Seasonal changes in gene expression at the sapwood-heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis.

Heartwood is a determining factor of wood quality and understanding the biology of heartwood may allow us to control its formation. Heartwood formation is a form of senescence that is accompanied by a variety of metabolic alterations in ray parenchyma cells at the sapwood-heartwood transition zone. Although senescence has been studied at the molecular level with respect to primary growth, the cell maturation and death events occurring during heartwood formation have been difficult to study because of their location and timing. Analysis of global gene expression patterns during the transition from sapwood to heartwood may offer a powerful means of identifying the mechanisms controlling heartwood formation. Previously, we developed cDNA microarrays carrying 2567 unigenes derived from the bark/cambium region, sapwood and transition zone of a mature black locust tree. Here, we describe the use of these microarrays to characterize seasonal changes in the expression patterns of 1873 genes from the transition zone of mature black locust trees. When samples collected in summer and fall were compared, 569 genes showed differential expression patterns: 293 genes were up-regulated (> twofold) in summer (July 5) and 276 genes were up-regulated in fall (November 27). More than 50% of the secondary and hormone metabolism-related genes on the microarrays were up-regulated in summer. Twenty-nine out of 55 genes involved in signal transduction were differentially regulated, suggesting that the ray parenchyma cells located in the innermost part of the trunk wood react to seasonal changes. We established the expression patterns of 349 novel genes (previously unknown or no-hit), of which 154 were up-regulated in summer and 195 were up-regulated in the fall.

Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia.

Wood is of critical importance to humans as a primary feedstock for biofuel, fiber, solid wood products, and various natural compounds including pharmaceuticals. The trunk wood of most tree species has two distinctly different regions: sapwood and heartwood. In addition to the major constituents, wood contains extraneous chemicals that can be removed by extraction with various solvents. The composition and the content of the extractives vary depending on such factors as, species, growth conditions, and time of year when the tree is cut. Despite the great commercial and keen scientific interest, little is known about the tree-specific biology of the formation of heartwood and its extractives. In order to gain insight on the molecular regulations of heartwood and its extractive formation, we carried out global examination of gene expression profiles across the trunk wood of black locust (Robinia pseudoacacia L.) trees. Of the 2,915 expressed sequenced tags (ESTs) that were generated and analyzed in the current study, 55.3% showed no match to known sequences. Cluster analysis of the ESTs identified a total of 2278 unigene sets, which were used to construct cDNA microarrays. Microarray hybridization analyses were then performed to survey the changes in gene expression profiles of trunk wood. The gene expression profiles of wood formation differ according to the region of trunk wood sampled, with highly expressed genes defining the metabolic and physiological processes characteristic of each region. For example, the gene encoding sugar transport had the highest expression in the sapwood, while the structural genes for flavonoid biosynthesis were up-regulated in the sapwood-heartwood transition zone. This analysis also established the expression patterns of 341 previously unknown genes.