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International Journal of Genomics

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International Journal of Genomics / 2002 / Article

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Research Article | Open Access

Volume 3 |Article ID 186124 | https://doi.org/10.1002/cfg.199

Leonel van Zyl, Sara von Arnold, Peter Bozhkov, Yongzhong Chen, Ulrika Egertsdotter, John MacKay, Ronald R. Sederoff, Jing Shen, Lyubov Zelena, David H. Clapham, "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", International Journal of Genomics, vol. 3, Article ID 186124, 13 pages, 2002. https://doi.org/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 and David H. Clapham2

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

2Department of Forest Genetics, Swedish University of Agricultural Sciences, Box 7027, Uppsala S-750 07, Sweden

3Institute of Paper Science and Technology, Forest Biology Group, 500 10th Street NW, Atlanta, GA 30318, USA

4Bioinformatics Research Center, Centennial Campus, North Carolina State University, Raleigh, NC 27695, USA

Received04 Mar 2002
Accepted14 Jun 2002

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.

Copyright © 2002 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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