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

摘要

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 sequenceconservation 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 threeconifer species was lower but sufficiently high (r2= 0.52 ? 0.63) to suggest that manypartial gene sequences are conserved in angiosperms and gymnosperms. Heterologousprobing was further used to identify tissue-specific gene expression over speciesboundaries. To evaluate the significance of differences in gene expression, conventionalparametric tests were compared with permutation tests after four methods ofnormalization. Permutation tests after Z-normalization provide the highest degreeof discrimination but may enhance the probability of type I errors. It is concludedthat arrays of cDNA from loblolly pine are useful for studies of gene expression inother pines or spruces.