"Frontmatter". In: Plant Genomics and Proteomics

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VERVIEW
“If the only tool you have is a hammer, then everything looks like a nail.”
This old adage really does apply to many scientific situations and has shaped
the historical investigations of plant form and function. When the tools were
ruler and microscope, growth studies and detailed structural descriptions
were all that were possible. As the molecular technology developed both the
range of studies and the way that questions can be framed have been greatly
expanded. As the technology improves old questions can be revisited and
new explanations can be suggested. 
The new tools that are available for investigating gene structure and
function have been steadily developed over the past 30 years. The molecu-
lar biology revolution for the characterization of genomes began with the
development of recombinant DNA techniques. Today the molecular tools
include various cloning vectors, the incorporation of robotics into high-
throughput methodologies, for example, in the area of DNA sequencing, 
and mass spectroscopy for the detailed characterization of proteins. The
application of these methodologies results in the generation of very large
amounts of data that need to be processed. Whereas in the past the actual
accumulation of the data was the rate-limiting step, the bottleneck is now
the ability to analyze all the data. 
The wealth of data generated by high-throughput methodologies will
advance our understanding of gene structure and function by the molecu-
Plant Genomics and Proteomics, by Christopher A. Cullis
ISBN 0-471-37314-1 Copyright © 2004 John Wiley & Sons, Inc.
2 3

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lar characterization of already existing variants. In addition, the ability to
change gene expression in vivo, by using insertional mutagenesis, RNA
interference, or other silencing mechanisms, will be crucial in determining
the specific function of a particular gene. Therefore, at the present time, 
techniques are available to identify gene expression at various stages of
development and/or in response to biotic or abiotic stresses and then to
develop the biological material to determine which of these observations or
structural entities are causal of the changes seen and which are simply the
downstream result of some earlier modulation of gene expression. 
This chapter considers the various techniques used in the acquisition of
genomic data. Broadly speaking, they cover the following main areas:
1. Methods of isolating and fractionating genomes into manageable-
sized pieces, with the associated automation and tracking systems
that are necessary to manage the experiments and to interpret the
results. Genome fractionation must occur at both the DNA and RNA
levels so that the actual expressed genomic regions can be deter-
mined. The cloning of both genomic DNAs and expressed RNAs is
therefore necessary. 
2. The development of microarray technology has opened up the pos-
sibilities of expression profiling, the visualization of the expression of
many genes simultaneously. 
3. The downstream processing of the RNAs into proteins and the 
modification of these proteins and their abundances can also be 
determined so that the effective contribution of any expressed 
RNAs can be more directly demonstrated. The development of 
metabolic profiling will continue to open up new avenues for 
understanding the function and contribution each of these proteins
to the phenotype. 
4. The informatics tools to analyze this wealth of molecular data.
5. The ability to select a particular gene or suite of genes and to selec-
tively interfere with their expression, to directly test whether the con-
clusions drawn from the molecular data actually hold up in practice.