RAPD-based screening of genomic libraries for positional cloning

Dioh, Waly; Tharreau, Didier; Lebrun, Marc

doi:10.1093/nar/25.24.5130

Cited by 11 publications

(10 citation statements)

References 4 publications

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“…The single copy RAPD marker OPE-Y13 that cosegregates with the avirulence gene ACE1 (Dioh et al, 2000) was used to screen a genomic cosmid library from avirulent progeny 96/0/76 (Dioh et al, 1997). The cosmid clone D31C12 was found to carry OPE-Y13.…”

Section: Cloning Of M Grisea Avirulence Gene Ace1mentioning

confidence: 99%

“…The actin encoding gene ACT1 was used as control in RT-PCR experiments. An EST corresponding to ACT1 was isolated from a M. grisea cDNA library prepared from mycelial RNA (Clergeot et al, 2001) and used to identify the corresponding cosmid from a 96/0/76 genomic library (Dioh et al, 1997).…”

Section: Rt-pcrmentioning

confidence: 99%

“…The cosmid library is described by Dioh et al (1997). For cosmid D31C12 subclones, cosmid DNA was digested with each of the following enzymes: BamHI, EcoRI, NotI, and XbaI and in double digests with BglII plus NotI and XbaI plus NotI, respectively.…”

Section: Plasmid Constructionsmentioning

confidence: 99%

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A Putative Polyketide Synthase/Peptide Synthetase fromMagnaporthe griseaSignals Pathogen Attack to Resistant Rice[W]

et al. 2004

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Isolates of the rice blast fungus Magnaporthe grisea that carry the gene encoding Avirulence Conferring Enzyme1 (ACE1) are specifically recognized by rice (Oryza sativa) cultivars carrying the resistance gene Pi33. This recognition enables resistant plants to activate a defense response. ACE1 was isolated by map-based cloning and encodes a putative hybrid between a polyketide synthase and a nonribosomal peptide synthetase, enzymes involved in microbial secondary metabolism. ACE1 is expressed exclusively during fungal penetration of host leaves, the time point at which plant defense reactions are triggered. Ace1 appears to be localized in the cytoplasm of the appressorium. Mutation of the putative catalytic site of the b-ketoacyl synthase domain of Ace1 abolishes recognition of the fungus by resistant rice. This suggests that Ace1 biosynthetic activity is required for avirulence. Our results are consistent with the hypothesis that the fungal signal recognized by resistant rice plants is the secondary metabolite whose synthesis depends on Ace1.

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Section: Cloning Of M Grisea Avirulence Gene Ace1mentioning

confidence: 99%

Section: Rt-pcrmentioning

confidence: 99%

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A Putative Polyketide Synthase/Peptide Synthetase fromMagnaporthe griseaSignals Pathogen Attack to Resistant Rice[W]

et al. 2004

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“…An alternative might be to separate chromosomes by pulsed-Weld electrophoresis and probe blots with labeled RAPD marker bands. However, this method could prove problematic as RAPDs can contain repeated sequences, which precludes screening by hybridization (Bohm and Zyprian, 1998;Dioh et al, 1997;Paran and Michelmore, 1993).…”

Section: Locusmentioning

confidence: 99%

Markers linked to vegetative incompatibility (vic) genes and a region of high heterogeneity and reduced recombination near the mating type locus (MAT) in Cryphonectria parasitica

Kubisiak

Milgroom

2006

Fungal Genetics and Biology

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“…After submission of this article, a note was published on the identification of cosmid clones linked to avirulence genes of the fungus Magnaporthe grisea by random amplified polymorphic DNA-based screening of a genomic library (25).…”

Section: Discussionmentioning

confidence: 99%

Screening for overlapping bacterial artificial chromosome clones by PCR analysis with an arbitrary primer

Xu¹,

Yang²,

Domingo³

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

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In this article, we used PCR analysis with arbitrary primers (AP-PCR) to screen for overlapping bacterial artificial chromosome (BAC) clones and assembly of contigs. A rice BAC library with three genome equivalents was used to prepare pooled BAC DNA. Twenty-two arbitrary primers were used to survey the pooled BAC DNAs and individual BAC DNAs. Each primer identified 1-10 loci, and the average was 4.4 loci. There were 1-5 overlapping clones in each locus, and the average was 2.5 clones. A total of 245 BAC clones were identified as overlapping by AP-PCR and the identities were confirmed by DNA-DNA hybridization. The 245 BAC clones were then assembled into 80 contigs and 17 single-clone loci. The results indicated that PCR analysis with arbitrary primers is a powerful tool in screening for overlapping BAC clones with high accuracy and efficiency. The use of AP-PCR analysis should speed up the construction of physical maps of the plant and animal genomes, as well as the rice genome.Intensive efforts are being made to construct high-resolution physical maps of human, animal, and plant genomes through the generation of ordered overlapping DNA fragments. Because of their capacity for housing large fragments of exogenous DNA, yeast artificial chromosomes (YAC) (1) and bacterial artificial chromosomes (BAC) (2) are used to generate contigs of large genomes. Several approaches are used to identify overlapping clones. DNA-DNA hybridization with mapped DNA markers, combined with chromosomal walking, is widely used to identify overlapping YAC clones. A YAC contig map of the human genome has been constructed by using this technique (3). In plants, physical maps of overlapping YAC clones of chromosomes 2 (4) and 4 (5) of Arabidopsis have been constructed by colony hybridization of YAC libraries. With the use of 1,383 DNA markers, the rice physical map of YAC covers about 50% of the rice genome (6). To obtain more complete coverage of the rice genome, a higher-density marker map is being constructed (7). Obviously, the major limitation of this approach to generate a physical map is the requirement of a high-density DNA marker map of the target genomes. Furthermore, repetitive DNA sequences present in eukaryote genomes and chimeric YAC clones create enormous difficulties in chromosome walking (6,8).Another approach to assemble overlapping clones is based on DNA fingerprinting of random clones (9, 10). The restriction fragments of each DNA clone show typical banding patterns when separated in high-resolution gels and͞or probed with DNA probes. Overlapping clones are identified by shared restriction fragments. By use of DNA fingerprinting of cosmid clones, a high-quality physical map of the nematode Caenorhabditis elegans genome was constructed (11). Though the DNA fingerprinting approach is effective in mapping a small genome, its application to a large genome such as the human genome can be difficult (3).Sequence tag site (STS) content mapping is used for the identification of YAC clones (12). Early application of the met...

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RAPD-based screening of genomic libraries for positional cloning

Cited by 11 publications

References 4 publications

A Putative Polyketide Synthase/Peptide Synthetase fromMagnaporthe griseaSignals Pathogen Attack to Resistant Rice[W]

A Putative Polyketide Synthase/Peptide Synthetase fromMagnaporthe griseaSignals Pathogen Attack to Resistant Rice[W]

Markers linked to vegetative incompatibility (vic) genes and a region of high heterogeneity and reduced recombination near the mating type locus (MAT) in Cryphonectria parasitica

Screening for overlapping bacterial artificial chromosome clones by PCR analysis with an arbitrary primer

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