QTL: their place in engineering tolerance of rice to salinity

Secondary salinization and its relationship to irrigation are strong incentives to improve the tolerance of crops to salinity and to drought. Achieving this through the pyramiding of physiological traits (phenotypic selection without knowledge of genotype) is feasible. However, wide application of this approach is limited by the practicalities of assessing not only the parents, but also large numbers of individuals and families in segregating generations. Genotypic information is required in the form of markers for any quantitative trait loci involved (marker-assisted selection) or of direct knowledge of the genes. In the absence of adequate candidate genes for salt tolerance, a quantitative trait locus/marker-assisted selection approach has been used here. Putative markers for ion transport and selectivity, identified from analysis of amplified fragment length polymorphism, had been discovered within a custom-made mapping population of rice. Here it is reported that none of these markers showed any association with similar traits in a closely related population of recombinant inbred lines or in selections of a cultivar. Whilst markers will be of value in using élite lines from the mapping population in backcrossing, this has to be considered alongside the effort required to develop and map any given population. This result cautions against any expectation of a general applicability of markers for physiological traits. It is concluded that direct knowledge of the genes involved is needed. This cannot be achieved at present by positional cloning. The elucidation of candidate genes is required. Here the problem lies not in the analysis of gene expression but in devising protocols in which only those genes of interest are differentially affected by the experimental treatments.