Abstract
The differential display technique was originally developed for the isolation of differentially expressed genes from eukaryotic tissues. We have adapted this technique for the isolation of cDNA markers from specific regions of the tomato genome. For this purpose, differential display was performed on RNA extracted from leaf tissue of nearly isogenic lines for the Tm-2a gene of tomato. On average, one out of 20 primer combinations resulted in a polymorphism at the cDNA level. When used as hybridization probes, all of these cDNA fragments were single or low copy and all of them were polymorphic on Southern hybridizations using DNA from the isogenic lines. Genetic mapping revealed in each case at least one locus in the introgressed segment on chromosome 9 of tomato. Thus, this technique might provide a way for the direct isolation of transcribed sequences from specific regions of any animal or plant genome for which such lines exist.
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Bauer D, Müller H, Reich J, Riedel H, Ahrenkiel V, Warthoe P, Strauss M (1993) Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR). Nucleic Acids Res 21:4272–4280
Devos KM, Gale MD (1992) The use of random amplified polymorphic DNA markers in wheat. Theor Appl Genet 84:567–572
Ganal MW, Young ND, Tanksley SD (1989) Pulsed field gel electrophoresis and physical mapping of large DNA fragments in the Tm-2a region of chromosome 9 in tomato. Mol Gen Genet 215:395–400
Gill KS, Gill BS (1991) A DNA fragment mapped within the submicroscopic deletion of Ph1: a chromosome pairing regulator gene in polyploid wheat. Genetics 129:257–259
Gill KS, Gill BS, Endo TR, Mukai Y (1993) Fine mapping of Ph1: a chromosome pairing regulator gene in polyploid wheat. Genetics 134:1231–1236
Giovannoni JJ, Wing RA, Ganal MW, Tanksley SD (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res 23:6553–6558
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Lazarus CM, Baulcombe DC, Martienssen RA (1985) Alphaamylase genes of wheat are two multigene families which are differentially expressed. Plant Mol Biol 5:13–24
Liang P, Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971
Liang P, Averbougk L, Pardee AB (1993) Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. Nucleic Acids Res 21:3269–3275
Lisitsyn N, Lisitsyn N, Wigler M (1993) Cloning the difference between two complex genomes. Science 259:946–951
Lisitsyn NA, Segre JA, Kusumi K, Lisitsyn NM, Nadeau JH, Frankel WN, Wigler MH, Lander ES (1994) Direct isolation of polymorphic markers linked to a trait by genetically directed representational difference analysis. Nature Genet 6:57–63
Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci USA 88:2336–2340
McCouch SR, Kochert G, Yu ZH, Wang ZY, Kush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829
Michelmore RW, Paran I, Kesseli RV (1991) Isolation of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832
Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448
Paran I, Kesseli R, Michelmore R (1991) Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce using near-isogenic lines. Genome 34:1021–1027
Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Roder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around the Tm-2a locus of tomato during backcross breeding. Theor Appl Genet 77:353–359
Young ND, Zamir D, Ganal MW, Tanksley SD (1988) Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the Tm-2a gene in tomato. Genetics 120:579–585
Zabeau M, Vos P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. European patent application 92402629.7, publication number 0534858A1
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Communicated by R. G. Herrmann
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Hannappel, U., Balzer, H.J. & Ganal, M.W. Direct isolation of cDNA sequences from specific chromosomal regions of the tomato genome by the differential display technique. Molec. Gen. Genet. 249, 19–24 (1995). https://doi.org/10.1007/BF00290231
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DOI: https://doi.org/10.1007/BF00290231