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

Comparative and Functional Genomics - Tập 3 Số 4 - Trang 306-318 - 2002
Leonel van Zyl1, Sara von Arnold2, Peter V. Bozhkov2, Yongzhong Chen2, Ulrika Egertsdotter3, John Mackay3, Ronald R. Sederoff1, Jing Shen4, Любов Зелена2, 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, S-750 07 Uppsala, 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

Tóm tắt

AbstractHybridization 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 John Wiley & Sons, Ltd.

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Comparative and Functional Genomics

Tập 3 Số 4

306-318

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