The use of functional genomics to understand components of plant metabolism and the regulation occurring at molecular, cellular and whole plant levels

The completion of the genome sequence of the small weed plant Arabidopsis thaliana (The Arabidopsis genome initiative 2000), and more recently of rice (Goff et al. 2002; Yu et al. 2002, 2005), has greatly changed the face of plant biology. Knowing the exact sequence and location of all the genes of a given organism is the first step towards understanding how all parts of a biological system work together. Information about the hypothesized function of an unknown gene may be deduced from its sequence homology to other genes of known function. However, genome sequencing projects have revealed the existence of a tremendous amount of biological diversity, with large proportion of genes sharing no homology to genes with known or hypothesized functions. In this respect functional genomics is the key approach to transforming quantity into quality (Borevitz and Ecker 2004; Holtfort et al. 2002). Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes. For efficient gene function analysis, researchers can choose from a multitude of different methods, most of them derived from genomic research performed on model organisms such as yeast, nematodes, flies and mice, not forgetting the technological spin-offs that were inspired by the human genome project. Arabidopsis populations, mutagenized by random insertion of T-DNA or transposon elements, have been generated with the aim to perform highthroughput reverse genetics studies and comprehensive forward genetics studies of the entire gene compendium (Alonso et al. 2003). Additionally, information about the spatial and temporal expression pattern of a gene can be gained from analysis of qualitative and quantitative changes of messenger RNAs, proteins, and metabolites. These techniques, able to simultaneously analyze large numbers of transcripts, proteins and chemical constituents, have led to the creation of new research fields within functional genomics, named transcriptomics, proteomics, and metabolomics. Each method has its inherent limitations and none of them alone is sufficient to assign a function to a gene of interest. However, the organization of the vast amount of data from the various approaches into central databases allows easy extraction and comparison of meaningful information. This chapter has the aim to highlight the major approaches that makes up modern plant functional genomics and to describe how they add a new dimension to the comprehension of plant biology with particular emphasis to the model plant, Arabidopsis thaliana.