Functional Genomics

In a first set of attempts to visualize the levels of gene expression in individual tissues, micro-array hybridization technologies have been developed. Here, a library of clones representing as many as possible of the expressed sequences of a genome is distributed by a robot as individual microspots on 1 x 1 cm filters, called microchips. In the case of the yeast (Saccharomyces cerevisiae) genome, such filters contain approximately 6,000 spots. For larger genomes, 10 to 100-fold more clones need to be spotted, but robots capable of applying 50,000 spots per square cm of filter are already available. Another approach (Argonne National Laboratories US together with Packard Motorola and the Engelhardt Institute Moscow) based on polyacrylamide gel pads seems also very promising. Hybridization of these filters with a labeled copy of the total mRNA population of a single cell type reveals the genes that are expressed in these cells. Comparing the variation in expression under different physiological conditions, stress situations, or during development will help us understand how a complex multicel-lular organism functions. Or, as is presently being explored for yeast, how the crosstalk between various biochemical pathways is functioning.3

Nevertheless, an alternative approach will be needed for ecological studies in the tropical forest because such an approach depends on the availability of a complete gene library and because such libraries do not exist for most of the species under study. In these cases, amplified fragment length polymor-phism4 (AFLP)-based mRNA profiling techniques are being developed. AFLP is a very efficient method for the comparison of genomes in taxonomic studies or for the analysis of the outcome of crosses in marker-assisted breeding. As such, the method has been used preferentially for studying plant and microbial genomes, although work with other organisms is currently in progress. mRNA profiling that is based on AFLP allows us to detect rare messengers (down to a level of one in five million). The method is also highly reproducible and can be used to distinguish the expression of different alleles in the case of heterozygotic organisms.

The rapid progress of these technologies should stimulate us to apply them now to forestry studies. Attempting to correlate on the one hand growth characteristics, pathogen resistance, wood quality, seed set and beneficial characteristics in general with the presence of characteristic messengers, on the other hand, is a great challenge.5 However, this information is urgently required because it lies at the basis of future tree selection programs.

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