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Functional genomics and cell wall biosynthesis in loblolly pine

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Abstract

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.

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References

  • Allona, I., Quinn, M., Shoop, E., Swope, K., St. Cyr, S., Carlis, J., Riedl, J., Retzel, E., Campbell, M.M., Sederoff, R. and Whetten, R. 1998. Analysis of xylem formation in pine by cDNA sequencing. Proc. Natl. Acad. Sci. USA 95: 9693–9698.

    Google Scholar 

  • Altschul, S.F., Madden, T.L., Schaffer, A.A, Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389–3402.

    Google Scholar 

  • Audic, S. and Claverie, J.M. 1997 The significance of digital gene expression profiles. Genome Res. 7: 986–995. Software available through http://igs-server.cnrs-mrs.fr

    Google Scholar 

  • Bennett, M.D. and Leitch, I.J. 1995. Nuclear DNA amounts in angiosperms. Ann. Bot. 76: 113–176.

    Google Scholar 

  • Biermann, C.J. 1993. Essentials of pulping and papermaking. Academic Press, San Diego, CA.

    Google Scholar 

  • Chapple, C. and Carpita, N. 1998. Plant cell walls as targets for biotechnology. Curr. Opin. Plant Biol. 1: 179–185.

    Google Scholar 

  • Diatchenko, L., Lau, Y.F., Campbell, A.P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E.D. and Siebert P.D. 1996. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA. 93: 6025–6030.

    Google Scholar 

  • Dhugga, K.S., Tiwari, S.C. and Ray, P.M. 1997. A reversibly glycosylated polypeptide (RGP1) possibly involved in plant cell wall synthesis: purification, gene cloning, and trans-Golgi localization. Proc. Natl. Acad. Sci. USA 94: 7679–7684.

    Google Scholar 

  • Dunnett, C.W. 1955. A multiple comparison procedure for comparing several treatments with a control. J. Am. Statist. Ass. 50: 1096–1121.

    Google Scholar 

  • Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863–14868.

    Google Scholar 

  • Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186–194.

    Google Scholar 

  • Friedman, N., Linial, M., Nachman, I. and Pe'er, D. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol., in press.

  • Harada, H. and Côté, W.A. 1985. The structure of wood. In: T. Higuchi (Ed.) Biosynthesis and Biodegradation of Wood Components, Academic Press, Orlando, FL, pp. 1–42.

    Google Scholar 

  • Higuchi, T. 1997. Biochemistry and Molecular Biology of Wood. Springer-Verlag, Berlin.

    Google Scholar 

  • Kamm, A., Doudrick, R.L., Heslop-Harrison, J.S. and Schmidt, T. 1996. The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc. Natl. Acad. Sci. USA 93: 2708–2713.

    Google Scholar 

  • Kerr, M.K. and Churchill, G.A. 2000. Experimental design for gene expression microarrays. Submitted; manuscript available at http://www.jax.org/research/churchill/pubs/index.html.

  • Kerr, M.K., Martin, M. and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. Submitted; manuscript available at http://www.jax.org/research/churchill/pubs/index.html.

  • Kinlaw, C.S., Ho, T., Gerttula, S.M., Gladstone, E. and Harry, D.E. 1996. Gene discovery in loblolly pine through cDNA sequencing. In: Somatic Cell Genetics and Molecular Genetics of Trees Forestry Sciences vol. 49), Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 175–182.

    Google Scholar 

  • Kinlaw, C. and Neale, D. 1997. Complex gene families in pine genomes. Trends Plant Sci. 2: 356–359.

    Google Scholar 

  • Kossack, D. 1989. The IFG copia-like element: characterization of a transposable element present in high copy number in Pinus and a history of the pines using IFG as a marker. Ph.D. dissertation, University of California at Davis, CA.

  • Kossack, D.S. and Kinlaw, C.S. 1999 IFG, a gypsy-like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol. Biol. 39: 417–426.

    Google Scholar 

  • Kriebel, H.B. 1985. DNA Sequence components of Pinus strobus nuclear genome. Can. J. For. Res. 15: 1–4.

    Google Scholar 

  • Lewin, M. and Goldstein, I.S. 1991. Wood Structure and Composition. Marcel Dekker, New York.

    Google Scholar 

  • Loopstra, C.A. and Sederoff, R.R. 1995. Xylem-specific gene expression in loblolly pine. Plant Mol. Biol. 27: 277–291.

    Google Scholar 

  • Loopstra, C.A., Puryear, J.D. and No, E.G. 2000. Purification and cloning of an arabinogalactan-protein from xylem of loblolly pine. Planta 210: 686–689.

    Google Scholar 

  • Megraw, R.A. 1985. Wood Quality Factors in Loblolly Pine: the influence of tree age, position in tree, and cultural practice on wood specific gravity, fiber length, and fibril angle. TAPPI Press, Atlanta, GA.

    Google Scholar 

  • Mellerowicz, E.J., Baucher, M., Sundberg, B. and Boerjan, W. 2001. Unravelling cell wall formation in the woody dicot stem. Plant Mol. Biol., this issue.

  • Meyer-Berthaud, B., Scheckler, S.E. and Wendt, J. 1999. Archaeopteris is the earliest known modern tree. Nature 398: 700–701.

    Google Scholar 

  • Murray, B.G. 1998. Nuclear DNA amounts in gymnosperms. Ann. Bot. 82: 3–15.

    Google Scholar 

  • Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R. and Tsui, K.W. 2000. On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. J. Comput. Biol., in press.

  • O'Malley, D., Whetten, R., Bao, W., Chen, C.-L. and Sederoff, R.R. 1993. The role of laccase in lignification. Plant J. 4: 751–757.

    Google Scholar 

  • O'Malley, D.M., Grattapaglia, D., Chaparro, J.X., Wilcox, P.L., Amerson, H.V., Liu, B.-H., Whetten, R., McKeand, S.E., Kuhlman, E.G., McCord, S., Crane, B. and Sederoff, R.R. 1996. Molecular markers, forest genetics and tree breeding. In: J.P Gustafson and R.B. Flavell (Eds.) Genomes of Plants and Animals: Proceedings of the 21st Stadler Symposium (Columbia, MO), Plenum, New York, pp. 87–102.

  • 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 

  • Reiter, W.D. 1998. The molecular analysis of cell wall components. Trends Plant Sci. 3: 27–32.

    Google Scholar 

  • Saltman, D., Thompson, L. and Bennett, K.M. 1998. Pulp and Paper Primer. TAPPI Press, Atlanta, GA.

    Google Scholar 

  • Schouten, J., de Kam, R.J., Fetter, K. and Hoge, J.H. 2000. Over-expression of Arabidopsis thaliana SKP1 homologues in yeast inactivates the Mig1 repressor by destabilising the F-box protein Grr1. Mol. Gen. Genet. 263: 309–319.

    Google Scholar 

  • Sederoff, R., Campbell, M., O'Malley, D. and Whetten, R. 1994. Genetic regulation of lignin biosynthesis and the potential modification of wood by genetic engineering in loblolly pine. Rec. Adv. Phytochem. 28: 313–355.

    Google Scholar 

  • Somerville, C. and Somerville, S. 1999. Plant functional genomics. Science 285: 380–383.

    Google Scholar 

  • Somssich, I.E., Wernert, P., Kiedrowski, S. and Hahlbrock, K. 1996. Arabidopsis thaliana defense-related protein ELI3 is an aromatic alcohol:NADP(+) oxidoreductase. Proc. Natl. Acad. Sci. USA 93: 14199–14203.

    Google Scholar 

  • Sterky, F., Regan, S., Karlsson, J., Hertzberg, M., Rohde, A., Holmberg, A., Amini, B., Bhalerao, R., Larsson, M., Villarroel, R., Van Montagu, M., Sandberg, G., Olsson, O., Teeri, T.T., Boerjan, W., Gustafsson, P., Uhlen, M., Sundberg, B. and Lundeberg, J. 1998. Gene discovery in the wood-forming tissues of poplar: analysis of 5692 expressed sequence tags. Proc. Natl. Acad. Sci. USA 95: 13330–13335.

    Google Scholar 

  • Timell, T.E. 1986 Compression Wood in Gymnosperms (3 vols.). Springer-Verlag, Berlin.

    Google Scholar 

  • Wakamiya, I., Newton, R.J., Johnston, J.S. and Price, H.J. 1993. Genome size and environmental factors in the genus Pinus.Am. J. Bot. 80: 1235–1241.

    Google Scholar 

  • Winzeler, E.A., Schena, M. and Davis, R.W. 1999. Fluorescence-based expression monitoring using microarrays. Meth. Enzymol. 306: 3–18.

    Google Scholar 

  • Wojtaszek, P. 2000. Genes and plant cell walls: a difficult relationship. Biol. Rev. Camb. Phil. Soc. 75: 437–475.

    Google Scholar 

  • Wolfinger, R.D., Gibson, G., Wolfinger, E.D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C. and Paules, R.S. 2000. Assessing gene significance from cDNA microarray expression data via mixed models. Manuscript available from http://statgen.ncsu.edu/ggibson/Publications/WGetc.pdf

  • Zhang, Y., Sederoff, R.R. and Allona, I. 2000. Differential expression of genes encoding cell wall proteins in vascular tissues from vertical and bent pine trees. Tree Physiol 20: 457–466.

    Google Scholar 

  • Zobel, B.J. and Sprague, J.R. 1998. Juvenile Wood in Forest Trees. Springer-Verlag, Berlin.

    Google Scholar 

  • Zobel, B.J. and van Buitenen, J. P.1989. Wood Variation: Its Causes and Control. Springer-Verlag, Berlin.

    Google Scholar 

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Authors and Affiliations

  1. Forest Biotechnology Group, North Carolina State University, 2500 Partners II, Centennial Campus, Campus Box 7247, Raleigh, NC , 27695, USA

    Ross Whetten, Ying-Hsuan Sun, Yi Zhang & Ron Sederoff

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  1. Ross Whetten
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  2. Ying-Hsuan Sun
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  3. Yi Zhang
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  4. Ron Sederoff
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Whetten, R., Sun, YH., Zhang, Y. et al. Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol Biol 47, 275–291 (2001). https://doi.org/10.1023/A:1010652003395

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