A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis

Abstract

Background: Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. The most serious problem affecting the quality and yield of solid wood products is the occurrence of end splitting in logs. Selection of E. grandis planting stock that exhibit preferred wood qualities is thus a priority of the South African forestry industry. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven different E. grandis trees.

Results: A 1578-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP clones and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated.

Conclusion: A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.

Figure 1

Hierarchical clustering of expression patterns. A. Hierarchical clustering of 1578 differentially expressed tissue profiles from the combined cDNA array. Relative expression levels (median centered and standardized values) are represented by a continuum with green signifying relative low expression of the ESTs, black indicating moderate expression (relative up-regulation) in the respective tissues, and red indicating high expression. The rows correspond to the quantified ESTs and columns to the respective E. grandis trees. LS: low splitting, HS: high splitting, H: high lignin, and L: low lignin, all collected from the lower-half of the stem. The transcripts have been divided into 10 expression pattern clusters as indicated by the numbers 1–10. B. Graphs of expression pattern clusters. Vertical axes in B represent standard deviation from the median expression level of each gene. The location of each cluster is indicated in A.