Heterologous Array Analysis in Pinaceae: Hybridization ofPinus taedacDNA Arrays with cDNA from Needles and Embryogenic Cultures ofP. taeda,P. sylvestrisorPicea abies

Autor: Jing Shen, David H. Clapham, Ronald R. Sederoff, Lyubov Zelena, Ulrika Egertsdotter, Yongzhong Chen, Sara von Arnold, Peter V. Bozhkov, Leonel van Zyl, John MacKay
Rok vydání: 2002
Předmět:
Zdroj: Comparative and Functional Genomics
Comparative and Functional Genomics, Vol 3, Iss 4, Pp 306-318 (2002)
ISSN: 1532-6268
1531-6912
Popis: 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 betweenPinusandPiceawe 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 ofPinus taedawere printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures ofPinus taeda,P. sylvestrisandPicea abies, and with labelled cDNA from leaves ofNicotiana 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.
Databáze: OpenAIRE
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