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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 22 (1993), S. 807-818 
    ISSN: 1573-5028
    Keywords: inverse PCR ; multigene family ; promoter ; potato ; U6snRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Using the inverse polymerase chain reaction (IPCR), 19 U6snRNA gene promoters were isolated from the potato genome. Analysis of their nucleotide sequences revealed the existence of two subfamilies. Promoters from class 1 harbour the typical sequence elements required for plant snRNA gene transcription whereas those from class 2 do not have a TATA box. Three promoters were fused to a modified U6snRNA-coding sequence to allow their acitivity to be monitored in tobacco protoplasts. Two of the promoters, one from either class, were found to be active. Comparison of potato U6snRNA gene promoter sequences with those found in other plant species showed various degrees of homology. In addition, the entire nucleotide sequences of seven potato U6snRNA genes and one pseudogene were determined. The overall frequency of nucleotide changes after PCR was found to be 1.15×10-3. The mutations appeared to be clustered in a distinct area and were all A-to-G/T-to-C substitutions.
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  • 2
    ISSN: 1573-5044
    Keywords: heritability ; protoplasts ; RFLPs ; Solanum tuberosum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genetics of tissue culture response in potato has been examined by analysing a sample of dihaploids (2n=2x=24) extracted from tetraploid parents (4n=4x=48). The genotypes were screened for rate of nodal multiplication, in vitro tuberisation, regeneration from leaf discs and protoplast plating efficiency. Significant differences were detected between dihaploids for the traits measured and this indicates that tissue culture response in the tetraploid parents must be in the heterozygous condition. Estimates of the broad sense heritabilities were calculated together with the number of genes or effective factors involved in the control of the traits. These estimates indicate that tissue culture response in potato is under relatively simple genetic control and “blocks of genes” may be located on specific chromosomes. The inheritance of RFLP markers in the segregating dihaploid population was also monitored and the potential of using molecular markers linked to gene(s) controlling tissue culture response is discussed.
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  • 3
    ISSN: 1615-6110
    Keywords: Angiosperms ; Rosaceae ; Rubus ; Chloroplast DNA ; restriction fragment length polymorphism ; cladistic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The variability in chloroplast DNA type of 20Rubus genotypes was examined by Southern hybridization. DNA extracted from theRubus accessions was digested with two restriction enzymes (EcoRI and EcoRV) and heterologous chloroplast DNA sequences from barley and pea were used as probes to detectRubus chloroplast DNA sequences on Southern blots ofRubus total DNA. Restriction fragment length polymorphism was detected and a total of 92 restriction fragments were generated by the probe/enzyme combinations examined. Cladistic principles based on the parsimony assumption were used to assemble a phylogenetic tree based on chloroplast restriction fragment length data. The phylogenetic tree grouped the taxonomically defined species and is in general agreement with information based on morphological criteria. However, the Japanese red raspberryR. illecebrosus was shown to have diverged considerably in terms of evolutionary time from other species in subg.Idaeobatus. Furthermore, the molecular approach provides a quantitative estimate of the relationship between species that is difficult to obtain from morphological data. In order to complement the chloroplast DNA information a ribosomal DNA probe was also included in the analysis and provided further information on the phylogenetic relationships withinRubus.
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  • 4
    ISSN: 1617-4623
    Keywords: Key words Bare-1  ;  Retrotransposons  ;  Barely  ;   Linkage analysis  ;  Sequence-Specific Amplification Polymorphisms (S-SAPs)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Retrotransposons are present in high copy number in many plant genomes. They show a considerable degree of sequence heterogeneity and insertional polymorphism, both within and between species. We describe here a polymerase chain reaction (PCR)-based method which exploits this polymorphism for the generation of molecular markers in barley. The method produces amplified fragments containing a Bare–1-like retrotransposon long terminal repeat (LTR) sequence at one end and a flanking host restriction site at the other. The level of polymorphism is higher than that revealed by amplified fragment length polymorphism (AFLP) in barley. Segregation data for 55 fragments, which were polymorphic in a doubled haploid barley population, were analysed alongside an existing framework of some 400 other markers. The markers showed a widespread distribution over the seven linkage groups, which is consistent with the distribution of the Bare–1 class of retrotransposons in the barley genome based on in situ hybridisation data. The potential applicability of this method to the mapping of other multicopy sequences in plants is discussed.
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  • 5
    ISSN: 1617-4623
    Keywords: Key words AFLP ; Barley ; Product homology ; Linkage maps
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Segregation of 850 polymorphic AFLP (amplified fragment length polymorphism) fragments was followed in three different doubled haploid (DH) barley populations, Dicktoo × Morex (DM), Igri × Franka (IF) and Blenheim × E224/3 (BE), which had previously been used to construct linkage maps using other molecular markers. The final maps consisted of 310, 655 and 474 markers, of which 234, 194 and 376, respectively, were AFLPs. A comparison of profiles from the parental lines identified 51 similar-sized AFLPs segregating in both DM and IF populations, 20 in the DM and BE populations and 18 in the IF and BE populations. Eight segregated in all three. Analysis of the complete datasets for each of the populations using Joinmap V.2. indicated that in general terms each of the AFLPs which were polymorphic in more than one population mapped to the same genetic locus. The number of co-dominant markers segregating in a single population ranged from 6% for DM to 12.6% for IF. These results are discussed in the context of using AFLP in genetic linkage and diversity studies.
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  • 6
    ISSN: 1617-4623
    Keywords: Key words AFLP ; Linkage map ; Solanum tuberosum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have constructed a partial linkage map in tetraploid potato which integrates simplex, duplex and double-simplex AFLP markers. The map consists of 231 maternal and 106 paternal markers with total map lengths of 990.9 cM and 484.6 cM. The longer of the two cumulative map lengths represents approximately 25% coverage of the genome. In tetraploids, much of the polymorphism between parental clones is masked by `dosage' which significantly reduces the number of individual markers that can be scored in a population. Consequently, the major advantage of using AFLPs – their high multiplex ratio – is reduced to the point where the use of alternative multi-allelic marker types would be significantly more efficient. The segregation data and map information have been used in a QTL analysis of late blight resistance, and a multi-allelic locus at the proximal end of chromosome VIII has been identified which contributes significantly to the expression of resistance. No late blight resistance genes or QTLs have previously been mapped to this location.
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  • 7
    ISSN: 1617-4623
    Keywords: Key words Simple sequence repeat ; Linkage map ; Single-strand hybridisation ; Triplex affinity capture ; Enriched library
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Solanum tuberosum L. DNA sequences containing simple sequence repeat (SSR) motifs were extracted from the EMBL database, cDNA and selectively enriched small-insert DNA libraries. Enrichment was achieved using either triplex affinity capture or single-strand hybridisation selection. One hundred and twelve primer pairs which successfully amplified products of the correct size from potato DNA were ultimately designed and synthesised. Ninety-eight of these revealed length polymorphisms in a panel of four diploid and two tetraploid clones, in agreement with the high information content of this class of markers which has been found in other species. All of the markers were assigned a quality score of 1–5 based on their potential usefulness. Eighty-nine loci from 65 of the primer pairs were located on two genetic linkage maps of potato by segregation analysis of the amplified alleles. Fifty-two of the SSRs were clearly single locus. The maps were aligned using 23 SSR primer pairs and 13 RFLP loci mapped in both populations. The markers described constitute a class which should replace Restriction Fragment Length Polymorphisms (RFLP) as the markers of choice for future genetic studies in potato. The sequences of the primers, together with other information on these markers are provided.
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  • 8
    ISSN: 1432-203X
    Keywords: Key words: potato, simple sequence repeats, somatic hybrids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We have utilised simple sequence repeat (SSR) polymorphism to analyse two sets of potential intra-specific hybrids of potato. Two primer pairs were used and both showed that one set of fusion products could not be true heterokaryons. In the other set, one of the primer pairs showed that unique bands in each of the parents were present in all of the hybrids, unambiguously demonstrating hybridity. This simple and robust, high-resolution assay can be used at the callus level and is amenable to automation, making it possible to reduce greatly the time required to screen a large number of potential somatic hybrids.
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  • 9
    ISSN: 1432-203X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phenetic relationships between 18 Coffea accessions representing 11 of the most important Coffea species employed in current breeding programmes were examined using RAPD markers and chloroplast and mitochondrial genome specific sequence tagged sites (STS). Estimates of variability based on the number of shared RAPD amplification products placed the species into three distinct groups which were consistent with derived chloroplast DNA phenotypes, the geographical origins of the species and previous studies based on morphological characteristics and RFLPs. C. eugenioides (2n = 2x = 22) exhibited the greatest similarity to the cultivated C. arabica (2n = 4x = 44) and may represent its maternal progenitor. The results are discussed in the context of strategies for Coffea improvement.
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  • 10
    ISSN: 1432-2242
    Keywords: Key words Barley ; BAC library ; P-loop genes ; Resistance-gene analog (RGA)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Modern cultivated barley is an important cereal crop with an estimated genome size of 5000 Mb. To develop the resources for positional cloning and structural genomic analyses in barley, we constructed a bacterial artificial chromosome (BAC) library for the cultivar Morex using the cloning enzyme HindIII. The library contains 313344 clones (816 384-well plates). A random sampling of 504 clones indicated an average insert size of 106 kbp (range=30–195 kbp) and 3.4% empty vectors. Screening the colony filters for chloroplast DNA content indicated an exceptionally low 1.5% contamination with chloroplast DNA. Thus, the library provides 6.3 haploid genome equivalents allowing a 〉99% probability of recovering any specific sequence of interest. High-density filters were gridded robotically using a Genetix Q-BOT in a 4×4 double-spotted array on 22.5-cm2 filters. Each set of 17 filters allows the entire library to be screened with 18432 clones represented per filter. Screening the library with 40 single copy probes identified an average 6.4 clones per probe, with a range of 1–13 clones per probe. A set of resistance-gene analog (RGA) sequences identified 121 RGA-containing BAC clones representing 20 different regions of the genome with an average of 6.1 clones per locus. Additional screening of the library with a P-loop disease resistance primer probe identified 459 positive BAC clones. These data indicate that this library is a valuable resource for structural genomic applications in barley.
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