In a higher plant, it is only a small proportion of cells within the root that exist in relation to the external salinity. Most cells in a plant are not exposed directly to the external salinity but to the result of how this interacts with the processes governing uptake and partitioning of ions in the plant as a whole. These are predictably different processes, at higher levels of organisation, than cell-based processes. The number, nature and chromosomal distribution of genes and regulatory elements affecting how a whole plant responds to salinity will determine both the strategy and the practicability of breeding for increased performance. While QTL for important traits for environmental stress response have been identified, there is little evidence as to the nature of the genetic information, other than in cold tolerance. The work on cold tolerance suggests the importance of signal perception and signalling pathways, but for salinity there is little indication of what genes might control or co-ordinate the response of whole plants to salinity. The identification of such genes by positional cloning alone is highly difficult with current mapping resolution. It is possible to use DNA markers for such genes without knowing what they are - but the transfer of markers across a range of genotypes may not be easy. It is proposed that are way forward is via the integration of map-based location of QTL and the identification of possible candidate genes via the increasing power of differential expression technologies such as micro-arrays.
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