"Frontmatter". In: Plant Genomics and Proteomics

CHAPTER
4
G
E N E
D
I S C O V E RY
O
VERVIEW
The ultimate aim of genomics is to identify the structure and function of all
the genes of all organisms. To be able to identify an end point in the attempt
to characterize all the genes in plants, it is important to first define what we
mean by a gene. The molecular definition of a gene has changed over the
years. Initially, a gene was defined as the nucleic acid sequence that defines
a peptide. Now the definition has to encompass many more features. These
features include the presence of gene families within a plant, alternative
splicing, RNA functioning without ever being translated into a protein, and
other confounding factors that together make a simple universal definition
more difficult. How different would two members of a gene family have to
be in their structure, their pattern of expression, and/or the substrate speci-
ficity of their product for them to be classified as two different genes? For
example, plants make many secondary products, groups of which are related
and made by enzymes that are very similar. Although, more than 1000
monoterpenes are made by minor variants of a single enzyme (The Ara-
bidopsis Genome Initiative, 2000), the number made by different species can
vary widely. Should each of these variants be counted as a different gene, or
the whole group as a single gene? Can the various distinguishable members
of a gene family expressed only in particular tissues or at specific develop-
mental stages be considered as separate genes because their expression is
separated in time and space? Without a redundancy of function, mutations
in each one of the members of the family may result in different phenotypes.
Therefore, each member of the gene family could be mapped as an inde-
pendent genetic locus, and so on this definition they could be considered as
individual genes (some resistance gene clusters contain related genes that
Plant Genomics and Proteomics, by Christopher A. Cullis
ISBN 0-471-37314-1 Copyright © 2004 John Wiley & Sons, Inc.
6 9

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would be classified as members of a gene family on the basis of sequence
similarity, but each of the genes has a different specificity and is considered
as a gene in its own right). Added to these considerations are the posttrans-
lational modifications that can occur on the proteins, which can result in
modifying their function. 
The identification of genes can start at various points in the process of
gathering information about genomes. They can be identified from their
presence in populations of RNAs, from an analysis of genomic sequence data
with gene finding programs, from comparisons with the genomic sequence
data from related organisms, or from their disruption with the subsequent
appearance of a phenotypic variant.
Therefore, the studies that enable gene discovery include:
∑ The cloning and sequencing of cDNAs to generate expressed
sequence tags 
∑ The cloning and sequencing of full-length cDNAs for understanding
gene structure
∑ The annotation of whole genomes
∑ The use of syntenic relationships between species
∑ The use of transposons or T-DNA for gene tagging and insertional
mutagenesis
∑ The use of chemical mutagens
∑ The expression of abnormal RNAs that induce epigenetic suppres-
sion of homologous genes (gene silencing) 
How can all the genes and their functions within a plant be discovered?
An example of such an attempt is the Arabidopsis 2010 program supported
by the National Science Foundation (Chory et al., 2000). The goal of this
program is the determination of the function of all the genes (currently esti-
mated at about 25,000) in Arabidopsis thaliana by the year 2010. This will be
accomplished by using the continued annotation of the complete Arabidop-
sis genome sequence. A complementary effort using the rice genome
sequence will enable an expansion and validation of the conclusions drawn
from the Arabidopsis genome to encompass the whole higher plant kingdom.
This explosion of DNA sequence information has created a unique oppor-
tunity to identify and investigate the function of all the plant genes.