markers ; genetic mapping ; marker-aided selection ; Pinus radiata ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Efficient construction of reasonable density genetic linkage maps is an essential component of QTL detection programmes. The AFLP technique has been used to produce genetic linkage maps in a range of species. We have developed protocols to generate reproducible AFLP profiles in Pinus radiata and have evaluated the inheritance and informativeness of AFLP markers in this important timber species. The large genome size of P. radiata necessitated increased levels of selection at both the pre-amplification and selective amplification steps of the AFLP protocol to generate reproducible AFLP profiles. Once optimised ca. 41.3 scorable AFLP bands were resolvable through denaturing gels, of which 48.4% were polymorphic in a screen of eight unrelated trees. This level of polymorphism is ca. three times higher than with RAPD markers. The total number of bands and the number of polymorphismic bands per PCR were ca. halved when AFLPs were electrophoresed on non-denaturing gels and stained with ethidium bromide. Using the protocols developed, AFLP is an efficient method for generating the DNA markers required for genetic linkage map construction in P. radiata.
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    URL: http://dx.doi.org/10.1023/A:1009612709760
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    Detection of genetic relationships among fourArtemia species using randomly amplified polymorphic DNA (RAPD) (1999)
    Springer
    International journal of salt lake research 8 (1999), S. 139-147 
    Details
    ISSN: 1573-8590
    Keywords: Artemia ; genetic polymorphism ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geography
    Notes: Abstract We have applied the technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among four species of brine shrimp:Artemia franciscana, A. urmiana, A. sinica, andA. parthenogenetica. Seventy ten-base synthetic oligonucleotides were used to amplify a total of 458 distinct fragments. DNA polymorphisms were found in all the species examined; the highest percentage of polymorphic bands was found inA. parthenogenetica, with 28.8 per cent. Each species was scored for the presence or absence of every amplification product and the data entered into a binary data matrix. Cluster analysis was then performed to create a dendrogram using UPGMA by the NTSYS program. There are significant differences between bisexual species and parthenogenetic populations.A. parthenogenetica provided 94 specific molecular markers, while bisexual species gave 27 specific molecular markers.A. sinica is a species distinct from the other Old World bisexual species.
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    URL: http://dx.doi.org/10.1007/BF02442127
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    Detection of genetic relationships among four Artemia species using randomly amplified polymorphic DNA (RAPD) (1999)
    Springer
    International journal of salt lake research 8 (1999), S. 139-147 
    Details
    ISSN: 1573-8590
    Keywords: Artemia ; genetic polymorphism ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geography
    Notes: Abstract We have applied the technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among four species of brine shrimp: Artemia franciscana, A. urmiana, A. sinica, and A. parthenogenetica. Seventy ten-base synthetic oligonucleotides were used to amplify a total of 458 distinct fragments. DNA polymorphisms were found in all the species examined; the highest percentage of polymorphic bands was found in A. parthenogenetica, with 28.8 per cent. Each species was scored for the presence or absence of every amplification product and the data entered into a binary data matrix. Cluster analysis was then performed to create a dendrogram using UPGMA by the NTSYS program. There are significant differences between bisexual species and parthenogenetic populations. A. parthenogenetica provided 94 specific molecular markers, while bisexual species gave 27 specific molecular markers. A. sinica is a species distinct from the other Old World bisexual species.
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    URL: http://dx.doi.org/10.1023/A:1009039815660
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    Gene and Genotypic Diversity of Phytophthora cinnamomi in South Africa and Australia Revealed by DNA Polymorphisms (1999)
    Springer
    European journal of plant pathology 105 (1999), S. 667-680 
    Details
    ISSN: 1573-8469
    Keywords: asexual reproduction ; mating types ; oomycetes ; origin ; RAPD ; RFLP ; population genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Phytophthora cinnamomi isolates from South Africa and Australia were compared to assess genetic differentiation between the two populations. These two populations were analysed for levels of phenotypic diversity using random amplified polymorphic DNAs (RAPDs) and gene and genotypic diversity using restriction fragment length polymorphisms (RFLPs). Sixteen RAPD markers from four decanucleotide Operon primers and 34 RFLP alleles from 15 putative loci were used. A few isolates from Papua New Guinea known to posses alleles different from Australian isolates were also included for comparative purposes. South African and Australian P. cinnamomi populations were almost identical with an extremely low level of genetic distance between them (Dm=0.003). Common features for the two populations include shared alleles, low levels of phenotypic/genotypic diversity, high clonality, and low observed and expected levels of heterozygosity. Furthermore, relatively high levels of genetic differentiation between mating type populations (Dm South Africa=0.020 and Dm Australia=0.025 respectively), negative fixation indices, and significant deviations from Hardy–Weinberg equilibrium, all provided evidence for the lack of frequent sexual reproduction in both populations. The data strongly suggest that both the South African and Australian P. cinnamomi populations are introduced.
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    URL: http://dx.doi.org/10.1023/A:1008755532135
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    Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation (1999)
    Springer
    Plant systematics and evolution 217 (1999), S. 313-332 
    Details
    ISSN: 1615-6110
    Keywords: Cucumis melo ; melon ; intra-specific classification ; RAPD ; Inter-SSR ; DNA fingerprinting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cucumis melo L. (melon) genotypes differ widely in morphological and biochemical traits. Intraspecific classification of such variability has been difficult, and most taxonomists still rely on the work of Naudin (1859). A collection of 54 accessions representing diverse genotypes from 23 countries was surveyed. Morphological traits related to the vegetative and flowering stages and mature fruit morphology and quality parameters, e.g., taste, aroma, sugar composition and pH, were scored. These were used to construct a “botanical-morphological” dendrogram that generally reflected the classification ofCucumis melo into several horticultural varieties. DNA polymorphism among the accessions was assessed using the Inter-SSR-PCR and RAPD techniques that detected abundant DNA polymorphism among melon genotypes. Cluster analysis indicated that the largest divergence was between North American and Europeancantalupensis andinodorus cultivars as one group, and the more “exotic” varieties:conomon, chito, dudaim, agrestis andmomordica, as a second group. The molecular phylogeny agreed, broadly, with the classification of melon into two subspecies, and did not contradict the division into “horticultural varieties”. It was apparent, however, that the infra-specific division is rather loose, molecular variation being distributed continuously between and within cultivar groups. We suggest that despite the morphological diversity, separation between varietal-groups may be based on a too small number of genes to enable unambiguous infra-specific classification based on DNA diversity.
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    URL: http://dx.doi.org/10.1007/BF00984373
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    Detection of molecular markers associated with linolenic and erucic acid levels in spring rapeseed (Brassica napur L.) (1999)
    Springer
    Euphytica 105 (1999), S. 173-181 
    Details
    ISSN: 1573-5060
    Keywords: Brassica napur ; doubled haploids ; RAPD ; linolenic acid ; erucic acid ; marker assisted selection ; rapeseed breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Undesirable characteristic of rapeseed oil is a relatively high level of linolenic acid (18:3), which is easily oxidized leading to rancidity and a shortened shelf life of the oil. Previous attempts to reduce linolenic acid levels in rapeseed oil through breeding have been impaired by complex genetics and strong environmental sensitivity of this trait. Therefore, our objective was to develop molecular markers for low linolenic acid that could facilitate the breeding of low linolenic rapeseed. Bulked segregant analysis was employed to identify two RAPD markers associated with 18:3 in a doubled haploid population segregating for linolenic and erucic acid levels. Based on analysis of individual DH lines, the markers RM350 and RM574, representing two independent loci, accounted for a total of 39% of the genetic variability in this population. This marker RM350 alone accounted for 25% genetic variation for this trait with no evidence of recombination. Significant interlocus interaction found between the markers RM350 and RM574 suggested that epistasis was involved in the genetic control of 18:3 level in this population. Another marker designated as RM322, which was independent of the other two, was found significantly associated with the erucic acid level and oil content. RAPD markers identified in this study should be a useful tool for the early detection of low linolenic, or low or high erucic acid genotypes in rapeseed breeding programs based on doubled haploids.
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    URL: http://dx.doi.org/10.1023/A:1003494217074
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    Identification of RAPD markers linked to fusarium crown and root rot resistance (Frl) in tomato (1999)
    Springer
    Euphytica 105 (1999), S. 205-210 
    Details
    ISSN: 1573-5060
    Keywords: crown rot ; fusarium crown and root rot ; genetic linkage ; Lycopersicon peruvianum ; molecular markers ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In tomato ( Lycopersicon esculentum Mill.) a single dominant gene ( Frl) on chromosome 9 confers resistance to fusarium crown and root rot (crown rot) incited by Fusarium oxysporum f. sp. radicis-lycopersici. To identify randomly amplified polymorphic DNA (RAPD) markers linked to Frl, crown rot susceptible and resistant tomato lines were screened for polymorphisms using 1000 random 10-mer primers and three reliable RAPD markers were found linked to Frl (UBC #'s 116, 194, and 655). A codominant polymorphic PCR marker of TG101, a restriction fragment length polymorphic (RFLP) marker linked to Frl, was developed to facilitate the linkage studies. Using TG101 and the four RAPD markers, on a Frl segregating backcross population of 950 plants indicated that all belong to the same linkage group. The polymorphic allele order was found to be TG101 – 655 – 116 – 194 – Frl. UBC 194 was found to be 5.1 cM from Frl in this population. Furthermore, it was the only marker found in the resistant genotypes ‘Mocis’ and Fla 7226, whereas resistant genotypes ‘Momor’, Ohio 89-1, and Fla 7464 all had UBC 194 and UBC #'s 116, 194, and 655.
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    Identification of a RAPD marker linked to a brown planthopper resistance gene in rice (1999)
    Springer
    Euphytica 107 (1999), S. 23-28 
    Details
    ISSN: 1573-5060
    Keywords: Bph-1 ; linkage analysis ; mapping ; RAPD ; RFLP ; rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract We report the tagging of a brown planthopper (BPH) resistance gene (Bph–1) in rice using RAPD and RFLP markers. The Korean rice variety ‘Gayabyeo’ has dominant duplicate genes including Bph–1 conferring resistance to biotype 1 of BPH. Bulked segregant RAPD analysis was employed for rapid identification of DNA markers linked to resistance genes. For tagging these two genes, an F2F3 population from a ‘Gayabyeo’ × ‘Nagdongbyeo’ cross was developed and evaluated for BPH resistance. Three bulked DNAs from two groups of homozygous BPH resistant (each for Bph–1 and the other unknown gene) and homozygous susceptible F2 plants were analyzed by RAPD using 140 random oligomers. One primer, OPD–7 yielded a 700-bp fragment that was present in Gayabyeo and resistant F2 plants (homozygous for Bph-1 locus) but absent in Nagdongbyeo and susceptible F2 plants. Cosegregation of this marker with Bph-1 was verified using an F2 population segregating for Bph-1. Chromosomal regions surrounding the Bph-1 were examined with additional RFLP and microsatellite markers on chromosome 12 to define the location of the RAPD marker and Bph-1. Use of this RAPD marker could facilitate early selection of resistant lines for BPH.
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    URL: http://dx.doi.org/10.1023/A:1003506830735
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    Protoplast regeneration and fusion in Cucumis: melon × cucumber (1995)
    Springer
    Plant cell, tissue and organ culture 43 (1995), S. 259-265 
    Details
    ISSN: 1573-5044
    Keywords: Asymmetric hybridization ; Cucumis melo ; C. sativus ; electrofusion ; Ploidy level ; RAPD ; somatic incompatibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The aim of this investigation was to develop a protocol to be used in asymmetric protoplast fusions with breeding material of melon and cucumber. Efficient methods for plant regeneration from unfused protoplasts of commercial melon lines were established and are reported. Ploidy levels of explant material and plants, regenerated from protoplasts were analyzed. Electrofusion was carried out between melon protoplasts and irradiated and non-irradiated donor protoplasts of cucumber. Although initial plating efficiencies of heterokaryons were high, development stopped after a few divisions. In control experiments, shoots were regenerated at high frequencies. In only two fusion experiments, development continued to the callus stage, but further development was not observed. When analyzed with PCR using arbitrary primers, the majority of these calli DNA were identical to the melon DNA. However, a few of the examined calli, although being mainly homologous to melon, were observed to have new bands corresponding to bands specific for cucumber. Due to sexual incompatibility, successful hybridization between cucumber and melon was never obtained by sexual crosses. We suggest that the failure to regenerate plants in our fused material could be explained partially by an analogous somatic incompatibility reaction.
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    URL: http://dx.doi.org/10.1007/BF00039953
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    Analyses of genetic diversity in Cuban rice varieties using isozyme, RAPD and AFLP markers (1999)
    Springer
    Euphytica 109 (1999), S. 107-115 
    Details
    ISSN: 1573-5060
    Keywords: AFLP ; DNA fingerprinting ; isozymes ; RAPD ; rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A survey of the genetic diversity among the major cuban rice cultivars was conducted using isozyme, RAPD and AFLP markers. Polymorphisms were detected for esterases, peroxidases, alcohol dehydrogenases and polyphenoloxidases systems; 21 RAPD primers and four AFLP primer combinations. Heterozygosity arithmetic mean value (Hav(p)), the effective multiplex ratio (EMR) and the marker index (MI), were calculated for isozyme, RAPD and AFLP markers. The mean value of genetic similarity among the different varieties was 0.92 for isozyme, 0.73 for RAPD and 0.58 for AFLP analyses. Thus, AFLP were able to detect polymorphisms with higher efficiency than RAPD (+15%) and isozyme (+34%). Data from the isozyme, RAPD and AFLP analyses were used to compute matrices of genetic similarities. The efficiency of the UPGMA for the estimation of genetic relatedness among varieties was supported by cophenetic correlation coefficients. The resulting values indicated that the distortion level for the estimated similarities was minimal. The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for isozyme and RAPD markers (r = 0.89), as well as for AFLP and RAPD markers (r = 0.82) were properly related. However, AFLP and isozyme data showed only moderate correlation (r = 0.63). Although the genetic variability found among the different cultivars was low, both RAPD and AFLP markers proved to be efficient tools in assessing the genetic diversity of rice genotypes.
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    URL: http://dx.doi.org/10.1023/A:1003672729948
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    Genetic diversity of plums characterized by random amplified polymorphic DNA (RAPD) analysis (1999)
    Springer
    Euphytica 109 (1999), S. 143-147 
    Details
    ISSN: 1573-5060
    Keywords: classification ; DNA ; plum varieties ; Prunus ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract We investigated the genetic diversity of 42 plum varieties by RAPD analysis. Twenty primers discriminated all plum varieties excepting two synonymous pairs: 'Botankyou and ‘Kelsey’, and ‘Chairn’ and ‘Tragedy’. Two North American plums, ‘Beach Plum’ and ‘Glow’, were genetically distinct from the other plums by cluster analysis. Overlaps observed between the ‘European plum group’ and the ‘Japanese plum group’, were perhaps due to intercrossing. We could also discriminate ‘Sordum’ from 'Late Sordum and ‘Bansei Sordum’, although ‘Late Sordum’ and ‘Bansei Sordum’ are thought to be derived from bud mutants of ‘Sordum’.
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    URL: http://dx.doi.org/10.1023/A:1003728201100
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    The genetic structure and conservation of aus, aman and boro rices from Bangladesh (1999)
    Springer
    Genetic resources and crop evolution 46 (1999), S. 587-598 
    Details
    ISSN: 1573-5109
    Keywords: diversity ; genetic resources ; GIS ; Oryza sativa ; RAPD ; rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A diverse set of 115 rice varieties from Bangladesh was surveyed using 35 polymorphic RAPD (randomly amplified polymorphic DNA) markers and the genetic structure of this germplasm, encompassing the principal rice ecotypes of Bangladesh (aus, aman and boro), was determined using multivariate analysis. The level of genetic diversity was evaluated and compared with the levels of diversity found within other rice growing areas of the world. Geographical information systems analysis using Atlas-GIS was employed to analyse and present the geographic distribution of genetic diversity across Bangladesh, and cluster analysis was used to test the efficiency of selection of material for a core collection.
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    URL: http://dx.doi.org/10.1023/A:1008749532171
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    Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers (1999)
    Springer
    Genetic resources and crop evolution 46 (1999), S. 547-555 
    Details
    ISSN: 1573-5109
    Keywords: core collection ; germplasm ; molecular marker ; potato ; RAPD ; Solanum phureja
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The potato crop originated in the Andean highlands where numerous farmer's varieties and non-cultivated wild species exist. An Andean potato collection is held in trust at the International Potato Center (CIP) to preserve the biodiversity of this crop and ensure the supply of germplasm for potato improvement worldwide. A core collection representing the biodiversity of the Andean potato germplasm is under construction using morphological, molecular, and geographic data. One of the eight cultivated potato species, Solanum phureja, has been genotyped using the RAPD technique. A protocol suitable for large germplasm collection genotyping has been developed to process numerous samples at reasonable costs. From 106 RAPD primers evaluated, we have selected 12 primers yielding 102 polymorphic markers, which unambiguously discriminated all 128 accessions but 2 that are possible duplicates. The S. phureja germplasm collected throughout the Andean countries appears to have a homogeneous genetic constitution. There was no clear geographic pattern as indicated by cluster analysis of the RAPD data. A sub-group of 20 accessions has been identified on the basis of the marker data and selected to maximize molecular (RAPD) variance and polymorphism. The probability of capturing equal amounts of marker polymorphism in this sub-group of 20 accessions by random sampling is less than 40%. This set accessions represents our first group of accessions that may constitute a core of the S. phureja collection. This tentative core will be challenged for diversity content by alternate markers and agronomic traits. Hence, the methodology for sampling less than 10% of the base collection, proposed for core collections by Brown (1989), can be based on molecular marker data provided cost-efficient fingerprints are developed.
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    URL: http://dx.doi.org/10.1023/A:1008724007888
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    RAPD divergence caused by microsite edaphic selection in wild barley (1999)
    Springer
    Genetica 105 (1999), S. 177-192 
    Details
    ISSN: 1573-6857
    Keywords: barley ; Hordeum spontaneum ; microsite ecology ; molecular edaphicdifferentiation ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Random amplified polymorphic DNA polymerase chain reaction (RAPDPCR) was used to assess genetic diversity in four subpopulations (86 individuals) of wild barley, Hordeum spontaneum, sampled from Tabigha microsite near the Sea of Galilee, Israel. The microsite consists of two 100 m transects that are topographically separated by 100 m, each equally subdivided into 50 m of basalt and terra rossa soil types. Despite the same macroclimate characterizing the area around the Sea of Galilee, the microsite offers two edaphically different microhabitats, with basalt being a more ecologically heterogeneous and broader-niche than the relatively drier but more homogeneous and narrow-niche terra rossa. Analysis of 118 putative loci revealed significant (P〈0.05) genetic differentiation in polymorphism (P0.05) between the two soils across the transects with P being higher in the more heterogeneous basalt (mean P0.05 = 0.902), than in terra rossa (mean P0.05 = 0.820). Gene diversity (He) was higher in basalt (mean He=0.371), than in terra rossa (mean He=0.259). Furthermore, unique alleles were confined to one soil type, either in one or both transects. Rare alleles were observed more frequently in terra rossa than basalt, and in transect II only. Gametic phase disequilibria showed a larger multilocus association of alleles in basalt than terra rossa, and in transect I than II. Spearman rank correlation (rs) revealed a strong association between specific loci and soil types, and transects. Also, analysis of multilocus organization revealed soil-specific multilocus-genotypes. Therefore, our results suggest an edaphically differentiated genetic structure, which corroborates the niche width-variation hypothesis, and can be explained, in part, by natural selection. This pattern of RAPD diversity is in agreement with allozyme and hordein protein diversities in the same subpopulations studied previously.
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    URL: http://dx.doi.org/10.1023/A:1003781711908
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    Application of DNA amplification fingerprinting (DAF) to mixed culture bioreactors (1995)
    Springer
    Journal of industrial microbiology and biotechnology 14 (1995), S. 10-16 
    Details
    ISSN: 1476-5535
    Keywords: DNA fingerprinting ; RAPD ; Community structure ; Polymerase chain reaction (PCR)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary The use of DNA amplification fingerprinting (DAF) as a tool for monitoring mixed microbial populations in bioreactors was evaluated. Short (8-mer or 10-mer) oligonucleotides were used to prime DNA extracts from various biological reactors during polymerase chain reaction (PCR) amplification. The reactors examined in this study included two sets of anaerobic stirred tank continuous flow bioreactors. One set of anaerobic reactors was operated under methanogenic conditions and one set was operated under sulfate-reducing conditions. The anaerobic reactor communities in the methanol-fed reactors showed extensive DAF homology. DAF was also applied to a fixed-film azo dye degrading reactor to examine the degree of uniformity of colonization of the substratum in representative regions of the reactor. This method is a quick and relatively inexpensive means of monitoring microbial community structure during biological processes. Since no cultivation of the sample is involved, the genetic profile of the community is not biased by outgrowth conditions. DAF profiles may be useful for comparisons of population changes over time or of bench-scale vs pilot-scale reactors but not adequate for assessing community diversity.
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    URL: http://dx.doi.org/10.1007/BF01570059
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    Variation of RAPD-fingerprint patterns using different DNA-extraction methods with Gram-positive bacteria (1995)
    Springer
    World journal of microbiology and biotechnology 11 (1995), S. 238-239 
    Details
    ISSN: 1573-0972
    Keywords: DNA extraction ; micro technique ; RAPD ; Staphylococcus ; Streptococcus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The effect of the DNA-extraction method used on fingerprint patterns of RAPD was studied usingStaphylococcus epidermidis andStreptococcus faecalis. The three methods tested (Chelex, microwave and phenol/chloroform) led to significantly different RAPD patterns. The microwave technique generated reproducible patterns and seems the most suitable for RAPD analysis of Gram-positive bacteria.
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    URL: http://dx.doi.org/10.1007/BF00704659
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    Allocation of random amplified polymorphic DNA markers and enzyme activities toAspergillus nidulans andAspergillus tetrazonus chromosomes (1995)
    Springer
    Antonie van Leeuwenhoek 68 (1995), S. 245-251 
    Details
    ISSN: 1572-9699
    Keywords: Aspergillus nidulans ; Aspergillus tetrazonus ; gene assignment ; isoenzyme analysis ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Chromosome-substituted haploid segregants of anA. nidulans × A. tetrazonus somatic hybrid were used to allocate several random amplified polymorphic DNA and isoenzyme markers to parental chromosomes. Twenty-six amplified DNA fragments, and nine isoenzyme activities, including lactate dehydrogenase, superoxide dismutase, and arylesterase isoenzymes were assigned to chromosomes. Chromosome-specific markers were found for eachA. nidulans andA. tetrazonus chromosome. These markers could be used to saturate the genetic map ofA. nidulans. The formation of two secondary metabolites was also assigned to chromosomes III and VIII. Attempts were made to allocate extracellular enzyme activities to parental chromosomes, mostly without success, possibly because multiple enzyme forms located on different chromosomes could be responsible for the production of an enzyme activity.
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    URL: http://dx.doi.org/10.1007/BF00871822
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    Determination of genetic variability by RAPD markers in cauliflower, cabbage and kale local cultivars from France (1995)
    Springer
    Genetic resources and crop evolution 42 (1995), S. 281-289 
    Details
    ISSN: 1573-5109
    Keywords: Collection ; diversity ; local cultivars ; RAPD ; genetic structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract RAPD markers were used to analyse the genetic variability among a cole crop cultivar collection from France and to identify possible duplicate accessions for facilitating the germplasm multiplication. We surveyed 24 cauliflower, 24 cabbage and 48 kale populations using 62, 100 and 89 RAPD markers respectively on 40 seed bulk samples per accession. Genetic distances were calculated on the basis of these markers. Using the phylogenetic package PAUP we compared the genetic clusters obtained for the RAPD markers with the groups based on morphologic and agronomic data. For cauliflowers and cabbages a drastic selection by growers led to an extensive differentiation of morphologic and precocity traits related to geographic origin, which matches the grouping based on RAPD markers. Furthermore, RAPDs detected in some cases misclassification of accessions in the collection. Kales formed an homogeneous group probably due to extensive genetic exchanges leading to a continuous diversity. For the other crops, different horticultural types were separated in several subgroups by the RAPD markers suggesting different genetic origins. RAPD markers provide a rapid and informative approach to analyze the genetic variability in a collection. It can be applied to autogamous (spring cauliflower) or allogamous (winter cauliflower) crops, even in cases where the intra-population diversity is extensive (cabbages).
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    URL: http://dx.doi.org/10.1007/BF02431263
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    Production of hybrid calluses via donor-recipient fusion between Microcitrus papuana and Citrus sinensis (1999)
    Springer
    Plant cell, tissue and organ culture 59 (1999), S. 81-87 
    Details
    ISSN: 1573-5044
    Keywords: asymmetric hybrid ; Citrus ; donor-recipient fusion ; Microcitrus ; RAPD ; X-ray
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract X-ray irradiated embryogenic protoplasts of Microcitrus papuana Swing. were electrically fused with iodoacetic acid-treated embryogenic protoplasts of Newhall navel orange [Citrus sinensis (L.) Osb.]. Seven cell lines were established by low-melting agarose embedding culture of fusion-treated protoplasts. Cytological examination of 4 cell lines showed that each cell line consisted of many aneuploid (45.10%, 38.98%, 32.69% and 34.85%, respectively) and diploid cells (52.94%, 59.33%, 63.46% and 62.12%. respectively), whereas only a few tetraploid cells (1.96%, 1.69%, 3.85% and 3.03%, respectively) were detected. Analyses of random amplified polymorphic DNA with four 10-mer primers confirmed the hybrid characteristics of the cell lines, which in combination with chromosome counting proved that the cell lines were asymmetric hybrids.
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    URL: http://dx.doi.org/10.1023/A:1006399302843
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    DNA analysis of potato + Solanum brevidens somatic hybrid lines (1999)
    Springer
    Euphytica 105 (1999), S. 103-107 
    Details
    ISSN: 1573-5060
    Keywords: Erwinia carotovora ; Solanum tuberosum ; somaclonal variation ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Three somatic hybrid lines between potato (cv. While Lady line no. Ke 79, 2n = 2x = 48) + Solanum brevidens (PI 218228, 2n = 2x = 24) were evaluated using randomly amplified polymorphic DNA (RAPD) markers. The lines originated from the same callus but showed different reactions to Erwinia carotovora ssp. carotovora, the cause of potato soft rot. By the use of 48 oligomer primers producing 99 scorable bands, DNA polymorphism were detected on 7 of 12 S. brevidens chromosomes. Loss of certain DNA segments on chromosome 5, 6, 9 and 11 were observed. Some of the variations could have taken place in early callus stage of development; others may have occurred after initiation of individual shoot regeneration. The possible involvement of missing RAPD products specific to one somatic hybrid that shows decreased resistance to bacterial soft rot is discussed.
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    URL: http://dx.doi.org/10.1023/A:1003451327553
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    Molecular analysis of Lathyrus sativus L. (grasspea) and related Lathyrus species (1999)
    Springer
    Euphytica 107 (1999), S. 167-176 
    Details
    ISSN: 1573-5060
    Keywords: genetic diversity ; Lathyrus ; L.sativus ; phylogenetic relationship ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Eight Lathyrus sativus L. accessions from a variety of geographic origins were used to study intraspecific genetic diversity using RAPD analysis. Fourteen decamer primers produced 64 amplification products, 50% of which were polymorphic between the samples. Jaccard's coefficient of genetic similarity was calculated between samples and a dendrogram was constructed by an unweighted pair-group method with arithmetical averages (UPGMA). The dendrogram showed that most of the L. sativus plants clustered into accessions or common geographical areas. The average genetic similarity coefficient within accessions was 0.12 and between accessions was 0.20, indicating a low level of intraspecific genetic variation. Interspecific genetic diversity and phylogenetic relationships of eight Lathyrus species, including L. sativus and Pisum sativum L. (field pea) were examined using 14 decamer primers which produced 283 amplification products. All amplification products were polymorphic across the nine species. In the dendrogram the Lathyrus species clustered into three distinct groups which correlated with the Sections Lathyrus, Clymenum and Linearicarpus. This supports traditional taxonomic classifications of the genus Lathyrus which are based on morphological traits. Of the species from Section Lathyrus, L. gorgoni and L. cicera were the most similar to L. sativus. The results suggest that a strategy of breeding for producing lines of L. sativus with increased genetic variation would be effectively achieved through hybrid production between accessions from wide geographic areas particularly the Mediterranean area and the Indian subcontinent. However, the most effective method would be introgression of germplasm from other species in Section Lathyrus.
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    Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers (1999)
    Springer
    Euphytica 110 (1999), S. 21-34 
    Details
    ISSN: 1573-5060
    Keywords: genetic diversity ; germplasm ; molecular markers ; RAPD ; sesame
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Fifty-eight accessions of sesame (Sesamum indicum L.), an important oil seed crop of the tropics and subtropics were analysed using random amplified polymorphic DNA (RAPD) technique. The material analysed comprised 36 collections from 18 different states of India and four adjoining countries of the Indian subcontinent, and 22 exotic accessions from 21 sesame growing countries around the world. The results from PCR amplifications with the selected 24 random 10-mer primers were statistically analysed. The value of Jaccard’s similarity coefficients ranged from 0.19 to 0.89. The results indicated the presence of high level of genetic diversity. However, the extent of genetic diversity was greater in the collections from Indian subcontinent as compared to the exotics. Among the Indian accessions, the collections from Rajasthan and North-eastern states were highly diverse. The phenetic analysis grouped 48 out of 58 accessions in six clusters and the remaining highly diverse accessions were placed outside these close-knit clusters. The Bootstrap estimates obtained by Wagner parsimony analysis were significant for seven out of 49 nodes in the majority-rule consensus tree (〈95% occurrence). The results of both the analyses were, however, broadly comparable when the constitution of the individual clusters were considered. The principal components analysis indicated that the first two components accounted for only 21% of the total variations and in order to explain 〈75% of variations 18 components were required. The high level of genetic diversity prevalent among the Indian collections is probably indicative of the nativity of this crop species. Similarly, the relatively lower level of polymorphism in exotic germplasm could be ascribed to the comparatively recent introductions of limited germplasm of this crop into some of the non-traditional sesame growing countries.
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    URL: http://dx.doi.org/10.1023/A:1003724732323
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    Genetic diversity of Prunus rootstocks analyzed by RAPD markers (1999)
    Springer
    Euphytica 110 (1999), S. 139-149 
    Details
    ISSN: 1573-5060
    Keywords: cultivar identification ; genetic diversity ; Prunus ; RAPD ; rootstocks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract We have used RAPD markers to characterize Prunus rootstocks from different species, both commercial, and selected clones from the breeding program at Aula Dei Experimental Station (Zaragoza, Spain). Molecular markers were used to study the genetic variation among different species, and within species. Forty one genotypes were used in this study. They included P. amygdalo-persica, and P. persica × P. davidiana hybrids; P. cerasifera, P. domestica, and P. insititia clones, and other diverse interspecific hybrids, which were divided in three groups according to postulated taxonomic classification. Diversity patterns obtained from 80 RAPD primers were evaluated in a representative subset of genotypes. This screening helped to identify 7 RAPD primers that were selected to produce a combined classification of the whole set of rootstock clones. This analysis successfully clustered rootstocks according to the classification scheme widely used to characterize Prunus clones, mainly based on morphological descriptors. Further than that, it supported the alleged origin of some interspecific materials, and confirmed a case of possible misclassification (‘Myrobalan 29 C’). A more thorough diversity analysis was conducted within each group of materials, using larger sets of primers (12–14). After this analysis, disjointed clusters were formed for P. amygdalo-persica and P. persica × P. davidiana hybrids in one group, and for Myrobalan (P. cerasifera) and Marianna (P. cerasifera × P. munsoniana) plums in another group. P. insititia and P. domestica clones, however, formed a jumbled cluster, possibly due to genetic interchange among them during their domestication and breeding history.
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    Genetic relationship among 19 accessions of six species of Chenopodium L., by Random Amplified Polymorphic DNA fragments (RAPD) (1999)
    Springer
    Euphytica 105 (1999), S. 25-32 
    Details
    ISSN: 1573-5060
    Keywords: Chenopodium ; genetic relationship ; molecular markers ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The RAPD technique was used to identify genetic relationships in 19 accessions, including six species of the genus Chenopodium. A dendrogram was constructed using UPGMA from 399 DNA markers. The molecular data clustered species and accessions into five different groups. Group 1 with three cultivated varieties of C. nuttalliae, Group 2 included eight cultivars and two wild varieties of C. quinoa, Group 3 with C. berlandieri and C. album, Group 4 with two accessions of C. pallidicaule, and Group 5 with 2 accessions of C. ambrosioides. The polymorphic patterns generated by RAPD profiles showed different degrees of genetic relationship among the species studied. A low level of intraspecific variation was found within the accessions of C. quinoa, C. nuttalliae, and C. pallidicaule. The RAPD markers were found to be a useful tool for detecting genetic variation within the genus Chenopodium.
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    URL: http://dx.doi.org/10.1023/A:1003480414735
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    The use of isozymes and PCR-based DNA polymorphism in aquatic weed management: a case-study on introduced and native clones of a hybrid complex (1999)
    Springer
    Hydrobiologia 415 (1999), S. 77-85 
    Details
    ISSN: 1573-5117
    Keywords: aquatic plants ; RAPD ; hybridization ; genetic diversity ; Scirpus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Enzyme polymorphisms have been widely used in aquatic plants since the 1980s. Studies on DNA polymorphisms are less numerous and a case-study using both methods on Scirpus is worked out. Along the unique freshwater tidal zone of the River Schelde (Belgium), clumps of Scirpus species are mostly scattered in small and fragmented locations on the dikes and mud flats. Most of these taxa are native S. triqueter, S. tabernaemontani or intermediate morphological forms. However, several cultivated strains of S. tabernaemontani have been introduced in recent years. Such ‘exotic’ strains have been planted to stabilize the muddy riverbanks and became well established and may perform better than the native hybrid complex. In order to determine the existing genetic diversity among these species and the possibility for genetic pollution, stems of 30 clumps from a series of locations along the tidal river were investigated for seven enzymes (SDH, PGM, EST, MNR, GOT, 6PGD and ME) and for markers at DNA level using random amplified polymorphic DNA's (RAPD) of 22 decanucleotides. Data analysis of the allozymes and of the amplified DNA fragments enabled us to classify unambiguously the different Scirpus taxa. Direct evidence of hybridization between S. triqueter and S. tabernaemontani could not be obtained, but the putative hybrids are genetically intermediate or close to S. triqueterwhen considering the DNA polymorphism. The introduced clones of S. tabernaemontani consisted of at least three groups of genotypes of which one was very related to the native ones. The escaped clumps could be assigned to a third introduced but less-related strain.
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    URL: http://dx.doi.org/10.1023/A:1003885403429
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    Genetic differentiation of endemic nile perch Lates stappersi (Centropomidae, Pisces) populations in Lake Tanganyika suggested by RAPD markers (1999)
    Springer
    Hydrobiologia 407 (1999), S. 141-148 
    Details
    ISSN: 1573-5117
    Keywords: RAPD ; nile perch ; Tanganyika ; endemic ; genetic differentiation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genetic differentiation of endemic nile perch (Lates stappersi) populations in Lake Tanganyika was studied using RAPD. DNA was extracted from alcohol stored muscle tissue by a salting method, without organic solvents. Three primers amplified 58 variable DNA fragments from 270 individuals from five localities. The genetic distances of local samples as inverse of bandsharing ranged from 0.097 to 0.312. The population sampled in Kigoma, close to the estuary of the Malagarazi river showed high values of genetic distance in pairwise comparisons with other sampled populations. Principal component analysis separated the main population and the 25 samples from Kigoma with high eigenvalues. Five individuals sampled in Kigoma were united with the main population, as confirmed by significant differences in band frequences. The local population in Kigoma had significantly different frequencies in 24 RAPD bands when compared to the pooled samples of Lates stappersi. No clearly diagnostic fragments were found. The genetic distance (1-F) between the Kigoma population and the united main stock was 0.195. Based on Slatkin's index on private alleles, the level of migration between Kigoma and all other sampling sites united, migration is restricted (Nm = 0.43) and allows genetic separation.
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    URL: http://dx.doi.org/10.1023/A:1003797700309
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    Genetic differentiation between Bruguiera gymnorhiza and B. sexangula in Sri Lanka (1999)
    Springer
    Hydrobiologia 413 (1999), S. 11-16 
    Details
    ISSN: 1573-5117
    Keywords: DNA ; RAPD ; genetic diversity ; Bruguiera ; Sri Lanka ; mangroves
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The identification of populations of Bruguiera sexangula, Bruguiera gymnorhiza and their putative hybrids in the field is difficult using only morphological and phenological characters. Using a PCR based technique, RAPD (Random Amplified Polymorphic DNA), the genetic variation of Bruguiera populations was studied from contrasting climatic and geographic regions along the southwest coastal region of Sri Lanka. Out of 45 primers screened, 20 primers allowed us to observe polymorphism, not only between species (interspecific) but also within the species (intraspecific). Analysis of RAPD data appears to be helpful in determining the genetic relationship among populations of B. gymnorhiza and B. sexangula. RAPD markers revealed that the two species are well separated without any hybrid position between the two taxa though they occur in mixed stands. Although sampling sizes of populations of this study were small, genetic variation among B. gymnorhiza and B. sexangula populations could be observed. For B. sexangula, it was possible to differentiate each of the three populations, even when using a small number of primers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003899028558
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  • 89
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    The development of multiple arbitrary amplicon profiling (MAAP) techniques (1995)
    Springer
    Human evolution 10 (1995), S. 69-80 
    Details
    ISSN: 1824-310X
    Keywords: AP-PCR ; RAPD ; DNA fingerprinting ; genetic markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In the wide panorama of modifications and applications of Polymerase Chain Reaction (PCR), genome analysis by randomtargeted primers has been increasingly used since its proposal in 1990. In this group of techniques, here collectively referred to as Multiple Arbitrary Amplicon Profiling (MAAP), one arbitrarily designed primer is used at low stringency to amplify DNA from any source. Fingerprints of various complexity are obtained and are tested to determine their suitability for genetic analysis both in bacteria and in different eukaryotes. Since MAAP does not require prior knowledge of DNA sequence, it has been mostly used to study poorly characterized genomes. In this review, we will outline MAAP technology, current methodology (annotated with drawbacks, confoundings and pitfalls), its wide range of applications, and its potential use in the study of the phylogenetic relationships and molecular taxonomy of non-human primates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02437516
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  • 90
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    Electronic Resource
    Tagging and combining bacterial blight resistance genes in rice using RAPD and RFLP markers (1995)
    Springer
    Molecular breeding 1 (1995), S. 375-387 
    Details
    ISSN: 1572-9788
    Keywords: disease resistance ; gene combination ; Oryza sativa L. ; RAPD ; RFLP ; Xanthomonas oryzae pv.oryzae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Four genes of rice,Oryza sativa L., conditioning resistance to the bacterial blight pathogenXanthomonas oryzae pv.oryzae (X. o. pv.oryzae), were tagged by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers. No recombinants were observed betweenxa-5 and RFLP marker lociRZ390, RG556 orRG207 on chromosome 5.Xa-3 andXa-4 were linked to RFLP locusXNpb181 at the top of chromosome 11, at distances of 2.3 cM and 1.7 cM, respectively. The nearest marker toXa-10, also located on chromosome 11, was the RAPD locusO07 2000 at a distance of 5.3 cM. From this study, the conventional map [19, 28] and two RFLP linkage maps of chromosome 11 [14, 26] were partially integrated. Using the RFLP and RAPD markers linked to the resistance genes, we selected rice lines homozygous for pairs of resistance genes,Xa-4 +xa-5 andXa-4 +Xa-10. Lines carryingXa-4 +xa-5 andXa-4 +Xa-10 were evaluated for reaction to eight strains of the bacterial blight pathogen, representing eight pathotypes and three genetic lineages. As expected, the lines carrying pairs of genes were resistant to more of the isolates than their single-gene parental lines. Lines carryingXa-4 +xa-5 were more resistant to isolates of race 4 than were either of the parental lines (‘quantitative complementation’). No such effects were seen forXa-4 +Xa-10. Thus, combinations of resistance genes provide broader spectra of resistance through both ordinary gene action expected and quantitative complementation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01248415
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  • 91
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    Electronic Resource
    Evidence of two genetic entities inBothriocephalus funiculus (Cestoda) detected by arbitrary-primer polymerase chain reaction random amplified polymorphic DNA fingerprinting (1995)
    Springer
    Parasitology research 81 (1995), S. 591-594 
    Details
    ISSN: 1432-1955
    Keywords: Biodiversity ; RAPD ; Evolution ; Parasitism ; Telcostean ; Cestoda
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The genetic diversity of two samples of Cestoda (Bothriocephalus funiculus, Renaud and Gabrion, 1984) parasitizing two sympatric teleostean species was assessed using random amplified polymorphic DNA (RAPD). A total of 72Bothriocephalus were analyzed individually, and electrophoretic analysis of the amplification products of 65 primers among the 68 tested revealed monomorphic patterns, reflecting the close genetic relatedness within and between the parasites of the two samples. However, 3 primers showed polymorphic patterns at 6 RAPD sites. Analysis of the distribution of these genomic fragments, assuming random mating, showed strong linkage disequilibria (only 8 genetic combinations were observed among the 32 expected). Two genetic entities displaying a high degree of host specificity were evidence within our two samples ofB. funiculus. This powerful molecular technique can be used as a diagnostic tool in studies concerning the biodiversity of related genetic entities and could have broad applications in parasitology.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00932026
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  • 92
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    Electronic Resource
    The use of an arbitrarily primed PCR product for the specific detection of Brucella (1999)
    Springer
    World journal of microbiology and biotechnology 15 (1999), S. 381-385 
    Details
    ISSN: 1573-0972
    Keywords: Brucella abortus ; Brucella melitensis ; polymerase chain reaction ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract A 1.3 kb Brucella-specific DNA fragment produced through the use of arbitrarily primed polymerase chain reaction (AP-PCR) was tested for its specificity by DNA–DNA hybridization to Brucella and non-Brucella bacteria. The digoxigenin (DIG)-labelled 1.3 kb DNA fragment hybridized with Brucella abortus and Brucella melitensis but did not hybridize with other non-Brucella bacteria tested. The sensitivity of the reaction was determined; as little as 150 fg DNA or 30 Brucella cells could be detected. The specificity and sensitivity of the 1.3 kb DNA fragment combined with the simplicity and speed of the technique suggest the potential of this fragment as a DNA probe for the quick and reliable detection of Brucella organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008975616874
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  • 93
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    Electronic Resource
    Molecular Fingerprinting Suggests Two Primary Outbreaks of Witches' Broom Disease (Crinipellis perniciosa) of Theobroma cacao in Bahia, Brazil (1999)
    Springer
    European journal of plant pathology 105 (1999), S. 167-175 
    Details
    ISSN: 1573-8469
    Keywords: genetic variability ; plant pathogen ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Crinipellis perniciosa (Stahel) Singer is the causal agent of witches' broom disease in the Sterculiaceae, Solanaceae, and Bixaceae families. The disease is endemic to the Brazilian Amazon, and was first reported infecting Theobroma cacao (cocoa) in the State of Bahia, Brazil, in 1989. Random amplified polymorphic DNA (RAPD) analyses were performed on 46 isolates of C. perniciosa from cocoa that were collected from 15 counties in Bahia and the Brazilian Amazon. A total of 258 RAPD loci from 20 primers and three mixed primers were analyzed. Of these loci, 108 (42%) were polymorphic, with an average of 4.7 polymorphic loci per primer produced. Genetic similarities were estimated using Nei and Li's index and UPGMA clustering. Bootstrap analysis divided the phenogram into four significantly different clusters: two groups contained isolates from Ariquemes and from Ouro Preto, Rondônia, and the other two separated the isolates from Bahia into two major groups of C. perniciosa, classified as Group 1 (G1) and Group 2 (G2). The two groups of isolates from Bahia differed for their genetic similarity with the isolates from the Brazilian Amazon. The geographic distribution of the groups in Bahia suggests two independent focal points of introduction. Ongoing programs to screen for resistant cocoa genotypes should consider both groups of isolates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008716000479
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