Rapid and reliable screening of a tomato YAC library exclusively based on PCR

Pillen, Klaus; Alpert, Kevin B.; Giovannoni, James J.; Ganal, Martin W.; Tanksley, Steven D.

doi:10.1007/bf02671903

Cited by 5 publications

(3 citation statements)

References 24 publications

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“…Using the Bs4-linked marker TG432, we screened two libraries according to Pillen et al (1996). One library was derived from the L. esculentum cultivars VFNT Cherry and Rio Grande-PtoR ).…”

Section: Yac Library Screenmentioning

confidence: 99%

Chromosome landing at the tomato Bs4 locus

et al. 2001

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The tomato (Lycopersicon esculentum) Bs4 gene confers resistance to strains of Xanthomonas campestris pathovar vesicatoria that express the avirulence protein AvrBs4. As part of a map-based cloning strategy for the isolation of Bs4, we converted Bs4-linked amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers into locus-specific sequence-tagged-site (STS) markers. The use of these markers for the analysis of 1972 meiotic events allowed high-resolution genetic mapping within a 1.2-cM interval containing the target gene. Two tomato yeast artificial chromosome (YAC) clones, each harboring inserts of approximately 250 kb, were identified using the marker most closely linked to Bs4. YAC end-specific markers were established and employed to construct a local YAC contig. The ratio of physical to genetic distance at Bs4 was calculated to be 280 kb/cM, revealing that recombination rates in this region are about three times higher than the genome-wide average. Mapping of YAC end-derived markers demonstrated that the Bs4 locus maps within a region of 250 kb, corresponding to a genetic interval of 0.9 cM.

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“…Using the Bs4-linked marker TG432, we screened two libraries according to Pillen et al (1996). One library was derived from the L. esculentum cultivars VFNT Cherry and Rio Grande-PtoR ).…”

Section: Yac Library Screenmentioning

confidence: 99%

Chromosome landing at the tomato Bs4 locus

et al. 2001

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“…Based on this sequence information, primers were designed and used for PCR ampli®cation of the corresponding locus from tomato. After con®rmation of the ampli®ed product by hybridization, DNA from the tomato YAC ) was screened via PCR according to Pillen et al (1996). Individual clones that gave the expected PCR products were puri®ed on selective plates, and chromosomal DNA was prepared in agarose-embedded blocks as described by Schwartz and Cantor (1984).…”

Section: Introductionmentioning

confidence: 99%

Map-based cloning of the tomato genomic region that spans the Sw-5 tospovirus resistance gene in tomato

Brommonschenkel

Tanksley

1997

Mol Gen Genet

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Two yeast artificial chromosomes (YACs) containing genomic DNA from tomato have been isolated using CT220, an RFLP marker which is tightly linked to the tomato spotted wilt virus resistance gene, Sw-5. High-resolution mapping of the YAC ends and internal YAC probes demonstrated that one of the YAC clones, TY257 (400 kb), spans Sw-5. By chromosome walking in a cosmid library, the position of Sw-5 has been delimited within the YAC to a maximal chromosomal segment of 100 kb, spanned by nine overlapping cosmid clones.

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“…Such markers are especially useful for preselecting recombinants in specific regions of the tomato genome for the purpose of highresolution mapping of genes targeted for map-based cloning (Alpert and Tanksley 1996). At the same time, they provide starting points for the rapid isolation of large insert clones from tomato DNA libraries, such as yeast artificial chromosomes (YACs) Bonnema et al 1996;Pillen et al 1996a) or bacterial artificial chromosomes (BACs) (Shizuya et al 1992) and binary BAC (BiBAC) clones (Hamilton et al 1996).Considerable effort is currently spent on the comparative mapping of highly conserved cDNA clones across a wide range of plant taxa. This has revealed that in limited regions, synteny exists even between distantly related plant species (Paterson et al.…”

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confidence: 99%

Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)

Ganal

Czihal²,

Hannappel³

et al. 1998

Genome Res.

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The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions.[cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos. AA824695-AA825005 and the dbEST Id database under accession nos. 1546519-1546862.] Molecular markers used in mapping experiments should ideally have a known function. This requirement is fulfilled best by the use of known genes in the form of genomic clones or cDNA clones. Many genetic maps based on molecular markers, such as RFLPs (restriction fragment length polymorphisms) include a number of known genes. However, the number of known genes available for a given organism is usually very limited. To circumvent this problem, many maps contain a large number of randomly selected cDNA clones. cDNAs have the additional advantage that they are frequently single or low copy and thus ideal for genetic mapping (Bernatzky and Tanksley 1986). Furthermore, they show a higher level of conservation between species than genomic clones (Zamir and Tanksley 1988) and allow more efficient cross-mapping in related species for the determination of synteny (Ahn and Tanksley 1993).In recent years random cDNA clones have attracted considerable interest, as the sequencing of such clones provides a means to obtain a fast catalog of expressed genes from a given organism without sequencing the entire genome. In plants, major efforts are now under way to sequence random cDNAs in Arabidopsis and rice Delseny et al. 1997). Many thousands of such fragments have been deposited in the respective databases. For ∼30%-40% of the cDNA sequences a possible function can be deduced based on homologies to known genes from bacteria, animals, or plants (Delseny et al. 1997).For all expressed genes, not only the DNA sequence and the possible function should be known but also their map position on the chromosomes. In the long term this will allow merging of the classical genetic map based on mutations with potential candidate genes for these mutants. A common repertoire of mapped cDNA clones will, in the future, enable us to study synteny even between distantly related species (Paterson et al. 1996) for which studies by cross-hybridization are very difficult. The availability of sequence information for mapped cDNA clones should make conclusions from hybridization studies more firm and testable.Tomato (Lycopersicon esculentum) has one of the most densely populated genetic maps among plants. Currently, >1000 RFLP markers have been published b...

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Rapid and reliable screening of a tomato YAC library exclusively based on PCR

Cited by 5 publications

References 24 publications

Chromosome landing at the tomato Bs4 locus

Chromosome landing at the tomato Bs4 locus

Map-based cloning of the tomato genomic region that spans the Sw-5 tospovirus resistance gene in tomato

Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)

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