Genetic and genomic approaches to develop rice germplasm for problem soils Abdelbagi M. Ismail Æ Sigrid Heuer Æ Michael J. Thomson Æ Matthias Wissuwa Received: 29 April 2007 / Accepted: 22 July 2007 / Published online: 17 August 2007 Ó Springer Science+Business Media B.V. 2007 Abstract Soils that contain toxic amounts of minerals or are deficient in essential plant nutrients are widespread globally and seriously constrain rice production. New methods are necessary to incorporate the complex adaptive traits associated with tolerance of these abiotic stresses, while simultaneously retaining the high yield potential of rice varieties when conditions are favorable. Significant progress in the genetic characterization of stress response pathways and recent advances in genomics have provided powerful tools for in-depth dissection of tolerance mech- anisms. Additionally, tolerance of most of these abiotic stresses in rice is controlled by a few QTLs with large effects despite the intricacy of the numerous traits involved. Genetic dissection of these QTLs and their incorporation into high-yielding varieties will significantly enhance and stabilize rice productivity in these problem soils. Current efforts at IRRI and in rice breeding programs worldwide are seeking to explore diverse germplasm col- lections and genetically dissect the causal mechanisms of tolerance to facilitate their use in breeding. This review focuses on salinity and P and Zn deficiency as the major problems encountered in rice soils, and examines current understanding of the mechanisms involved and efforts toward germplasm improvement. Keywords Abiotic stresses Á Marker-assisted breeding Á Problem soils Á Oryza sativa Á Rice Á Salinity Introduction Soils that contain toxic amounts of minerals or are deficient in essential plant nutrients are widespread globally and seriously constraining rice production. These problem soils comprise a considerable proportion of rice production areas, which are invariably associated with poverty due to low and unstable productivity. Moreover, it was estimated that about 100 million ha of land suited to rice production in South and Southeast Asia are currently unused because of these soil problems (Senadhira 1994). These areas are potential targets for extra food production to eliminate global hunger and poverty if sufficiently exploited. High- yielding stress-tolerant rice varieties are expected to pro- vide a yield increase of about 2 t ha À1 on these soils (Ponnamperuma 1994). The coexistence of multiple abiotic stresses (Table 1) and the complexity of traits involved in tolerance of a particular stress hampered past efforts to develop tolerant high-yielding rice varieties. New methods are necessary to genetically dissect and incorporate these complex adaptive traits while simultaneously retaining the high yield potential of rice varieties, which could be achieved if the genes responsible for tolerance of these stresses were identified. Our understanding of the physiological and molecular bases of plant perception of environmental stresses and the adaptive responses to these stresses has advanced sub- stantially in recent years. Significant progress in the genetic characterization of stress response pathways and recent genomic advances have provided powerful tools for in- depth trait dissection, initially with the model plant Arabidopsis but more recently with other plant species (Zhu 2003; Zhang et al. 2004; Bohnert et al. 2006). As an important food crop, rice has a rich history of genetic investigation, a large collection of germplasm adapted to A. M. Ismail (&) Á S. Heuer Á M. J. Thomson International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines e-mail: abdelbagi.ismail@cgiar.org M. Wissuwa Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan 123 Plant Mol Biol (2007) 65:547–570 DOI 10.1007/s11103-007-9215-2