Molecular marker technology has progressed rapidly over the last decade and is beginning to be incorporated into breeding programs worldwide. As the technology is still relatively expensive, it is unlikely that marker-assisted selection (MAS) can be applied on a routine basis in the large populations that breeders normally handle. It will be particularly appropriate for improving the efficiency of selection for specific objectives in high-potential populations. This article focuses on the abiotic stresses, which uniquely delineate the rainfed lowland ecosystem. Drought resistance is the most complicated trait required for rainfed lowland cultivars, Quantitative trait loci (QTL) for root-related characters such as depth and thickness have been mapped in three populations involving crosses between susceptible lowland cultivars and upland japonica cultivars. A locus conferring dehydration tolerance from the drought susceptible cultivar CO39 has been mapped on chromosome 8. Genetic studies of submergence tolerance have concentrated on the 'FR13A' source, The majority of this tolerance derives from a single gene mapped on chromosome 9, although several other QTL have also been described. QTL for tolerance to adverse soils are being mapped, with loci for salinity and iron toxicity being identified. MAS can be used to transfer important QTL into cultivars with the broadest range of adaptation. As an example, MAS could be used to introduce QTL for tolerance to submergence and drought into a cultivar that produces high yields in a specific region. As the cost of MAS technology declines, the process can be applied to ever smaller eco-geographic regions. In the future, molecular marker technology will enable the identification of specific genes conferring increased yield as well as resistance to biotic and abiotic stresses. This will give breeders an unprecedented ability to tailor cultivars to the specific environments where they will be grown. Published by Elsevier Science B.V.
