Advertisement

Theoretical and Applied Genetics

, Volume 82, Issue 2, pp 209–216 | Cite as

Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction

  • S. Weining
  • P. Langridge
Originals

Summary

The polymerase chain reaction (PCR) can be used to detect polymorphisms in the length of amplified sequences between the annealing sites of two synthetic DNA primers. When the distance varies between two individuals then the banding pattern generated by the PCR reaction is essentially a genetic polymorphism and can be mapped in the same way as other genetic markers. This procedure has been used in a number of eukaryotes. Here we report the use of PCR to detect genetic polymorphisms in cereals. Known gene sequences can be used to design primers and detect polymorphic PCR products. This is demonstrated with primers to the α-amylase gene family. A second approach is to use semi-random primers to target diverse regions of the genome. For this purpose the consensus sequences at the intron-exon splice junctions were used. The targeting of the intronexon splice junctions in conjunction with primers of random and defined sequences, such as α-amylase, provides a source of extensive variation in PCR products. These polymorphisms can be mapped as standard genetic markers.

Key words

α-Amylase Cereal DNA Genome mapping Intron splice junction Polymerase chain reaction 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Baulcombe DC, Huttly AK, Martienssen RA, Barker RF, Jarvis MG (1987) A novel wheat α-amylase gene (α-Amy3). Mol Gen Genet 209:33–40Google Scholar
  2. Botstein D, White RL, Skonic M, David RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedGoogle Scholar
  3. Brown JW (1986) A catalogue of splice junction and putative branch point sequences from plant introns. Nucleic Acids Res 14:9549–9559Google Scholar
  4. Brown JW, Feix G, Frendewey D (1986) Accurate in vitro splicing of two pre-mRNA plant introns in a HeLa cell nuclear extract. EMBO J 5:2749–2758Google Scholar
  5. Chandler PM, Zwar JA, Jacobsen JV, Higgins TJV, Inglis AS (1984) The effects of gibberellic acid and abscisic acid on α-amylase mRNA levels in barley aleurone layers studies using an α-amylase cDNA clone. Plant Mol Biol 3:407–418Google Scholar
  6. D'Ovidio, R, Tanzarella OA, Porceddu E (1990) Rapid and efficient detection of genetic polymorphism in wheat hrough amplification by polymerase chain reaction. Plant Mol Biol 15:169–171Google Scholar
  7. Erlich HA (1989) PCR technology: principles and applications for DNA amplification. Stockton Press, New YorkGoogle Scholar
  8. Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–269PubMedGoogle Scholar
  9. Goodall GJ, Filipowicz W (1989) The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58:473–483Google Scholar
  10. Hawkins JD (1988) A survey on intron and exon length. Nucleic Acids Res 16:9893–9905Google Scholar
  11. Huttly AK, Martienssen RA, Baulcombe DC (1988) Sequence heterogeneity and differential expression of the α-Amy2 gene family in wheat. Mol Gen Genet 214:232–240Google Scholar
  12. Huynh TV, Young RA, Davis RW (1985) Constructing and screening cDNA libraries in λgt10 and λgt11. In: Glover DM (ed) DNA cloning: a practical approach, vol 1. IRL press, Oxford, pp 49–78Google Scholar
  13. Islam AKRM, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174Google Scholar
  14. Kan Y, Dozy A (1978) Antenatenal diagnosis of sickle-cell anaemia by DNA analysis of amniotic-fluid cells. Lancet 2:910–912Google Scholar
  15. Knox CAP, Sonthayanaon B, Chandra GR, Muthukrishnan S (1987) Structure and organization of two divergent α-amylase genes from barley. Plant Mol Biol 9:3–17Google Scholar
  16. Lai EC, Stein JP, Catterall JF, Woo SLC, Mace ML, Means AR, O'malley BW (1979) Molecular structure and flanking nucleotide sequences of the natural chicken ovomucoid gene. Cell 18:829–842Google Scholar
  17. Lazarus CM, Baucombe DC, Martienssen RA (1985) α-Amylase genes of wheat are two multigene families which are differentially expressed. Plant Mol Biol 5:13–24Google Scholar
  18. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401Google Scholar
  19. Maniatis T, Fritsch EF Sambrook, J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.Google Scholar
  20. Mullis KB, Faloona F (1987) Specific synthesis of DNA in vitro via a polymerase catalysed chain reaction. Methods Enzymol 155:335–350Google Scholar
  21. Muthukrishnan S, Gill BS, Swegle M, Chandra GR (1984) Structural genes for α-amylase are located on barley chromosomes 1 and 6. J Biol Chem 259:13637–13639Google Scholar
  22. Nelson DV, Ledbetter SA, Corbo L, Victoria MF, Ramiro RS, Webster TD, Ledbetter DH, Caskey CT (1989) Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci USA 86:6686–6690Google Scholar
  23. Saiki RK (1989) The design and optimization of the PCR. In: Erlich HA (1989) PCR technology: principles and applications for DNA amplification. Stockton Press, New York, pp 7–15Google Scholar
  24. Saiki RK, Scarf S, Faloona F, Mullks KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle-cell anemia. Science 230:1350–1354PubMedGoogle Scholar
  25. Skolnick MH, Wallace RB (1988) Simultaneous analysis of multiple polymorphic loci using amplified sequence polymorphism (ASPs). Genomics 2:273–279Google Scholar
  26. Sommer R, Tautz D (1989) Minimal homology requirement for PCR. Nucleic Acids Res 17:6749Google Scholar
  27. Streeck RE, Hobom G (1975) Mapping of cleavage sites for restriction endonucleases in λdv plasmid. Eur J Biochem 57:596–606Google Scholar
  28. Tanksley SD, Orton TJ (1983) Isozymes in plant genetics and breeding. Elsevier, AmsterdamGoogle Scholar
  29. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Bio/technology 7:258–264Google Scholar
  30. Tautz D (1989) Hypervariability of simple sequences as a general sources for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedGoogle Scholar
  31. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396PubMedGoogle Scholar
  32. 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 18:6531–6535PubMedGoogle Scholar
  33. Wyman A, White R (1980) A highly polymorphic locus in human DNA. Proc Natl Acad Sci USA 77:6754–6758PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1991

Authors and Affiliations

  • S. Weining
    • 1
  • P. Langridge
    • 1
  1. 1.Centre for Cereal Biotechnology, Waite Agricultural Research Institute, University of AdelaideGlen OsmondAustralia

Personalised recommendations