Skip to main content
NCBI home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2002 Aug;3(4):306–318. doi: 10.1002/cfg.199

Heterologous Array Analysis in Pinaceae: Hybridization of Pinus Taeda cDNA Arrays With cDNA From Needles and Embryogenic Cultures of P. Taeda, P. Sylvestris or Picea Abies

Leonel van Zyl 1, Sara von Arnold 2, Peter Bozhkov 2, Yongzhong Chen 2, Ulrika Egertsdotter 3, John MacKay 3, Ronald R Sederoff 1, Jing Shen 4, Lyubov Zelena 2, David H Clapham 2,✉
PMCID: PMC2448427  PMID: 18629264

Abstract

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.

Full Text

The Full Text of this article is available as a PDF (196.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allona I., Quinn M., Shoop E., Swope K., St Cyr S., Carlis J., Riedl J., Retzel E., Campbell M. M., Sederoff R. Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9693–9698. doi: 10.1073/pnas.95.16.9693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Gagneux P., Varki A. Genetic differences between humans and great apes. Mol Phylogenet Evol. 2001 Jan;18(1):2–13. doi: 10.1006/mpev.2000.0799. [DOI] [PubMed] [Google Scholar]
  3. Gibbons A. Which of our genes makes us human? Science. 1998 Sep 4;281(5382):1432–1434. doi: 10.1126/science.281.5382.1432. [DOI] [PubMed] [Google Scholar]
  4. Girke T., Todd J., Ruuska S., White J., Benning C., Ohlrogge J. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 2000 Dec;124(4):1570–1581. doi: 10.1104/pp.124.4.1570. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hegde P., Qi R., Abernathy K., Gay C., Dharap S., Gaspard R., Hughes J. E., Snesrud E., Lee N., Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556 passim. doi: 10.2144/00293bi01. [DOI] [PubMed] [Google Scholar]
  6. Heller R. A., Schena M., Chai A., Shalon D., Bedilion T., Gilmore J., Woolley D. E., Davis R. W. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2150–2155. doi: 10.1073/pnas.94.6.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hertzberg M., Sievertzon M., Aspeborg H., Nilsson P., Sandberg G., Lundeberg J. cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol. Plant J. 2001 Mar;25(5):585–591. doi: 10.1046/j.1365-313x.2001.00972.x. [DOI] [PubMed] [Google Scholar]
  8. Kerr M. K., Martin M., Churchill G. A. Analysis of variance for gene expression microarray data. J Comput Biol. 2000;7(6):819–837. doi: 10.1089/10665270050514954. [DOI] [PubMed] [Google Scholar]
  9. Lee M. L., Kuo F. C., Whitmore G. A., Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9834–9839. doi: 10.1073/pnas.97.18.9834. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Logemann J., Schell J., Willmitzer L. Improved method for the isolation of RNA from plant tissues. Anal Biochem. 1987 May 15;163(1):16–20. doi: 10.1016/0003-2697(87)90086-8. [DOI] [PubMed] [Google Scholar]
  11. Maleck K., Levine A., Eulgem T., Morgan A., Schmid J., Lawton K. A., Dangl J. L., Dietrich R. A. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet. 2000 Dec;26(4):403–410. doi: 10.1038/82521. [DOI] [PubMed] [Google Scholar]
  12. Richmond C. S., Glasner J. D., Mau R., Jin H., Blattner F. R. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 1999 Oct 1;27(19):3821–3835. doi: 10.1093/nar/27.19.3821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Richmond T., Somerville S. Chasing the dream: plant EST microarrays. Curr Opin Plant Biol. 2000 Apr;3(2):108–116. doi: 10.1016/s1369-5266(99)00049-7. [DOI] [PubMed] [Google Scholar]
  14. Ruan Y., Gilmore J., Conner T. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 1998 Sep;15(6):821–833. doi: 10.1046/j.1365-313x.1998.00254.x. [DOI] [PubMed] [Google Scholar]
  15. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  16. Whetten R., Sun Y. H., Zhang Y., Sederoff R. Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol Biol. 2001 Sep;47(1-2):275–291. [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES