Project name: Evolution of Gene Expression in Spruce (Genus Picea)

Description: Diversification of defense-related compounds is a plant defense mechanism against the diverse array of natural enemies in the course of evolution, and is known to involve various sources of tissue. Here a large-scale survey of gene expression is conducted from three different sources of tissue; needles, phloem with the attached bark, and xylem, with an emphasis on the expression of the secondary metabolites of the core phenylpropanoid pathway and derivative pathways, taken together as phenolic defense-related compounds. Five species of spruce; P. abies, P. glauca, P. jezoensis, P. mariana, and P. omorika, spanning much of their known phylogeny, are chosen for cross-species microarray hybridizations.The objectives are: first) to explore the tissue-related differences in the expression of phenolic genes and their coherent role in tree defense; second) to describe the diversification trends in the expression of phenolic gene families with respect to their position in the pathway; and third) to infer the mode of evolution underlying the expression of the selected genes.Overall design: Trees at the arboretum of Kalamalka Research Station, Vernon, BC, Canada (http://www.for.gov.bc.ca/hre/forgen/rstations.htm#Kalamalka_Research_Station) were designated for sampling. Three biological replicates of Black spruce (Picea mariana), Jezo spruce (P. jezoensis), Norway spruce (P. abies), Serbian spruce (P. omorika), and White spruce (P. glauca) were sampled. The bark and the attached phloem were separated from inner layers, and the xylem tissue was scraped off. The fresh current-year needles were pooled from different aerial branches on the mid-afternoon of Apr. 24, 2007, flash-frozen in liquid nitrogen, and transferred into separate containers.A modified loop design was decided for gene expression profiling with 15 cross-species hybridizations per each source of tissue (total of 45 slides) using the Treenomix third generation cDNA microarray platform (GEO accession #: GPL5423). Array350 kit (Genisphere, Hatfield, USA) was chosen for the microarray hybridizations of needle and bark/phloem sources of tissue. Due to the lower yield of RNA extraction, microarray hybridization of the xylem tissue used Array900 (Genisphere, Hatfield, USA).The slides were scanned with a ProScanArray scanner (PerkinElmer, Downers Grove, IL, USA), and the scanned TIF images were processed by ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA)to quantify spot intensities. The spot intensities were normalized with the variance stabilizing (VSN) method, and the normalized log channel intensities were analyzed by fitting a linear mixed effects model.

Data type: Transcriptome or Gene expression

Sample scope: Multispecies

Relevance: Agricultural

Release date: 2009-10-10

Last updated: 2009-10-02