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Molecular Breeding

, Volume 12, Issue 2, pp 107–118 | Cite as

Sequence variation in two lignin biosynthesis genes, cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase 2 (CAD2)

  • Fiona S. Poke
  • René E. Vaillancourt
  • Robert C. Elliott
  • James B. Reid
Article

Abstract

Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase 2 (CAD2) are genes which may influence variation in lignin content and composition within plants. Sequence variation within these genes may be responsible for changes in enzyme activity and/or specificity, which could cause variation in lignin content or composition. This study examines sequence variation within these two genes in Eucalyptus globulus, an important species used in pulp and paper-making. Twenty-one single nucleotide polymorphisms (SNPs) were identified in the exons of CCR, of which nine were neutral mutations and 12 were missense mutations. Six of the missense mutations affected highly conserved amino acids within the protein sequence of CCR. Eight SNPs were identified in the CAD2 exons, six of which were neutral mutations and two which were missense mutations. One of the missense mutations affected a highly conserved amino acid within the protein sequence. In addition, 32 SNPs were identified in the CCR introns along with four insertion/deletions and two polyA length variation regions. Polymorphism affecting highly conserved amino acids may alter enzyme function and this molecular variation may be linked to variation in lignin profiles. Selecting positive alleles which produce favourable lignin profiles would be advantageous in tree breeding programs.

Candidate genes Eucalypt genetics Eucalyptus globulus Lignin Single nucleotide polymorphism 

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References

  1. Baucher M., Monties B., Van Montagu M. and Boerjan W. 1998. Biosynthesis and genetic engineering of lignin. Crit. Rev. Plant Sci. 17: 125–197.Google Scholar
  2. Boudet A.-M., Chabannes M., Goffner D., Lapierre C., Piquemal J., Petit-Conil M. et al. 1998. Controlled down-regulation of genes involved in the last steps of lignin synthesis may significantly change the lignin profiles of plants. In: Proceedings of the Molecular Breeding of Woody Species. Tokyo, Japan, pp. 1–21.Google Scholar
  3. De Melis L.E., Whiteman P.H. and Stevenson T.W. 1999. Isolation and characterisation of a cDNA clone encoding cinnamyl alcohol dehydrogenase in Eucalyptus globulus Labill. Plant Sci. 143: 173–182.Google Scholar
  4. Dimmel D.R., MacKay J.J., Althen E.M., Parks C. and Sederoff R.R. 2001. Pulping and bleaching of CAD-deficient wood. J. Wood Chem. Technol. 21: 1–17.Google Scholar
  5. Doyle J.J. and Doyle J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13–15.Google Scholar
  6. Dutkowski G.W. and Potts B.M. 1999. Geographic patterns of genetic variation in Eucalyptus globulus ssp. globulus and a revised racial classification. Aust. J. Bot. 47: 237–263.Google Scholar
  7. Gardiner C.A. and Crawford D.F. 1987. 1987 Seed collections of Eucalyptus globulus subsp. globulus for tree improvement purposes. CSIRO Division of Forest Research, Canberra.Google Scholar
  8. Gardiner C.A. and Crawford D.F. 1988. 1988 Seed collections of Eucalyptus globulus subsp. globulus Labill. for tree improvement purposes. CSIRO Division of Forestry and Forest Products, Canberra.Google Scholar
  9. Gaut B.S. and Clegg M.T. 1993. Molecular evolution of the Adh1 locus in the genus Zea. Proc. Natl. Acad. Sci. USA 90: 5095–5099.Google Scholar
  10. Gion J.M., Boudet C., Grima-Pettenati J., Pichavant F.H., Plomion C., Baillères H. et al. 2001. A candidate genes approach identifies CCR, PAL and C4H as loci for syringyl/guaiacyl ratio in a interspecific hybrid between E. urophylla and E. grandis. In: Barros S. (ed.), Developing the Eucalypt of the Future. Proceedings of IUFRO International Symposium 10-15th September 2001, Valdivia, Chile.Google Scholar
  11. Goffner D., Campbell M.M., Campargue C., Clastre M., Borderies G., Boudet A. et al. 1994. Purification and characterisation of cinnamoyl-coenzyme A:NADP oxidoreductase in Eucalyptus gunnii. Plant Physiol. 106: 625–632.Google Scholar
  12. Goffner D., Joffroy I., Grima-Pettenati J., Halpin C., Knight M.E., Schuch W. et al. 1992. Purification and characterization of isoforms of cinnamyl alcohol dehydrogenase from Eucalyptus xylem. Planta 188: 48–53.Google Scholar
  13. Grima-Pettenati J., Feuillet C., Goffner D., Borderies G. and Boudet A.M. 1993. Molecular cloning and expression of a Eucalyptus gunnii cDNA clone encoding cinnamyl alcohol dehydrogenase. Plant Mol. Biol. 21: 1085–1095.Google Scholar
  14. Hawkins S., Goffner D. and Boudet A.M. 1994. Cinnamyl alcohol dehydrogenase polymorphism and its potential role in the control of lignin heterogeneity. In: International Symposium on Natural Phenols in Plant Resistance. Weihenstephan, Germany, pp. 280–286.Google Scholar
  15. Hibberd A.I., Wearne R.H. and Wallis A.F.A. 1999. Effect of variation in the aromatic units of lignin in plantation eucalypt woods on pulping quality. In: Proceedings 53rd Appita annual conference. APPITA, Rotorua, New Zealand, pp. 19–22.Google Scholar
  16. Jones L., Ennos A.R. and Turner S.R. 2001. Cloning and characterization of irregular xylem4 (irx4): a severely lignin-deficient mutant of Arabidopsis. Plant J. 26: 205–216.Google Scholar
  17. Kawabe A., Yamane K. and Miyashita N.T. 2000. DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arabidopsis thaliana. Genetics 156: 1339–1347.Google Scholar
  18. Lacombe E., Hawkins S., Van Doorsselaere J., Piquemal J., Goffner D., Poeydomenge O. et al. 1997. Cinnamoyl coA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. Plant J. 11: 429–441.Google Scholar
  19. Lewin B. 1997. Genes VI. Oxford University Press, New York.Google Scholar
  20. Mackay T.F. 2001. Quantitative trait loci in Drosophila. Nat. Rev. Genet. 2: 11–20.Google Scholar
  21. McCarthy L.C., Hosford D.A., Riley J.H., Bird M.I., White N.J., Hewett D.R. et al. 2001. Single-nucleotide polymorphism alleles in the insulin receptor gene are associated with typical migraine. Genomics 78: 135–149.Google Scholar
  22. Miranda I. and Pereira H. 2001. Provenance effect on wood chemical composition and pulp yield for Eucalyptus globulus Labill. Appita J. 54: 347–351.Google Scholar
  23. Nesbitt K.A., Potts B.M., Vaillancourt R.E., West A.K. and Reid J.B. 1995. Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae). Hered. 74: 628–637.Google Scholar
  24. Ohta T. 1993. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. USA 90: 4548–4551.Google Scholar
  25. Pichon M., Courbou I., Beckert M., Boudet A.M. and Grima-Pettenati J. 1998. Cloning and characterisation of two maize cDNAs encoding cinnamoyl-coA reductase (CCR) and differential expression of the corresponding genes. Plant Mol. Biol. 38: 671–676.Google Scholar
  26. Piquemal J., Lapierre C., Myton K., O'Connell A., Schuch W., Grima-Pettenati J. et al. 1998. Down-regulation of cinnamoyl-coA reductase induces significant changes of lignin profiles in transgenic tobacco plants. Plant J. 13: 71–83.Google Scholar
  27. Potts B.M., Barbour R.C., Hingston A. and Vaillancourt R.E. 2003. Turner Review No. 6: Genetic pollution of native eucalypt gene pools, identifying the risks. Aust. J. Bot. 51: 1–25.Google Scholar
  28. Rafalski A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94–100.Google Scholar
  29. Ralph J., MacKay J.J., Hatfield R.D., O'Malley D.M., Whetten R.W. and Sederoff R.R. 1997. Abnormal lignin in a loblolly pine mutant. Science 277: 235–239.Google Scholar
  30. Rodrigues J., Meier D., Faix O. and Pereira H. 1999. Determination of tree to tree variation in syringyl/guaiacyl ratio of Eucalyptus globulus wood lignin by analytical pyrolysis. J. Anal. Appl. Pyrolysis 48: 121–128.Google Scholar
  31. Singh S.V., Kumari R. and Guha S.R.D. 1982. Lignin composition and its influence on kinetics of kraft pulping tropical hardwoods. Indian Pulp Paper 1: 5–16.Google Scholar
  32. Syvånen A.-C., Landegren U., Isaksson A., Gyllensten U. and Brookes A. 1999. Enthusiasm mixed with scepticism about single-nucleotide polymorphism markers for dissecting complex disorders. Eur. J. Human Genetics 7: 98–101.Google Scholar
  33. Tenaillon M.I., Sawkins M.C., Long A.D., Gaut R.L., Doebley J.F. and Gaut B.S. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98: 9161–9166.Google Scholar
  34. Terauchi R., Terachi T. and Miyashita N.T. 1997. DNA polymorphism at the Pgi locus of a wild yam, Dioscorea tokoro. Genetics 147: 1899–1914.Google Scholar
  35. Wallis A.F.A., Wearne R.H. and Wright P.J. 1996. Analytical characteristics of plantation eucalypt woods relating to kraft pulp yields. Appita J. 49: 427–432.Google Scholar
  36. Wood M.S., Stephens N.C., Allison B.K. and Howell C.I. 2001. Plantations of Australia - A Report from the National Plantation Inventory and the National Farm Forest Inventory. Bureau of Rural Sciences, Canberra.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Fiona S. Poke
    • 1
    • 2
  • René E. Vaillancourt
    • 1
    • 2
  • Robert C. Elliott
    • 2
  • James B. Reid
    • 1
    • 2
  1. 1.Cooperative Research Centre for Sustainable Production ForestryUniversity of TasmaniaAustralia
  2. 2.School of Plant ScienceUniversity of TasmaniaHobartAustralia

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