Skip to main content
Log in

Partial sequencing and mapping of clones from two maize cDNA libraries

  • Research Article
  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

As one component of a maize genome project, we report the analysis of a number of randomly selected cDNAs, by a combination of measuring mRNA expression, ‘single-pass’ sequencing (SPS), and genome mapping. Etiolated seedling (490) and membrane-free polysomal endosperm cDNA clones (576) were evaluated for their transcription levels by hybridizing with a probe prepared from total mRNA and categorized as corresponding to abundantly or rarely expressed mRNAs and as either constitutive or tissue-specific. A total of 313 clones from the two libraries were submitted to ‘single-pass’ sequencing from the presumed 5′ end of the mRNA and the nucleotide sequence compared with the GenBank database. About 61% of the clones showed no significant similarities within GenBank, 14% of the clones exhibited a high degree of similarity, while the remaining 25% exhibited a lesser degree of similarity. The chromosomal location of more than 300 clones was determined by RFLP mapping using standard populations. The results demonstrate that a combination of analyses provides synergistic information in eventually deducing the actual function of these types of clones.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Ploymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter C: Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651–1656 (1991).

    PubMed  Google Scholar 

  2. Adams MD, Dubnick M, Kerlavage AR, Moreno R, Kelley JM, Utterback TR, Nagle JW, Fields C, Venter JC: Sequence identification of 2375 human brain genes. Nature 355: 632–634 (1992).

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  4. Aarts MGM, Dirkse WG, Stiekema WJ, Pereira A: Transposon tagging of a male sterility gene in Arabidopsis. Science 363: 715–717 (1993).

    Google Scholar 

  5. Boguski MS, Lowe TMJ, Tolstoshev CM: dbEST-database for ‘expressed sequence tags”. Nature Genet 4: 332–333, 1993.

    Article  PubMed  Google Scholar 

  6. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW: Gene mapping with recombinant inbreds in maize. Genetics 118: 519–526 (1988).

    PubMed  Google Scholar 

  7. Clark L, Carbon J: Isolation of a yeast centromere and construction of small functional circular chromosomes. Nature 287: 504–509 (1980).

    PubMed  Google Scholar 

  8. Chomzynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenolchloroform extraction. Analytical Biochem 162: 156–159 (1987).

    Article  Google Scholar 

  9. CoeJr EH, Neuffer MG, Hoisington DA: The Genetics of Corn. In: Sprague GF, Dudley JW (eds) Corn and Corn Improvement, 3rd ed., pp. 81–258. ASA, CSSA, SSSA Publishers, Madison, WI (1988).

    Google Scholar 

  10. Joshi CP: An inspection of the domain between putative TATA box and translation start site in 79 plants. Nucl Acid Res 15: 6643–6653 (1987).

    Google Scholar 

  11. Habben JE, Kirleis AW, Larkins BA: The origin of lysine-containing proteins in opaque-2 maize endosperm. Plant Mol Biol 23: 825–838 (1993).

    Article  PubMed  Google Scholar 

  12. Helentjaris T: A geneticlinkage map for maize based on RFLPs. Trends Genet 3: 217–221 (1987).

    Article  Google Scholar 

  13. Hodge R, Paul W, Draper J, Scott R: Cold-plaque screening: a simple technique for the isolation of low abundance, differentially expressed transcripts from conventional libraries. Plant J 2: 257–260 (1992).

    Google Scholar 

  14. Hofte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon M, Charpenteau JL, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu DY, Mache R, Raynal M, Cooke R, Grellet F, Delseny M, Parmentier Y, Marcillac GD, Gigot C, Fleck J, Philipps G, Axelos M, Bardet C, Tremousaygue, Lescure G: An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 4: 1051–1061 (1993).

    Article  PubMed  Google Scholar 

  15. Hoog C: Isolation of large number of novel mammalian genes by a differential cDNA library screening strategy. Nucl Acids Res 19: 6123–6127 (1991).

    PubMed  Google Scholar 

  16. Keith CS, Hoang DO, Barrett BM, Feigelman B, Nelson MC, Thai H, Baysdorfer C: Partial sequence-analysis of 130 randomly selected maize cDNA clones. Plant Physiol 101: 329–332 (1993).

    Article  PubMed  Google Scholar 

  17. Kouchi H, Hata S: Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development. Mol Gen Genet 238: 106–109 (1993).

    PubMed  Google Scholar 

  18. Ma H, Yanofsky MF, Meyerowitz EM: AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Devel 5: 484–495 (1991).

    PubMed  Google Scholar 

  19. McCreery T, Helentjaris T: Production of hybridization probes by the PCR utilizing digoxigenin-modified nucleotides. In: Isaac PG (ed) Protocols for Nucleic Acid Analysis by Nonradioactive Probes, pp. 67–72. Humana Press, New Jersey (1994).

    Google Scholar 

  20. McCreery T, Helentjaris T: Hybridization of digoxigenin-labeled probes to Southern Blots and detection by chemiluminescence. In: Isaac PG (ed) Protocols for Nucleic Acid Analysis by Nonradioactive Probes, pp. 107–112. Humana Press, New Jersey (1994).

    Google Scholar 

  21. Neuffer MG, Jones L, Zuber MS: The Mutants of Maize. Crop Science Society of America, Wisconsin (1968).

    Google Scholar 

  22. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467 (1977).

    PubMed  Google Scholar 

  23. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).

    Google Scholar 

  24. Shattuck-Eidens DM, Bell RN, Neuhausen SL, Helentjaris T: DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing. Genetics 126: 207–217 (1990).

    PubMed  Google Scholar 

  25. Park YS, Kwak JM, Kwon OY, Kim YS, Lee DS, Cho MJ, Lee HH, Nam HG: Generation of expressed sequence tags of random root cDNA clones of Brassica napus by single-run partial sequencing. Plant Physiol 103: 359–370 (1993).

    PubMed  Google Scholar 

  26. Singleton CK, Delude RL, Ken R, Manning SS, McPherson CE: Structure, expression, and regulation of members of the developmentally controlled V and H gene classes from Dictyotelium. Devel Genet 12: 88–97 (1991).

    Google Scholar 

  27. Uchimiya H, Kidou SI, Shimazaki T, Aotsuka S, Takamatsu S, Nishi R, Hashimoto H, Matsubayashi Y, Kidou N, Umeda M, Kato A: Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice (Oryza sativa L). Plant J 2: 1005–1009 (1992).

    Google Scholar 

  28. Waterston R, Martin C, Craxton M, Huynh C, Coulson A, Hillier L, Durbin R, Green P, Shownkeen R, Halloran N, Metzstein M, Hawkins T, Wilson R, Berks M, Du Z, Thomas K, Thierrymieg J, Sulston J: A survey of expressed genes in Caenorhabditis elegans. Nature Genet 1: 114–123 (1992).

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shen, B., Carneiro, N., Torres-Jerez, I. et al. Partial sequencing and mapping of clones from two maize cDNA libraries. Plant Mol Biol 26, 1085–1101 (1994). https://doi.org/10.1007/BF00040691

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00040691

Key words

Navigation