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Cloning of a specific ripening-related gene from the multiple of ripening-related genes identified from a single band excised from a cDNA-AFLP gel

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Abstract

High-throughput methods such as amplified fragment length polymorphism (AFLP) analysis of complementary DNA (cDNA) and cDNA microarrays are useful for identifying ripening-related cDNAs from grapevine. Here we describe the identification and cloning of a gene that is transcriptionally activated at the onset of grape berry ripening. In addition, we describe the presence of multiple ripening-related genes in a single band excised from a cDNA-AFLP gel and the additional steps implemented to identify a specific ripening-related gene. In total, 7 cDNAs were identified in the band excised from the cDNA-AFLP gel. All 7 cDNAs were shown to be ripening regulated during berry development, though most were characterised by low levels of expression during berry ripening. These results highlight the limitation placed on the isolation of a specific sequence from a cDNA-AFLP gel and the steps that can be taken to overcome this limitation.

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Abbreviations

AFLP:

amplified fragment length polymorphism

cDNA:

complementary DNA

DDRT-PCR:

differential display reverse transcription PCR

PCR:

polymerase chain reaction

References

  • Aiello LP, Robinson GS, Lin Y-W, Nishio Y, and King GL (1994) Identification of multiple genes in bovine retinal pericytes altered by exposure to elevated levels of glucose by using mRNA differential display. Proc Natl Acad Sci USA 91: 6231–6235.

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.

    PubMed  CAS  Google Scholar 

  • Bachem CWB, Van Der Hoeven RS, De Bruijn SM, Vreugdenhil D, Zabeau M, and Visser RGF (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9: 745–753.

    Article  PubMed  CAS  Google Scholar 

  • Baldwin D, Crane V, and Rice D (1999) A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol 2: 96–103.

    Article  PubMed  CAS  Google Scholar 

  • Bauer D, Müller H, Reich J, Riedel H, Ahrenkiel V, Warthoe P, and Strauss M (1993) Identification of diffentially expressed mRNA species by an improved display technique (DDRT-PCR). Nucleic Acids Res 21: 4272–4280.

    Article  PubMed  CAS  Google Scholar 

  • Breyne P and Zabeau M (2001) Genome-wide expression analysis of plant cell cycle modulated genes. Curr Opin Plant Biol 4: 136–142.

    Article  PubMed  CAS  Google Scholar 

  • Callard D, Bernard L, and Mazzolini L (1994) A method for the elimination of false positives generated by the mRNA differential display technique. BioTechniques 16: 1096–1103.

    PubMed  CAS  Google Scholar 

  • Davies C and Robinson SP (2000) Differential screening indicates a dramatic change in mRNA profiles during grape berry ripening. Cloning and characterization of cDNAs encoding putative cell wall and stress response proteins. Plant Physiol 122: 803–812.

    Article  PubMed  CAS  Google Scholar 

  • Debouck C (1995) Differential display or dismay? Curr Opin Biotechnol 6: 597–599.

    Article  CAS  Google Scholar 

  • Donson J, Fang Y, Espiritu-Santo G, Xing W, Salazar A, Miyamoto S, Armendarez V, and Volkmuth W (2002) Comprehensive gene expression analysis by transcript profiling. Plant Mol Biol 48: 75–97.

    Article  PubMed  CAS  Google Scholar 

  • Fischer A, Saedler H, and Theissen G (1995) Restriction fragment length polymorphism-coupled domain-directed differential display: a highly efficient technique for expression analysis of multigene families. Proc Natl Acad Sci USA 92: 5331–5335.

    Article  PubMed  CAS  Google Scholar 

  • Gery S and Lavi S (1997) Purification and cloning of differential display products. BioTechniques 23: 198–202.

    PubMed  CAS  Google Scholar 

  • Gray J, Picton S, Shabbeer J, Schuch W, and Grierson D (1992) Molecular biology of fruit ripening and its manipulation with antisense genes. Plant Mol Biol 19: 69–87.

    Article  PubMed  CAS  Google Scholar 

  • Habu Y, Fukado-Tanaka S, Hisatomi Y, and Iida S (1997) Amplified restriction fragment length polymorphism-based mRNA fingerprinting using a single restriction enzyme that recognizes a 4-bp sequence. Biochem Biophys Res Comm 234: 516–521.

    Article  PubMed  CAS  Google Scholar 

  • Kawamoto S, Ohnishi T, Kita H, Chisaka O, and Okubo K (1999) Expression profiling by iAFLP: a PCR based method for genome-wide gene expression profiling. Genome Res 9: 1305–1312.

    Article  PubMed  CAS  Google Scholar 

  • Li F, Barnathan ES, and Karikó K (1994) Rapid method for screening and cloning of cDNAs generated in differential mRNA display: application of Northern blot for affinity capturing of cDNAs. Nucleic Acids Res 22: 1764–1765.

    Article  PubMed  CAS  Google Scholar 

  • Liang P and Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257: 967–971.

    Article  PubMed  CAS  Google Scholar 

  • Liang P, Averboukh L, Keyomarsi K, Sager R, and Pardee A (1992) Differential display and cloning of messenger RNAs from human breast cancer versus mammary epithelial cells. Cancer Res 52: 6966–6968.

    PubMed  CAS  Google Scholar 

  • Liang P, Averboukh L, and Pardee AB (1993) Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimisation. Nucleic Acids Res 21: 3269–3275.

    Article  PubMed  CAS  Google Scholar 

  • Linskens MHK, Feng J, Andrews WH, Enlow BE, Saati SM, Tonkin LA, Funk WD, and Villeponteau B (1995) Cataloging altered gene expression in young and senescent cells using enhanced differential display. Nucleic Acids Res 23: 3244–3251.

    Article  PubMed  CAS  Google Scholar 

  • Liu C and Raghothama KG (1995) Cloning and characterisation of pTPS11, a cDNA (GenBank U34808) for a phosphate-starvation induced gene from tomato. Plant Physiol 109: 1126–1127.

    Article  Google Scholar 

  • Martin KJ, Kwan C-P, O'Hara MJ, Pardee AB, and Sager R (1998) Identification and verification of differential display cDNAs using gene-specific primers and hybridisation arrays. BioTechniques 24: 1018–1026.

    PubMed  CAS  Google Scholar 

  • McClelland M, Mathieu-Daude F, and Welsh J (1995) RNA fingerprinting and differential display using arbitrarily primer PCR. Trends Genet 11: 242–246.

    Article  PubMed  CAS  Google Scholar 

  • Men AE and Gresshoff PM (1998) Efficient cloning of DAF polymorphic markers from silver-stained polyacrylamide gels. Biotechniques 24: 593–595.

    PubMed  CAS  Google Scholar 

  • Miele G, MacRae L, McBride D, Manson J, and Clinton M (1998) Elimination of false positives generated through PCR re-amplification of differential display cDNA. BioTechniques 25: 138–144.

    PubMed  CAS  Google Scholar 

  • Oh BJ, Balint DE, and Giovannoni JJ (1995) A modified procedure for PCR-based differential display and demonstration of use in plants for isolation of genes related to fruit ripening. Plant Mol Biol Rep 13: 70–81.

    Article  CAS  Google Scholar 

  • Sargent T (1987) Isolation of differentially expressed genes. In: Abelson J and Simon M (eds), Methods in Enzymology, volume 152, pp 423–432. Academic Press, New York.

    Google Scholar 

  • Shimkets RA, Lowe DG, Tai JT, Sehl P, Jin H, Yang R, Predki PF, Rothberg BE, Murtha MT, and Roth ME (1999) Gene expression analysis by transcript profiling coupled to a gene database query. Nat Biotechnol 17: 798–803.

    Article  PubMed  CAS  Google Scholar 

  • Sutcliffe JG, Foye PE, Erlander MG, Hilbush BS, Bodzin LJ, Durham JT, and Hasel KW (2000) TOGA: an automated parsing technology for analysing expression of nearly all genes. Proc Natl Acad Sci USA 97: 1976–1981

    Article  PubMed  CAS  Google Scholar 

  • Venter M, Burger AL, and Botha FC (2001) Molecular analysis of fruit ripening: the identification of differentially expressed sequences inVitis vinifera using cDNA-AFLP technology. Vitis 40: 191–196.

    CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, and Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407–4414.

    Article  PubMed  CAS  Google Scholar 

  • Wan JS, Sharp SJ, Poirier GM, Wagaman PC, Chambers J, Pyati J, Hom Y, Galindo JE, Huvar A, Peterson PA, Jackson MR, and Erlander MG (1996) Cloning of differentially expressed mRNAs. Nat Biotechnol 14: 1685–1691.

    Article  PubMed  CAS  Google Scholar 

  • Wang X, and Feuerstein GZ (1995) Direct sequencing of DNA isolated from mRNA differential display. BioTechniques 18: 448–453.

    PubMed  CAS  Google Scholar 

  • Wilkinson JQ, Lanahan MB, Conner TW, and Klee HJ (1995) Identification of mRNAs with enhanced expression in ripening strawberry fruit using polymerase chain reaction differential display. Plant Mol Biol 27: 1097–1108.

    Article  PubMed  CAS  Google Scholar 

  • Woodhead M, Taylor MA, Brennan R, McNicol RJ, and Davies HV (1997) Cloning and characterisation of the cDNA clones of five genes that are differentially expressed during ripening in the fruit of blackcurrent (Ribes nigrum L.). J Plant Physiol 153: 381–393.

    Article  Google Scholar 

  • Zegzouti H, Marty C, Jones B, Bouquin T, Latché A, Pech JC, and Bouzayen M (1997) Improved screening of cDNAs generated by mRNA differential display enables the selection of true positives and the isolation of weakly expressed messages. Plant Mol Biol 15: 236–245.

    Article  CAS  Google Scholar 

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Author notes

  1. Frederik C. Botha

    Present address: South African Sugarcane Research Institute, Private Bag X02, 4300, Mount Edgecombe, Republic of South Africa

Authors and Affiliations

  1. Institute for Plant Biotechnology, Stellenbosch University, P/Bag X1, Matieland, Stellenbosch, Republic of South Africa

    Anita L. Burger & Frederik C. Botha

  2. Biotechnology division, ARC Infruitec-Nietvoorbij, P/Bag X5026, 7599, Stellenbosch, Republic of South Africa

    Anita L. Burger

Authors
  1. Anita L. Burger
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  2. Frederik C. Botha
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Correspondence to Anita L. Burger.

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Burger, A.L., Botha, F.C. Cloning of a specific ripening-related gene from the multiple of ripening-related genes identified from a single band excised from a cDNA-AFLP gel. Plant Mol Biol Rep 22, 225–236 (2004). https://doi.org/10.1007/BF02773133

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