The present focus on genomics-type plant biology has been ushered in by the
generation of the Arabidopsis sequencing project initiated in the end of 1980s,
mirrored on the coincidental focus on bacterial, yeast, and animal, human in
particular, genome sequencing projects. Genome sequences have become essential
requisites for anchoring ESTs and expression profiles, and even more significantly,
for determining which protein and pathways are present in an
organism. The recognition of syntenic relationships between species is increasingly
exploited for comparative genomics analyses (Bennetzen, 2002). Similar
comprehensive data collection methods have emerged for proteins and metabolites,
with improvements in tools and technologies continuous or accelerating.
Sequences and dynamic expression profiles are only a starting point: the number
of predicted reading frames is continuously increasing as predictive bioinformatics
tools improve, as additional reading frames, dismissed or not recognized in the
past, are confirmed by their presence, and as the siRNAs, RNA genes that selectively
silence particular transcripts, are now being added as novel, important
components of gene expression regulation. The number of splicing variants,
leading to different protein sequences from one gene, can be expected to increase
as well. Within this multitude of genes will be many functions relevant for ion and
metabolic homeostasis under saline conditions, as well as specialized pathways
for other abiotic stresses; functions that underlie the multigenic trait that is stress
tolerance or resistance. In S. cerevisiae, the model that has most crucially contributed
to our understanding of salt stress tolerance, more than 500 genes confer a ‘‘severe salt phenotype’’ to the cells when deleted (http://www.yeastgenome.
org/cache/genome-wide-analysis.html) (Hohmann, 2002; Serrano et al., 1999).
More than 400 of these genes have homologues in Arabidopsis. Even when trivial
causes, for example, the deletion of a ribosomal protein gene or an essential RNA
polymerase subunit, are excluded, the genes that are essential for yeast cell
survival identify many different functional categories, most likely in any cell.
The most promising way forward will, most likely, be to identify the stressrelevant
genes in model species through mutagenesis and forward screens and
tilling methods (Henikoff et al., 2004; Tani et al., 2004). This strategy will be especially
useful when the population of tagged mutants carries a reporter gene that reports
altered responses to stress (Ishitani et al., 1997). A second opportunity is to become
more aware of evolutionarily related naturally stress tolerant species that are relatives
of established glycophytic model species. In comparisons of gene and protein
expression patterns, and by determining divergent gene numbers (paralogues of
ubiquitous genes), we can learn about the underlying functions that determine
different plant life styles (Bressan et al., 2002; Inan et al., 2004; Taji et al., 2004).
Additionally, the immediate future will be characterized by high throughput
localization studies for all or most of the
salinity stress-related transcripts and
proteins, using, for example, cell ablation techniques combined with microarray
analysis, and cellular and subcellular painting of transcripts and proteins by highthroughput in situ and real-time, in vivo fluorescence detection and localization
methods. Eventually, we will have a virtual representation of all transcripts,
proteins, and major metabolites during the life of a number of model species
from seed to seed under optimal conditions, and when challenged by abiotic
This information when combined with classical and marker-assisted breeding
and correlating quantitative trati loci (QTL) regions with genome information
may enable us to generate stress tolerant species and lines of crops that rely on
the immense genetic variability that exists in plants (Koyama et al., 2001; Loudet et al., 2003; Tuberosa et al., 2002).