high-tech molecular analyses, genetic studies, and newly developed computational strat-
egies. The financial and intellectual commitments made toward completion of deciphering
the human genome were instrumental in leading to development of new technologies for
large-scale analysis of genes and proteins. Those technological developments continue
today, and are being applied to analysis of every class of organism—including important
crop plants.
Although all plant families and species have their specific traits that make them unique,
there are many genes that are conserved across species. In fact, there are many genes with
conserved functions across plants and animals. By determining the function of a given gene
in one species, it might allow us take a reasonable guess about the function of the corre-
sponding, orhomologous, gene in another species. For this reason, some plants that are
viewed as models attract a lot of attention. For example, the speciesArabidopsis thaliana
is a small, fast-growing member of the mustard family, and has a relatively small
genome confined to just five chromosomes. For these reasons, it serves as a good model
for studies of plant development and response to the environment. TheArabidopsis
genome was the first plant to be fully sequenced, and its genome of approximately 120
million bp was reported in 2000. Having the complete genome of a plant, even one of
no value as a crop such asArabidopsis, has proved very valuable in determining the
function of individual genes. As genomic DNA sequence information from crop
plants continues to increase, the similarities and differences among gene structures and
presence in different plant species is becoming clearer. It is hoped that by comparing the
structures of these different genomes, the gene regions that are important for valuable
traits can be identified.
From a technical perspective, improved methods have made it increasingly feasible to
determine DNA sequences of an organism. However, although knowledge of the
genomic sequence of a species is a valuable tool, it does not necessarily tell us about the
function of genes or how they contribute to phenotype. It can be particularly difficult to
associate specific genes with valuable traits, especially when the gene might have a
minor, but important, effect on a trait. Therefore, genomic approaches to understanding
gene functions or patterns of gene expression are being widely applied. Gene expression
studies are typically aimed at indicating presence of a particular mRNA transcript. For
most genes, their ultimate function is dependent on the presence of the mRNA transcript
whose nucleotide sequence information can be translated into amino acid sequence.
Expression of many genes is regulated at the level of mRNA accumulation and can be
associated with their ultimate function in the plant. For example, many genes thought to be
involved in plant defense against pathogens will have greatly increased amounts of their
encoded mRNAs during infection by a pathogen. To study this phenomenon, scientists
often take the approach of inoculating a plant with a pathogen, and then measuring
mRNA transcript levels. If a given gene isupregulatedat the level of mRNA accumulation,
then this gene is a good candidate for one involved in defense responses. By measuring
large numbers of transcripts under certain sets of environmental conditions, profiles of
gene expression begin to emerge and gene sets involved in plant defenses (or other
traits) can be identified.
A common technique for measuring mRNA transcript accumulation of large numbers of
genes is a DNAmicroarray(Alba et al. 2004). This technique takes advantage of the ability
of two nucleotide segments with complementary sequences to bind together, orhybridize.
If one of the sequences is somehow tagged with a label that can be measured, then the
amount of binding can be quantified. In a DNA microarray, specific sequences are typically
8.2. IDENTIFYING GENES OF INTEREST VIA GENOMIC STUDIES 195