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1.
Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.) 总被引:26,自引:0,他引:26
Microsatellite markers containing simple sequence repeats (SSR) are a valuable tool for genetic analysis. Our objective is to augment the existing RFLP map of rice with simple sequence length polymorphisms (SSLP). In this study, we describe 20 new microsatellite markers that have been assigned to positions along the rice chromosomes, characterized for their allelic diversity in cultivated and wild rice, and tested for amplification in distantly related species. Our results indicate that the genomic distribution of microsatellites in rice appears to be random, with no obvious bias for, or clustering in particular regions, that mapping results are identical in intersubspecific and interspecific populations, and that amplification in wild relatives ofOryza sativa is reliable in species most closely related to cultivated rice but becomes less successful as the genetic distance increases. Sequence analysis of SSLP alleles in three relatedindica varieties demonstrated the clustering of complex arrays of SSR motifs in a single 300-bp region with independent variation in each. Two microsatellite markers amplified multiple loci that were mapped onto independent rice chromosomes, suggesting the presence of duplicated regions within the rice genome. The availability of increasing numbers of mapped SSLP markers can be expected to increase the power and resolution of genome analysis in rice. 相似文献
2.
Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.) 总被引:37,自引:0,他引:37
M. W. Blair O. Panaud S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(5):780-792
Inter-simple sequence repeat (ISSR) amplification was used to analyze microsatellite motif frequency in the rice genome and
to evaluate genetic diversity among rice cultivars. A total of 32 primers, containing different simple sequence repeat (SSR)
motifs, were tested for amplification on a panel of 59 varieties, representative of the diversity of cultivated rice (Oryza sativa L.). The ISSR analysis provided insights into the organization, frequency and levels of polymorphism of different simple
sequence repeats in rice. The more common dinucleotide motifs were more amenable to ISSR analysis than the more infrequent
tri-, tetra- and penta-nucleotide motifs. The ISSR results suggested that within the dinucleotide class, the poly(GA) motif
was more common than the poly(GT) motif and that the frequency and clustering of specific tri- and tetra-nucleotide simple
sequence repeats was variable and motif-specific. Furthermore, trinucleotide ISSR markers were found to be less polymorphic
than either dinucleotide or certain tetranucleotide ISSR markers, suggesting which motifs would be better targets for microsatellite
marker development. The ISSR amplification pattern was used to group the rice genotypes by cluster analysis. These results
were compared to surveys of the same varieties for amplified fragment length polymorphism (AFLP), restriction fragment length
polymorphism (RFLP) and isozyme markers. The ISSR fingerprint could be used to differentiate the genotypes belonging to either
Japonica or Indica sub species of cultivated rice and to dissect finer levels of diversity within each subspecies. A higher percentage of polymorphic
bands was produced with the ISSR technique than the AFLP method, based on a similar PCR reaction. Therefore, ISSR amplification
proved to be a valuable method for determining genetic variability among rice varieties and for rapidly identifying cultivars.
This efficient genetic fingerprinting technique would be useful for characterizing the large numbers of rice accessions held
in national and international germplasm centers.
Received: 25 May 1998 / Accepted: 17 September 1998 相似文献
3.
Identification of an active LTR retrotransposon in rice 总被引:2,自引:0,他引:2
4.
Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among 11 Quercus species 总被引:1,自引:0,他引:1
V. Zoldos D. Papes M. Cerbah O. Panaud V. Besendorfer S. Siljak-Yakovlev 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(6):969-977
Genomes of 11 Quercus species were characterized using cytogenetic (Giemsa C-banding, fluorochrome banding), molecular-cytogenetic (fluorescence in situ hybridization, FISH, to ribosomal genes) and molecular (dot-blot for ribosomal gene-copy number assessment) techniques. Ribosomal
genes are the first DNA sequences to be physically mapped in oaks, and the copy number of the 18S-5.8S-26 S rRNA genes is
estimated for the first time. Oak karyotypes were analysed on the basis of DAPI banding and FISH patterns; five marker chromosomes
were found. In addition, chromosomal organization of ribosomal genes with respect to AT- and GC-differentiated heterochromatin
was studied. Fluorochrome staining produced very similar CMA/DAPI banding patterns, and the position and number of ribosomal
loci were identical for all the species studied. The 18S-5.8S-26 S rRNA genes in oak complements were represented by a major
locus at the subterminal secondary constriction (SC) of the only subtelocentric chromosome pair and a minor locus at paracentromeric
SC of one metacentric pair. The only 5 S rDNA locus was revealed at the paracentromeric region of the second largest metacentric
pair. A striking karyotypic similarity, shown by both fluorochrome banding and FISH patterns, implies close genome relationships
among oak species no matter their geographic origin (European or American) or their ecophysiology (deciduous or evergreens).
Dot-blot analysis gave preliminary evidence for different copy numbers of 18S-5.8S-26 S rRNA genes in diploid genomes of Q. cerris, Q. ilex, Q. petraea, Q. pubescens and Q. robur (2700, 1300, 2200, 4000 and 2200 copies, respectively) that was correlated with the size polymorphism of the major locus.
Received: 26 February 1999 / Accepted: 16 March 1999 相似文献
5.
Zoldos V Siljak-Yakovlev S Papes D Sarr A Panaud O 《Molecular genetics and genomics : MGG》2001,265(2):234-241
Very similar genome sizes, similar karyotypes and heterochromatin organisation, and identical number/position of ribosomal loci characterise the common oak (Q. robur) and the cork oak (Q. suber), two distantly related oak species. Representational Difference Analysis (RDA) was used to subtract the genome of Q. suber from the genome of Q. robur in order to search for genome differentiation. A library of 400 clones (bearing RDA fragments) representing genome differences between the two species was obtained. Seven Q. robur-specific DNA sequences were analysed with respect to their molecular and chromosome organisation. All belong to the dispersed repetitive component of the genome, as revealed by Southern hybridisation and in situ hybridisation. They are present in the Q. robur genome in between 100 and 700 copies, and are distributed along the length of almost all chromosomes. A search for homologies between RDA fragments and sequences in Genbank revealed similarities of all RDA fragments with known retrotransposons. The RDA fragments were also tested for their presence/absence in the genomes of six additional oak species belonging to different phylogenetic groups, in order to examine the evolutionary dynamics of these DNA sequences. 相似文献
6.
Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources. 相似文献
7.
M. Le Thierry d’Ennequin O. Panaud B. Toupance A. Sarr 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(7):1061-1066
AFLP markers were used to assess genetic diversity and patterns of geographic variation among 39 accessions of foxtail millet
(Setaria italica) and 22 accessions of green foxtail millet (S. viridis), its putative wild progenitor. A high level of polymorphism was revealed. Dendrograms based on Nei and Li distances from
a neighbour joining procedure were constructed using 160 polymorphic bands. Bootstrap values revealed that no specific geographic
structure can be extracted from these data. The high level of diversity among Chinese accessions was consistent with the hypothesis
of a centre of domestication in China. The results also showed that accessions from Eastern Europe and Africa form two distinct
clusters. The narrow genetic basis of these two gene pools may be the result of local-adaptation.
Received: 1 June 1999 / Accepted: 16 September 1999 相似文献
8.
Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza 总被引:1,自引:0,他引:1
Ammiraju JS Zuccolo A Yu Y Song X Piegu B Chevalier F Walling JG Ma J Talag J Brar DS SanMiguel PJ Jiang N Jackson SA Panaud O Wing RA 《The Plant journal : for cell and molecular biology》2007,52(2):342-351
Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza. 相似文献
9.
An improved protocol for non-radioactive labelling and detection of rice and tomato DNA is described. The procedure includes
the use of polymerase chain reaction for the incorporation of digoxigenin-dUTP in the DNA molecule and the use of a chemiluminescent
compound (AMPPD) for the signal detection. 相似文献