© 2004 "New directions for a diverse planet". Proceedings of the 4th International Crop Science Congress, 26 Sep – 1 Oct 2004, Brisbane, Australia. Published on CDROM. Web site www.cropscience.org.au 1 Abiotic stress tolerance in rice for Asia: progress and the future H.R. Lafitte, A. Ismail, J. Bennett International Rice Research Institute, DAPO 7777, Metro Manila, Philippines. www.irri.cgiar.org Email addresses: R.Lafitte@cgiar.org Abdelbagi.Ismail@cgiar.org J.Bennett@cgiar.org Abstract Various abiotic stresses limit rice production in rainfed environments, which comprise about 45% of the global rice area. Important stresses include water deficit, submergence, salinity, and deficiencies of P and Zn. In recent years, advances in physiology, molecular biology, and genetics have greatly improved our understanding of how rice responds to these stresses and the basis of varietal differences in tolerance. Progress has relied on the application of rather specific phenotypic screens that allow the effects of stress to be distinguished from general differences in adaptation of diverse parents. QTLs have been identified that explain a considerable portion of observed variation, and in some cases, the genes underlying specific QTLs have been identified. Transformation has been used to assess the effects of altered expression of specific stress-related genes, allowing confirmation of the importance of particular metabolic pathways. Through expression profiling of many genes simultaneously, it has been possible to identify three types of stress-responsive gene networks: early signaling pathways, adaptive responses, and genes that reflect downstream results of damage. For crop improvement, the identification of useful allelic variation for genes in the second group may be the most promising approach. Once such genes or gene combinations are identified, either molecular approaches or trait-specific physiological screens can be used to search for these superior alleles. Marker-assisted backcrossing can then be applied to incorporate these alleles into agronomically superior germplasm. Media summary Abiotic stresses such as drought, salinity, submergence, and nutrient deficiencies limit rice production. Recent advances in our understanding of the physiology and molecular biology of stress tolerance in rice are being used to develop improved rice varieties. Key words Drought, flooding, salt, Oryza sativa, gene expression Introduction Over half of the world’s population depends on rice as a staple crop; in Asia, rice supplies 30 – 80% of the daily calories consumed (Narciso and Hossain 2002). Rice is an anomaly among the domesticated cereals – a tropical C 3 grass that evolved in a semi-aquatic, low-radiation habitat. As such, rice carries an odd portfolio of tolerances and susceptibilities to abiotic stresses as compared to other crops. Rice thrives in waterlogged soil and can tolerate submergence at levels that would kill other crops, is moderately tolerant of salinity and soil acidity, but is highly sensitive to drought and cold. Even where rice response to stress is superior to other crops, however, many rice-growing environments demand still greater tolerance than is found in most improved germplasm. In tropical regions, rice is grown in monsoon climates that are subject to intermittent submergence (water depths of 0.5 to 1 m that cover the foliage), drought, and, in coastal regions, salinity. Rice is also grown in the tropics during the dry season where adequate irrigation is available, and the crop may suffer from low temperatures at seeding and high temperatures at flowering. In temperate regions, where virtually all rice is fully irrigated, low temperature is also a major abiotic stress affecting rice production. Where rice is grown in unflooded soils in the humid tropics, the crop is affected by water deficit, soil acidity, and deficiency of P and Zn. Complementing the agronomic need for greater tolerance to abiotic stress in important rice-growing regions is the unique role of rice in the genomic era of plant science. Rice has the smallest genome among the cultivated cereals, and it conserves much of the gene content and, to some extent, gene order present in other species (Gale and Devos 2001). The amplification of the genome in other species appears to have occurred largely through the duplication and rearrangement of an ancestral gene complement, which is most closely preserved in rice. The full rice genome has now been sequenced (Goff et al. 2002), allowing the identification and localization of genes related to stress tolerance. The rice system can be used to