Update on Genomics Functional Genomics in Plants

The sequencing of the first genome of a higher plant, Arabidopsis, is progressing at a rapid pace. As we are writing these words, almost one-third of the estimated 100 Mb is available in public databases, and with appropriate funding the complete genome sequence is predicted to be finished by the year 2001. Sequencing programs for other plant genomes such as rice are planned, and with new generations of more efficient sequencing machines (Marshall and Pennisi, 1998), the sequence of several other plant genomes may become available in the coming decade. In the wake of these sequencing efforts, plant research enters an exciting period in which genome-wide approaches are becoming an integral part of plant biology, with potentially highly rewarding but as yet unpredictable biotechnological applications. This is reflected by the current frenzy with which new agricultural biotechnical companies are being founded and the rate at which existing companies are investing in the development of tools to exploit and further expand this wealth of information. The term functional genomics can be referred to as the “development and application of global (genome-wide or system-wide) experimental approaches to assess gene function by making use of the information and reagents provided by structural genomics” (Hieter and Boguski, 1997). With these approaches the focus of the analysis is shifted from individual components to biological systems. It involves the use of high-throughput methods for the study of large numbers of genes (ideally the entire set) in parallel. Gene “function” can be considered from several points of view: it can mean biochemical function (e.g. protein kinase), cellular function (e.g. a role in a signal transduction pathway), developmental function (e.g. a role in pattern formation), or adaptive function (the contribution of the gene product to the fitness of the organism). Having identified a new sequence, the comparison with sequence databases is the simplest way to obtain (essentially biochemical) functional information. Currently, about 50% of newly identified genes show sequence similarity to previously described genes. However, computerized analyses are generally not sufficient to define gene function with a high level of confidence, and experimental confirmation is needed in most cases. Indirect information on cellular or developmental function can be obtained from spatial and temporal expression patterns; for example, the presence of mRNA and/or protein in different cell types, during development, during pathogen infection, or in different environments. The subcellular localization and posttranslational modifications of proteins can be informative as well. Knocking out or overexpressing the gene permits the gene sequence to be linked to a phenotype from which a cellular role or a role in development may be deduced. Finally, the fitness of plants carrying mutations or natural variants for the gene can be compared in different environments with wild-type plants to study the adaptive function. In this Update we provide a review of the ever-growing toolbox for the global study of gene function in plants, indicating the potential and the limitations of the different techniques. Where appropriate, we will also draw a parallel with the more advanced technologies in bacterial, yeast, and animal systems.