A genomics approach towards salt stress tolerance
Introduction
For at least 8 000 years, mankind has manipulated plant species from subtropical regions to grow under diverse climatic conditions. The results of this activity provide all our food, feed and fiber. Domestication extended to just a few hundred species, with maybe ten of these providing the majority of all foods. Selection, increasingly based on scientific criteria, has allowed us to keep pace with population growth 〚9〛. Population growth, changes in lifestyle, competition for fresh water between farmers and cities, and possible global environmental changes have led to alarmist projections that seem to argue for additional strategies by which food supply can be guaranteed 〚32〛. Areas where food production is problematic coincide largely with places where water is a precious commodity, prolonged droughts are frequent, where saline and marginal soils are found and where temperature extremes compromise production. Moreover, the increased productivity achieved in irrigated agriculture has become a double-edged sword, because salinization following prolonged irrigation is unavoidable 〚13〛, 〚37〛. These considerations have galvanized strong interest in studying plant abiotic stress responses and understanding the meaning of stress tolerance as a biological phenomenon.
Understanding abiotic stress tolerance, not to mention breeding for stress tolerance, proved difficult because of the trait’s multigenicity. As a consequence no traditional crop lines exist that combine tolerance to high salinity or drought with high yield, which represents yet another complex trait. Many physiological studies have analyzed the problem. In the search for tolerance mechanisms, plant biologists have generated hypotheses by interpreting correlative evidence from many species based on biochemical and biophysical principles that govern stress tolerance or resistance 〚27〛 These insights provided guiding principles for moving from physiology to protein and enzyme analysis, genetic structure, gene function and gene expression studies, finally culminating in transgenic and mutant generation and analyses.
The last decade has brought a sea change in our views about stress sensitivity fueled by results from molecular genetics. Changes in the expression of individual genes and proteins induced by stress have been monitored under different conditions. As of the year 2000, the sequence of the Arabidopsis thaliana genome is nearly completed, and soon we will have a catalog of plant gene expression exceeding a million transcripts (http://www.ncbi.nlm.nih.gov/dbEST/index.html) 〚28〛, 〚44〛, 〚45〛. While numbers are important, more important is that from the molecular analysis of these transcripts, collected as ESTs (expressed sequence tags), the frequency and type of transcribed genes are obtained for organs, tissues and cells during development and under various perturbations. Such expression profiles are augmented by the analysis of EST-derived microarrays or oligonucleotide-based DNA-chips both providing information on changes in the expression levels over time or during experimental perturbations of the plants 〚7〛, 〚39〛, 〚50〛. Accompanying these activities has been yet another breakthrough, whose impact on stress biology and crop breeding will be, we think, even more profound. In A. thaliana, rice and corn saturation mutagenesis seems to have been achieved 〚4〛, 〚31〛, 〚36〛. The resulting mutants make possible proof of concept experiments on a large scale.
Here we present an initial set of data from an ongoing project that is focussing on defining the complete gene set associated with salinity stress. In addition, we report on Arabidopsis mutants with altered stress sensing and signal transduction characteristics. New technologies are employed to advance understanding: large-scale EST preparation and expression profiling, microarray analysis identifying target genes whose expression is stress-regulated, and the generation of mutants in stress-relevant signal transduction and response pathways. As the first results emerge, additional strategies can be employed that target the analysis of the many functionally unknown genes or transcripts, which are regulated when plants experience abiotic stress.
Section snippets
Results and discussion
For continued vegetative growth and the development of reproductive organs under osmotic and ionic stress conditions, plants must, above all, obtain water. To satisfy this essential need, each of many adaptive mechanisms that have been detected as plant defenses must be subordinate to this goal. When stomata are closed to limit water loss, a series of events adjusts photosynthesis, carbon fixation and carbohydrate transport, initiating processes that maintain the integrity of the photosynthetic
Conclusion
With the instrumentation in place that allows large-scale DNA sequencing, genome-wide analysis of the transcriptome, and large-scale analysis of all proteins in a cell, we must learn to utilize the bioinformatics tools that are essential if we wish to sort and understand the data avalanche. The extent to which biology is presently driven by these new technologies and by the need for sophisticated bioinformatics tools requires a new mindset. We have arrived at a threshold that permits the
Libraries from stressed plantsand EST sequencing
Our main objective was to obtain cDNA libraries from different tissues of salt-stressed plants to be used for the generation of EST sequences. Up to now, approximately fifty cDNA libraries have been generated, listed at stress-genomics.org (see also table I). They include cDNA libraries from the non-plant models Synechocystis sp. PCC6803, Saccharomyces cerevisiae, Aspergillus nidulans and Dunaliella salina. The plant models for which cDNA libraries have been established are Arabidopsis thaliana
Acknowledgements
We thank the technical staff and students in our laboratories, who have been essential in making high-throughput DNA preparation, analysis of ESTs, and mutant generation possible, especially Rashid Abduraham, Inna Akselrod, Adam Barb, Alison Berne, Susan Brazille, Amanda Breen, Davi Bufford, Juang-Hong Chong, Michael Dellinger, Monica Dennis, Andrea Hanlon, Xiaojing Jin, Melissa Knue, Julianne Lazarr, Saul Leite, Fang Li, Xianghui Liu, Heather McLaughlin, Jeson Martajaja, Jessica Martinez,
References (50)
- et al.
The distribution of T-DNA in the genomes of transgenic Arabidopsis and rice
FEBS Lett.
(2000) - et al.
Genomic approaches to plant stress tolerance
Curr. Opin. Plant Biol.
(2000) - et al.
Molecular genetic improvement of salt tolerance in plants
Biotechnol. Annu. Rev.
(1997) - et al.
DNA microarrays for studies of higher plants and other photosynthetic organisms
Trends Plant Sci.
(1999) - et al.
Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project
Curr. Opin. Biotechnol.
(2000) - et al.
Chasing the dream: plant EST microarrays
Curr. Opin. Plant Biol.
(2000) - et al.
Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways
Curr. Opin. Plant Biol.
(2000) - et al.
The application of DNA microarrays in gene expression analysis
J. Biotechnol.
(2000) Construction of specific mutations in photosystem-II photosynthetic reaction center be genetic engineering methods in Synechocystis-6803
Methods Enzymol.
(1988)- et al.
Growth and development of Mesembryanthemum crystallinum (Aizoaceae)
New Phytol.
(1998)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Nucleic Acids Res.
Salt tolerance conferred by overexpression of a vacuolar Na+/H+ antiport in Arabidopsis
Science
Molecular mechanisms of salinity tolerance
The highly abundant chlorophyll-protein complex of iron-deficient Synechococcus sp. PCC7942 (CP43') is encoded by the isiA gene
Plant Physiol.
Cluster analysis and display of genome-wide expression patterns
Proc. Natl. Acad. Sci. USA
Feeding the Ten Billion
Base-calling of automated sequencer traces using Phred. II. Error probabilities
Genome Res.
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
Genome Res.
Systematic changes in gene expression patterns following adaptive evolution in yeast
Proc. Natl. Acad. Sci. USA
Breeding for salinity tolerance in crop plants: Where next?
Aust. J. Plant Physiol.
Mapping quantitative trait loci for tolerance to abiotic stresses in maize
J. Exp. Zool.
The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3
Proc. Natl. Acad. Sci. USA
The involvement of cytokinins in plant responses to environmental stress
Plant Growth Regul.
Plant cellular and molecular responses to high salinity
Annu. Rev. Plant Physiol. Plant Mol. Biol.
Regulation of light harvesting in green plants
Annu. Rev. Plant Physiol. Plant Mol. Biol.
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Contributed experimental data from ongoing sub-projects within the stress genomics consortium.