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
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.
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.
Drought, flooding, salt, Oryza sativa, gene expression
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 C3 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 assign function to genes, so that homologues can be identified in other species with more cumbersome genomes, but with possibly greater stress tolerance. The syntenic relationship between genomes has encouraged the application of functional genomic approaches to rice, in order to better understand general plant processes, disease resistance, and tolerance to abiotic stress.
The objectives of this paper are to briefly review recent efforts to better understand rice adaptation to several common abiotic stresses and to highlight efforts to integrate results of advances in physiology and molecular biology into rice breeding programs.
Drought is generally avoided in irrigated rice production systems, but it is a consistent feature across much of the 63.5 million hectares of rainfed rice sown annually, most of which is in tropical Asia, Africa, and Latin America (Narciso and Hossain 2002). Farmers have been selecting those plants that survived drought events for centuries, and there is a wealth of genetic variation for response to water deficit among traditional cultivars (Mackill et al. 1996). There are few examples, however, of improved cultivars that combine acceptable yield potential and drought tolerance. The immediate difficulty lies in reliably measuring drought tolerance. Like other seed-producing crops, rice is more susceptible to damage from water deficit at particular growth stages. A given level of drought at the vegetative stage can cause a moderate reduction in yield, but the same stress can eliminate yield entirely if it coincides with pollen meiosis or fertilization (O'Toole 1982). In some cases, superior response to vegetative stage stress is associated with better performance under reproductive stage stress, but in many cases the strategies that appear to be successful at the reproductive stage may be counterproductive when stress occurs at flowering (Pantuwan et al. 2002). Direct selection for improved yield under drought has been hampered by the unpredictability of drought events, which mean that selection pressure is generally inconsistent, and possibly contradictory, across years. Progress has been made, however, through the inclusion of tolerant parents in crossing (Chang et al. 1982; Pinheiro 2003). More recently, the use of managed environments and targeted multilocation testing has been implemented to facilitate progress in breeding drought tolerant rice (Fischer et al. 2003). The success of these initiatives will be known within the next few years.
Rice varieties differ greatly in their ability to tolerate aerobic soil and moisture deficit. The greatest ability to grow and produce some grain with chronic moderate water deficit is found in japonica varieties from upland ecosystems such as those found in hilly Southeast Asia and Africa (Mackill et al. 1996). Examples include Azucena from the Philippines and Moroberekan from Guinea. Notable levels of drought tolerance are also observed in the early-maturing aus and indica varieties traditionally grown in the plateau region of Eastern India, such as N22 and Dehula (Lafitte and Courtois 2002). While these cultivars usually escape drought through early maturity, they can also produce some grain when rains fail around flowering, indicating that they avoid or tolerate drought. Varieties adapted to anaerobic systems tend to stop growing as soil moisture declines, and leaves roll or senesce, effectively shedding excess radiation. This is associated with limited deep rooting and water extraction in many lowland varieties (Lilley and Fukai 1994). Some lowland cultivars have impressive levels of tolerance of tissue water deficit (Lilley and Ludlow 1996) and perform well in screens for leaf survival with vegetative stage stress (De Datta et al. 1988). Certain cultivars, such as Nam Sagui 19 from Thailand, combine both tissue tolerance and grain yielding ability in an indica genetic background, and these have served as important parental lines in breeding programs.
The physiological basis of genetic variation in drought response is not clear, in part because so many different measures of tolerance have been reported. If tolerance is defined as the ability to maintain leaf area and growth under prolonged vegetative stage stress, the main basis of variation appears to be constitutive root system architecture and its associated tillering habit that allows maintenance of more favorable plant water status (Nguyen et al. 1997), though in the field the impact of root system is easily confounded by plant size effects (Mitchell 1998). Differences have also been observed in the adaptive response of root distribution to soil drying (Azhiri-Sigari et al. 2000; Liu et al. 2004b). The mechanisms underlying genetic variation in both constitutive and adaptive root distribution may be sensitivity to signals, particularly auxin, that influence root elongation and branching (Bao et al. 2004; Ge et al. 2004). When drought tolerance is defined as the ability to flower and produce grain under water deficit, additional mechanisms may become important. Delayed flowering under drought is associated with an apparent delay in floral development when stress occurs between panicle initiation and pollen meiosis (from 30 to 10 d before heading). With the onset of stress occurring from 10 to 5 d before heading, flowering is slowed mainly due to slower elongation of the panicle and supporting tissues (A. Kathiresan, pers. comm.). Genetic variation in flowering delay under drought has been reported, and only part of this variation depended on measured plant water status (Pantuwan et al. 2002). Drought also affects the process of starch deposition in pollen grains, which normally begins about 3 days before anthesis, contributing to reduced anther dehiscence. Genetic variation for the tolerance of anther dehiscence to low water status has been observed (Liu et al. 2004a). Panicle desiccation can occur when drought coincides with heading; variety-specific mechanisms that can refill cavitated xylem elements in shoots may be important to limit panicle failure (Stiller et al. 2003). Unfortunately, we have little information about genetic variation in the final drought-sensitive processes of fertilization and early embryo establishment, other than the observation that varieties that better maintain shoot water potential have an advantage. As new methods are applied to the study of drought during the reproductive stage, we expect to discover additional mechanisms that allow some varieties to set grain despite unfavorable shoot water potentials.
Molecular approaches to drought tolerance have been widely applied to rice, beginning with QTL analysis. The rice genetic map is well covered by microsatellite markers (McCouch et al. 2003), and rice researchers worldwide have developed diverse mapping populations and related databases (see (Ware et al. 2002)). Mapping studies have been successful in identifying genetic regions associated with highly heritable traits such as plant height and flowering date, and in some cases it has been possible to identify the specific gene underlying a QTL (Ishimaru et al. 2004). QTLs have also been identified for some secondary traits that are expected to be associated with drought response, such as rooting depth, membrane stability, and osmotic adjustment (Table 1). Where tolerance is measured as yield under drought, however, few strong and repeatable QTLs have been identified. As more studies are published using realistic stress levels and adequate documentation of the dynamics of drought development, it should be possible to focus on some key QTLs that appear to be important across environments or populations. To date, however, it has not been possible to identify sufficiently large and discrete QTLs for performance under drought to justify marker-assisted selection. Instead, the results of QTL studies will probably be most usefully applied to the identification of promising genetic regions for the identification of candidate genes. Nonetheless, modifications of QTL mapping strategies still hold promise to deliver a product that will be more directly useful for cultivar improvement – these include linkage disequilibrium studies and the use of the advanced-backcross QTL approach that combines selection and QTL identification in closely related backcross lines.
Many studies report changes in the expression of individual genes when rice is challenged by drought stress, and they frequently respond to other abiotic and biotic stresses as well. These include such diverse genes as MAP kinase (Agrawal et al. 2003), DREB genes (Dubouzet et al. 2003), calcium-dependent protein kinase (Saijo et al. 2001), an endo-1,3-glucanase (Akiyama and Pillai 2001), a translation elongation factor (Li Zi and Chen Shou 1999), and glutathione reductase (Kaminaka et al. 1998). Transformation studies have demonstrated that altering the expression of a number of different genes from different pathways can affect the response of rice to water deficit or dehydration (Table 2). These include genes associated with diverse functions, such as water uptake (aquaporins) (Martre et al. 2002), signaling (kinases) (Saijo et al. 2001) (Liu et al. 2003), membrane integrity (LEA protein) (Xu et al. 1996) (Rohila et al. 2002) (Babu et al. 2004), and carbohydrate metabolism (TPS) (Jang et al. 2003). The effect of transformation on grain production under stress has not been well documented.
Because of the very large number of genes that change expression under drought stress, genomic approaches that can follow transcriptional changes in thousands of genes at a time hold great promise. Few genomic studies on drought have been published for rice, and these are mostly based on seedling responses to desiccation (Rabbani et al. 2003). Other studies have focused on expression profiling after application of other treatments that share some effects with drought, such as exogenous ABA or exposure to salt, usually applied to seedlings or callus (Yazaki et al. 2004). In maize, expression profiling experiments on reproductive tissues has been successful in highlighting important pathways that responded to stress (Yu and Setter 2003; Zinselmeier et al. 2002). For rice, microarray analysis has been used to identify differences in gene regulation in panicles of tolerant and susceptible varieties grown under stress in field conditions (Kathiresan et al. 2004). In addition to direct effects of drought on gene expression, there are changes in post-translational modifications such as protein phosphorylation. Advances in proteomics and metabolomics provide opportunities to follow these changes as well (Koller et al. 2002).
Excess water is a common constraint throughout the rainfed rice production areas as in South and Southeast Asia and tropical Africa. While rice is adapted to waterlogged conditions because of the well-developed aerenchyma that facilitates oxygen diffusion and prevents anoxia in roots, complete submergence can be lethal. Out of 40 million ha in Asia grown under rainfed lowlands, about 15 million ha are frequently damaged by submergence (Huke and Huke 1997). Submergence stress can also damage crops in irrigated areas due to high rainfall and/or impeded drainage, particularly early in the season. The annual average yield loss from submergence is estimated at about 80 kg/ha (Dey and Upadhaya 1996). In general, two types of flooding cause damage to rice: flash flooding that results in complete inundation of short duration, and long-term flooding, where water stagnates for up to few months (deepwater and tidal-flood areas).
The effect of flash-flooding interacts with growth stage. Germination is highly sensitive to flooding. Variability in ability to germinate under water and in coleoptile elongation under anoxia have been observed in rice. This was related to the rate of alcoholic fermentation and enhanced activity of starch degrading enzymes (Setter et al. 1994). During later vegetative development, rice can adapt to complete submergence through processes that provide necessary energy for maintenance metabolism and minimize losses. Under short-term flooding, extension growth is detrimental because it hastens energy depletion and increases mortality. Tall plants also tend to lodge when the water level recedes resulting in additional yield losses and poor grain quality. Mechanisms associated with such tolerance were recently reviewed (Ella et al. 2003; Jackson and Ram 2003; Ram et al. 2002; Setter et al. 1997).
Most existing rice cultivars are seriously damaged if they are completely submerged for more than 3 d; however, a few tolerant cultivars can withstand complete submergence for 10 to 14 d, such as FR13A, FR13B, Goda Heenati, Kurkaruppan, BKNFR76106-16-0-1-0 and Thavalu. FR13A was released in the 1940s in Orissa, India, as a pure line selection from the local variety Dhullaputia (Mackill et al. 1996). This cultivar is probably the most frequently used in genetics and physiological studies and as a standard against which other breeding lines are often compared. Breeding to further improve tolerance to submergence in rice along with yield potential has been on going for over three decades (HilleRisLambers and Vergara 1982; Mackill 1986; Singh and Dwivedi 1996). The initial work focused on transferring tolerance from traditional landraces into semi-dwarf breeding lines. However, the traditional donors were low yielding, tall and had low grain quality. Tolerant breeding lines with improved agronomic characteristics have now been developed (Mackill et al. 1993; Mackill and Xu 1996), and some breeding lines such as IR49830-7 had yield equivalent to the irrigated checks. Other new breeding lines with adequate tolerance to submergence have been recommended for release in India (Singh et al. 1998).
Genetic studies suggested both simple and quantitative inheritance for submergence tolerance (Suprihatno and Coffman 1981). Using a population developed from a cross between an indica submergence tolerant line (IR40931-26) and a susceptible japonica line (PI543851) a major QTL was mapped to chromosome 9, designated as Sub1 (Xu and Mackill 1996). This QTL accounted for about 70% of the phenotypic variation in submergence tolerance in the population studied. The donor line for this QTL was derived from FR13A and had a similar level of tolerance (Mackill et al. 1993). In a subsequent study (Nandi et al. 1997) the importance of Sub1 in submergence tolerance was confirmed and 4 additional QTLs were identified on 4 different chromosomes. Moreover, the Sub1 locus has been fine mapped, paving the way for its positional cloning (Xu et al. 2000). Markers linked to this gene are currently being used to incorporate Sub1 into existing popular varieties. The dramatic effect of Sub1 on what is essentially a quantitative trait suggests a regulatory locus rather than a specific enzyme. The identity will likely be evident after cloning the putative gene, which is currently underway.
The development of submergence tolerant cultivars has required the use of stress-specific screens, because direct evaluation of tolerance is not as simple as it might seem. Results depend strongly on the depth and duration of submergence, age of seedlings, and water temperature. Because of these complexities, alternative indirect screening approaches have been developed using traits known to be associated with submergence tolerance such as extent of underwater shoot elongation, shoot carbohydrate storage and extent of chlorophyll retention, all of which are correlated significantly with seedling survival. Our recent studies using cultivars that contrast in initial carbohydrate content as well as in elongation ability showed that initial carbohydrate content is not, on its own, a good indicator for submergence tolerance, though post submergence non-structural carbohydrates, which is the outcome of both elongation ability and the initial carbohydrate contents, is a better indicator of tolerance (Das et al., 2004). Tolerant varieties were also found to have greater ability to retain their chlorophyll content during and after submergence. This is found in studies where chlorophyll degradation was prevented by blocking the action of ethylene that accumulates during submergence (Ella et al. 2003). Monitoring chlorophyll content few days after submergence could constitute an efficient method of screening particularly if it could be done non-destructively. Extent of leaf florescence could also be used indirectly as an indicator of initial chlorophyll degradation. The potential of these traits to provide a reliable screening technique warrant further validation.
In deepwater areas, water depth can exceed 100 cm and stagnate for several months. Elongation ability of leaves and internodes under these conditions are essential to keep pace with the rising water and to escape complete submergence, thus ensuring O2 supply and access to CO2 and light (Setter et al. 1997). Flooding increases ethylene concentration in plant tissue both due to enhanced synthesis as well as entrapment. Rice adapted to deepwater conditions appears to differ from lowland rice in its response to interactions between ethylene and GA (Van der Straeten et al. 2001).
Traditional varieties adapted to deepwater environments such as Jalmagna, Baisbish and Rayada 16-3, are low yielding due to their low-tillering ability, long droopy leaves, susceptibility to lodging, and poor grain quality (Mallik et al. 1995). Improved varieties should combine yield and quality attributes with elongation ability, but progress has been rather slow. Artificial screening ponds and rapid generation advancement can accelerate breeding efficiency. Recently, progress has been made in developing lines with facultative elongation ability, broad and thick leaves, heavy panicles and stiff culms for deep-water conditions. Some lines with reasonable yield and grain quality have been released, such as “Prachinburi2” in Thailand. This new class of breeding lines elongate only with rising water and have greater yield.
Using a population developed from a cross between Jalmagna and IR74, three main QTLs for elongation ability were identified. The most important was QIne1, which mapped near sd-1 on chromosome 1. Two other QTLs mapped on chromosomes 4 and 5 (Sripongpangkul et al. 2000). Fine-mapping and tagging of these QTLs should facilitate their efficient incorporation into modern popular varieties using marker-aided selection.
Salt stress is a major constraint to cereal production worldwide. In Asia alone, 21.5 million ha are affected, of which 12 million ha are saline and 9.5 million ha are alkaline/sodic. Rice is a salt-sensitive crop, but it is the only cereal that has been recommended as a desalinization crop because of its ability to grow well under flooded conditions, and because the standing water in rice fields can help leach the salts from the topsoil to a level low enough for subsequent crops (Bhumbla and Abrol 1978). Despite its high sensitivity to salinity, considerable variation in tolerance was observed in rice (Akbar et al. 1972; Flowers and Yeo 1981).
Rice is comparatively tolerant of salt stress during germination, active tillering, and towards maturity and is sensitive during early seedling and reproductive stages. The physiological bases of salt tolerance during early seedling stage are fairly well understood; key traits include high seedling vigor, salt exclusion at the root level, compartmentation of ions in structural and older tissues, high tissue tolerance, responsive stomata that close within minutes after exposure to salt stress but partially reopen after a period of acclimation, and upregulation of antioxidant systems, particularly the ascorbate/glutathione pathway of oxidative stress tolerance. During reproductive development, tolerant genotypes tend to exclude salt from flag leaves and developing panicles (Yeo and Flowers 1986, A. Ismail, unpublished data). Although these traits are essentially independent, none of the known salt-tolerant landraces combine favorably more than few of them and there is considerable variation in the extent of expression of particular traits among cultivars, suggesting the likelihood of identifying even better donors and alleles of useful genes. Salinity tolerance at the seedling and reproductive stages are only weakly associated; hence, pyramiding of contributing traits at both stages is needed for developing resilient salt-tolerant cultivars (Moradi et al. 2003). Salt tolerance of rice can, therefore, be improved beyond the present phenotypic range by use of physiological criteria to select independently for individual contributing traits or ultimately by tagging genes controlling critical steps in pathways underlying each of these traits to permit their subsequent combination in superior genotypes.
Few attempts have been made to identify QTLs associated with salinity tolerance in rice. For example, seven QTLs for seedling traits associated with salt stress were identified and were mapped to five different chromosomes (Prasad et al. 2000). A major gene for salt tolerance was mapped on chromosome 7, using an F2 population derived from a salt-tolerant japonica rice mutant, M-20 and the sensitive original variety 77-170 (Zhang et al. 1995). The QTLs associated with different mechanisms of salinity tolerance in rice independently govern the uptake of Na and K and Na:K selectivity and are mapped on different chromosomes (Koyama et al. 2001). A major QTL designated ‘Saltol” was mapped on chromosome 1 using a population generated from a cross between the sensitive variety IR29 and a tolerant landrace, Pokkali. This QTL accounted for more than 70% of the variation in salt uptake in this population (Bonilla et al. 2002) and is now being mapped to within 1 cM using a large set of NILs. Candidate BAC clones from the physical map have also been identified. Marker assisted backcrossing is currently being used to incorporate this QTL into popular varieties sensitive to salt stress.
The genes underlying difference in tolerance are myriad, because of the large number of mechanisms that result in tolerance. One mechanism to avoid toxic concentrations of harmful salts in the cytoplasm is to transport them to the apoplast. This is achieved through active processes involving a gene family of Na+/H+ antiporters that transport sodium out of the cell or sequester it in vacuoles (Blumwald et al. 2000). Evidence for the role of these antiporters in tolerance to salt stress has recently accumulated from a number of independent studies. For example, overexpression of the vacuolar Na+/H+ antiporters (AtNHX1) from Arapidopsis in tomato (Zhang and Blumwald 2001) and canola (Zhang et al. 2001) permitted the transgenic plants to grow in up to 200 mM NaCl, which is extremely high for xerophytic plants. A potassium transporter from Arapidopsis (AtHKT1) is involved in Na+ recirculation from shoots to roots (Berthomieu et al. 2003), probably by mediating Na+ loading into the phloem sap in shoots and unloading in roots. This mechanism could play a crucial role in plant tolerance to salt stress by removing large amounts of Na+ from the shoot. The central role of root membrane transporters in determining response to salinity has been demonstrated in large-scale expression studies in roots (Maathuis et al. 2003).
Allelic variation in one copy of a small family of H+ ATPase genes from 77-170 correlated with a QTL for salt tolerance located on chromosome 12 (Zhang et al. 1999). Transcripts of this gene were found to accumulate in roots of a salt tolerant mutant M-20, suggesting that it may restrict salt uptake into roots. In addition to these examples, there are reports of significant improvements in salinity tolerance associated with over-expression of other genes such as superoxide dismutase in Arabidopsis (Gao et al. 2003) and a calcium-dependent protein kinase in rice (Saijo et al. 2000). The opportunities to improved rice salinity tolerance through the incorporation and pyramiding of superior alleles of these various mechanisms appears very promising.
Insufficient plant-available soil phosphorus is a major constraint for rice production. This is particularly apparent under upland conditions, which are commonly characterized by infertile, highly acidic, P-fixing soils, normally in areas where little or no fertilizer is applied. Even under lowland conditions, P deficiency is a main factor limiting performance of modern rice varieties and is likely to become increasingly important as P is removed from soils under intensive rice production (De Datta et al. 1990). The lack of locally available P sources and the high cost of importing and transporting fertilizers prevent many resource-poor rice farmers from applying P. Some rice soils can quickly fix up to 90% of the added P fertilizer into less soluble forms (Dobermann et al. 1998). An attractive, cost-effective and sustainable strategy is to develop rice cultivars capable of extracting higher proportion of fixed P. Genetic variability among lowland (Wissuwa and Ae 2001b) and upland (Fageria et al. 1988) rice cultivars in their ability to exploit soil and fertilizer P were observed. Variation in uptake in the range of 0.6 to 12.9 mg P plant-1 was reported, and with the traditional landraces being superior to modern varieties. Hence, genetic variation in tolerance to P deficiency could effectively be exploited for rice improvement.
Two main types of mechanisms confer tolerance to P deficiency; internal mechanisms associated with efficient use of P by plant tissue; and external mechanisms that allow greater P uptake by plant roots. Genetic variation in external efficiency is probably the most important mechanism for P deficiency tolerance in rice (Hedley et al. 1994; Wissuwa and Ae 1999). Morphological characteristics such as root length, surface area, fineness, and density of root hairs are found to influence P uptake in many crop species (Kirk and Du 1997; Otani and Ae 1996). A model was recently developed to critically test the contribution of these traits (Wissuwa 2003). Small changes in root growth-related parameters were found to exert large effects on P uptake. For example, a 22% increase in root fineness or in internal efficiency of root dry matter production could triple P uptake, suggesting that large genotypic differences in P-uptake could be caused by small changes in tolerance mechanisms that are difficult to detect.
Under flooded conditions rice roots can acidify soils in their immediate vicinity through release of H+ from roots or from oxidation of Fe2+ by root-released O2 (Saleque and Kirk 1995), making soil-bound P more available. Mechanisms of P solubilization in aerobic soils are probably different and mainly involve the secretion of low molecular weight organic acids, such as citrate, that increase P availability through the formation of soluble metal-citrate chelates (Kirk et al. 1999). Chelating agents such as organic acids may help solubilize P in the soil by dissolving Al and Fe solid phases on which P is held. High rates of release of P-solubilizing organic acid anions from roots in response to P-deficiency have been reported (Kirk et al. 1999).
Although genotypic differences in P deficiency tolerance in rice were reported long ago, efforts were limited to screening available varieties rather than developing new genotypes especially adapted to P deficient soils. The fact that traditional varieties were more superior to modern varieties (Wissuwa and Ae 2001b) indicates the need for such breeding programs to incorporate P-deficiency tolerance into modern cultivars. However, tolerance to P-deficiency is quantitatively inherited with both additive and dominant effects (Chaubey et al. 1994) and as with other quantitative traits, progress through conventional approaches will be slow. More rapid progress in breeding may be achieved through the application of modern molecular approaches.
Attempts have been made to detect QTLs controlling P-deficiency tolerance in rice, and four QTLs have been identified for P-uptake. One major QTL (Pup1) was mapped on chromosome 12 (Wissuwa and Ae 1999; Wissuwa et al. 1998). Pup1 was found to triple P uptake under P-deficient soils, with no apparent effect when P was not limiting (Wissuwa and Ae 2001a). At present, Pup1 is fine-mapped in a 0.4 cM interval, which, on the rice physical map, spans 3 BACs that have been fully sequenced. Physiological studies suggest that the Pup1 gene is expressed in root tissue, where it either leads to higher root growth per unit P uptake (higher internal efficiency) or improves P uptake per root surface area (external efficiency; Wissuwa and Ismail, unpublished). The availability of rice genome sequence data will facilitate efforts to clone the Pup1 locus if potential target genes can be identified based on hypothetical gene function or expression. Work is currently ongoing to identify and characterize the putative candidate genes in this region and to develop a MAS strategy for its incorporation into modern varieties.
Understanding the mechanisms by which phosphate is transported across the plasma membrane and into the plant symplast has advanced considerably over the past few years, and genes encoding P transporters were isolated from different plant species (Rausch and Bucher 2002; Smith 2002). Plants have multiple phosphate transporter genes, eight of which have been isolated from barley alone. Two types of phosphate transporters were generally identified; low affinity transporters with constitutive expression and high affinity transporters whose expression is up regulated under P deficiency. Strategies for increasing nutrient uptake by over-expressing these genes are likely in situations where reasonable phosphate concentration can be maintained at the outer surface of the plasmalemma. Another possibility is that manipulating the expression of these genes might improve internal efficiency by mobilization of phosphate within the plant (Smith 2002). Exploring the rice genome for better alleles of these genes could also be useful for breeding.
Zinc (Zn) deficiency is the most common nutrient problem for rice next to nitrogen and phosphorus, with as much as 50% of all lowland rice soils being affected (White and Zasoski 1999). Deficiency is normally associated with continual soil wetness and occurs particularly in alkaline, organic and poorly drained soils (Yoshida et al. 1973) (Forno et al. 1975). It is also associated with high bicarbonate content and high levels of available phosphate and silica. The use of high levels of fertilizers with antagonistic effects on Zn availability and intensive cultivation of modern rice cultivars have exacerbated the deficiency problem over the past several years.
Zinc deficiency in rice occurs in the first few weeks after soil flooding. Surviving plants can then recover spontaneously within 6-8 wk, although the vegetative stage might be prolonged and yield is usually seriously affected. The mechanism of Zn solubilization in soils low in available Zn is similar to the mechanism of P solubilization, and results from acidification of the rhizosphere in the vicinity of roots by H+ released from the roots or generated in the oxidation of iron by O2 released by roots (Kirk and Bajita 1995).
In soils where Zn deficiency occurs as a consequence of Zn fixation rather than inherently low Zn, developing cultivars that use Zn more efficiently or possess the ability to solubilize soil bound Zn sources of low availability to plants is probably the most prudent solution, since Zn fertilizers are not widely available and expensive. Noticeable differences between rice cultivars in ability to extract Zn and grow under low Zn conditions have been observed (Neue 1994; Yang et al. 1994). There is no apparent yield cost associated with Zn-deficiency tolerance, and tolerant genotypes often show tolerance to both salinity and P deficiency, though the basis of this cross-tolerance is not known. However, despite this variability, no serious breeding programs have yet been initiated to incorporate this trait into elite breeding lines and varieties. Studies of the inheritance of this trait and unraveling of the physiological mechanisms underlying the observed genetic variation are prerequisites for a successful breeding program. Limited efforts are now underway to map this trait and to pave the way for further physiological and molecular exploration.
Our knowledge of how rice genes respond to stress is increasing daily. Our understanding of how these changes translate into plant growth and crop level differences in performance under stress lags behind, and will require a focused effort at synthesis in order to convert the exciting results of genomics into tools and guidelines that plant breeders can use. The most direct application will be in marker-aided selection, though novel high-throughput trait-based screens for use in breeding programs may also emerge from this effort. Marker-assisted selection of progeny from crosses between tolerant, low-yielding cultivars and susceptible, high yield-potential lines theoretically allows for much greater efficiency in a breeding program, because extensive unreliable phenotypic screening can be eliminated, and linkage drag can be effectively reduced. In practice, the identification of suitable markers has been slowed by the low repeatability and precision of QTLs for abiotic stress tolerance. It is rare to identify a single QTL that accounts for most of the observed variation in a given cross and screening system. Nonetheless, exceptions such as Sub1 and Pup1 have been identified through a combination of appropriate parental crosses, careful phenotyping, and dedicated fine-mapping studies.
Future progress may be more rapid if we can effectively use advances in genomics. For example, the costly and time-consuming process of fine-mapping may be circumvented by considering the stress-responsive candidate genes that underlie a given QTL (Ishimaru et al. 2004; Wayne and McIntyre 2002). A strong putative candidate region can be used directly in breeding, however, even if final gene identity is not known, as long as its position is confirmed through association with phenotype in mapping populations (Thorup et al. 2000, Ramalingam et al. 2003). In this case, the actual identity of the candidate is not confirmed, but there a breeder may have sufficient confidence to use a tightly linked marker as a selection tool. The final validation of a specific candidate gene will require additional steps such as transformation or the evaluation of targeted knock-out mutants (Glazier et al. 2002). Knowledge of gene identity is required for the generation of gene-based molecular markers and to justify the search for allelic variants of the gene using molecular techniques or tightly targeted phenotypic screens.
One intriguing aspect of the information emerging from genomic studies of abiotic stress response is the large number of genes that respond to multiple stresses, both biotic and abiotic. These can be roughly grouped into those related to initial stress perception, those that modify processes in response to the signal, and the downstream results of that modification, with some overlap between groups (Figure 1). Various studies have demonstrated that common genes are activated by such diverse stresses as wounding, pathogen attack, salt stress, and high temperature in both Arabidopsis (Cheong et al. 2002) and rice (Rabbani et al. 2003). Protein kinases (Agrawal et al. 2003), transcription factors (Dubouzet et al. 2003), and genes associated with hormone metabolism (Chen et al. 2002) particularly show this non-specific response. These genes may also be important in development (Cooper et al. 2003). Such genes that act early in the stress sensing and transduction processes appear to be finely tuned to allow responses to a variety of stresses, some of which act antagonistically (Xiong and Yang 2003). While it is tempting to search for superior alleles of such upstream master switches, these very upstream genes may not be appropriate targets for modification in improving abiotic stress tolerance, because they may restrict the ability of the plant to respond to other environmental challenges or to the combined stresses that characterize real environments. On the other hand, a rice cultivar tolerant to salt shock differed from its susceptible counterpart in its rapid response to stress imposition, suggesting that the immediacy of response to early upstream changes may also have adaptive significance (Kawasaki et al. 2001). Stress-responsive genes that change expression primarily as a result of damage are probably not good targets for crop improvement. The challenge before us, then, is to identify those genes underlying responses in the middle group (Figure 1) that respond to the primary stress signal with an adaptive response that is itself compatible with yield, such as the maintenance of plant hydraulic conductance and seed development under drought, sequestration of toxic ions under salt stress, or the repression of ethylene synthesis under submergence. Once such genes and processes are identified, the search for improved allelic forms among global genebanks and wild relatives can begin in earnest.
Table 1. Selected traits related to abiotic stress tolerance that have been mapped on the rice genome through QTL studies
Leaf rolling/drying under drought
Scored for field-grown plants at vegetative stage
Courtois et al. 2000; Price et al. 2002b
Root architecture (constitutive)
Root thickness, maximim root length, root weight or length distribution measured for plants grown in soil in containers
Courtois et al. 2003; Kamoshita et al. 2002; Price et al. 2002a; Venuprasad et al. 2002; Zheng et al. 2003
Percentage of roots that penetrate a physical barrier for plants grown in soil in containers
Ali et al. 2000; Ray et al. 1996; Zheng et al. 2000
Membrane stability under drought
Leaf segments collected from plants stressed to 60% RWC, membrane stability based on electrical conductance of solution
Tripathy et al. 2000
Osmotic adjustment under drought
Plants stressed to 60% RWC in soil-filled pots
Lilley et al. 1996; Robin et al. 2003
Height and heading date under drought
Measured in multiple field locations, some with drought
Li et al. 2003b
Yield and yield components under drought
Lines grown in the field with managed drought stress
Babu et al. 2003; Lafitte et al. 2004; Lanceras et al. 2004
Seedling survival after submergence
Nandi et al. 1997; Xu et al. 2000
Seedling growth with high salinity; ion accumulation in seedlings
Bonilla et al. 2002; Koyama et al. 2001; Lin et al. 2004; Prasad et al. 2000
Tolerance to phosphorus deficiency
Plant growth in low-P field
Wissuwa et al. 1998
Table 2. Candidate genes for drought tolerance with effect confirmed through transformation studies in rice and/or supported by coincidence with QTL region
Confirmation of effect in transgenic/ QTL results
Trehalose-6-phosphate synthase and phosphatase
Development and meristem growth (van Dijken et al. 2004)
Recovery of leaves after severe dehydration
Lee et al. 2003
Leaf wilting and growth in 5-wk old plants in pots subjected to two 4-d drying cycles
Garg et al. 2002
Membrane stabilization (Koag et al. 2003)
Favorable water status and superior growth during gradual stress in soil-filled pots
Babu et al. 2004
Water channel activity (Javot and Maurel 2002)
Higher hydraulic conductance and water potential in seedlings under PEG stress
Lian et al. 2004
Regulate cell wall expansion (Li et al. 2003a)
Taller than wild type under normal conditions
Choi et al. 2003
OsEXP2 mapped to same interval as QTL for seminal root length
Zheng et al. 2003
Arginine decarboxylase (adc)
Produces putrescine, which may have protective role
Wilting and rolling of leaves with PEG treatment
Capell et al. 2004
Figure 1. Conceptual grouping of plant responses to stress into gene activation for upstream signal transduction, adaptive responses that allow the plant to change and moderate or survive the stress, and downstream responses that result from successful adaptation or unsuccessful responses (damage). Some examples are shown for each group. Allelic variation in genes that underlie the adaptive responses should be useful in breeding programs for improved stress tolerance.
Agrawal GK, Tamogami S, Iwahashi H, Agrawal VP and Rakwal R (2003) Transient regulation of jasmonic acid-inducible rice MAP kinase gene (OsBWMK1) by diverse biotic and abiotic stresses. Plant Physiology and Biochemistry 41, 355-361.
Akbar M, Yabuno T and Nakao S (1972) Breeding for saline resistant varieties of rice I. Variability for salt tolerance among some rice varieties. Japanese Journal Breeding 22, 277-284.
Akiyama T and Pillai MA (2001) Molecular cloning, characterization and in vitro expression of a novel endo-1,3-beta-glucanase up-regulated by ABA and drought stress in rice (Oryza sativa L.). Plant Science 161, 1089-1098.
Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S and Nguyen HT (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theoretical and Applied Genetics 101, 756-766.
Azhiri-Sigari T, Yamauchi A, Kamoshita A and Wade L (2000) Genotypic variation in response of rainfed lowland rice to drought and rewatering II. Root growth. Plant Production Science 3, 180-188.
Babu RC, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ and Nguyen HT (2003) Genetic analysis of drought resistance in rice by molecular markers: Association between secondary traits and field performance. Crop Science 43, 1457-1469.
Babu RC, Zhang JX, Blum A, Ho THD, Wu R and Nguyen HT (2004) HVA1, a LEA gene from barley confers dehydration tolerance in transgenic rice (Oryza sativa L.) via cell membrane protection. Plant Science 166, 855-862.
Bao F, Shen JJ, Brady SR, Muday GK, Asami T and Yang ZB (2004) Brassinosteroids interact with auxin to promote lateral root development in Arabidopsis. Plant Physiology 134, 1624-1631.
Berthomieu P, Conéjéro G, Nublat A, Brackenbury W, Lambert C, Savio C, Uozumi N, Oiki S, Yamada K, Cellier F, Gosti F, Simonneau T, Essah P, Tester M, Very A-A, Sentenac H and Casse F (2003) Functional analysis of AtHKT1 in Arabidopsis shows that Na+ recirculation by the phloem is crucial for salt tolerance. EBMO Journal 22, 2004-2014.
Bhumbla D and Abrol I (1978) Saline and sodic soils. In 'Soils and Rice' pp. 719-738. (International Rice Research Institute: Manila, Philippines)
Blumwald E, Aharon G and Apse M (2000) Sodium transport in plant cells. Biochemica Biophysica Acta 1465, 140-151.
Bonilla P, Dvorak J, Mackill D, Deal K and Gregorio G (2002) RFLP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philippine Journal of Agricultural Science 85, 68-76.
Capell T, Bassie L and Christou P (2004) Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress. PNAS 101, 9909-9914.
Chang TT, Loresto GC, O'Toole JC and Armenta-Soto JL (1982) Strategy and methodology of breeding rice for drought-prone areas. In 'Drought Resistance in Crops with Emphasis on Rice'. (Ed. IRRI) pp. 218-244. (IRRI: Los Banos)
Chaubey C, Senadhira D and Gregorio G (1994) Genetic analysis of tolerance for phosphorus deficiency in rice (Oryza sativa L.). Theoretical Applied Genetics 89, 313-317.
Chen WQ, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou GZ, Whitham SA, Budworth PR, Tao Y, Xie ZY, Chen X, Lam S, Kreps JA, Harper JF, Si-Ammour A, Mauch-Mani B, Heinlein M, Kobayashi K, Hohn T, Dangl JL, Wang X and Zhu T (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 14, 559-574.
Cheong Y, Chang H, Gupta R, Wang X, Zhu T and Luan S (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabiclopsis. Plant Physiology 129, 661-677.
Choi DS, Lee Y, Cho HT and Kende H (2003) Regulation of expansin gene expression affects growth and development in transgenic rice plants. Plant Cell 15, 1386-1398.
Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbuhl P, Ellero C, Goff SA and Glazebrook J (2003) A network of rice genes associated with stress response and seed development. PNAS 100, 4945-4950.
Courtois B, McLaren G, Sinha PK, Prasad K, Yadav R and Shen L (2000) Mapping QTLs associated with drought avoidance in upland rice. Molecular Breeding 6, 55-66.
Courtois B, Shen L, Petalcorin W, Car and ang S, Mauleon RandLi Z (2003) Locating QTLs controlling constitutive root traits in the rice population IAC 165 x Co39. Euphytica 134, 335-345.
Das KK, Sarkar RK, Ismail AM (2004) Elongation ability and non-structural carbohydrate levels in relation to submergence tolerance in rice. Plant Sci. in press
De Datta S, Biswas T and Charoenchamratcheep C (1990) Phosphorus requirements and management for lowland rice. In 'Phosphorus requirements for sustainable agriculture in Asia and Oceania' pp. 307-323. (International Rice Research Institute: Manila, Philippines)
De Datta SK, Malabuyoc JA and Aragon EL (1988) A field screening technique for evaluating rice germplasm for drought tolerance during the vegetative stage. Field Crops Research 19, 123-134.
Dey M and Upadhaya H (1996) Yield loss due to drought, cold and submergence in Asia. In 'Rice Research in Asia: Progress and Priorities'. (Eds R Evenson, R Herdt and M Hossain) pp. 291-303. (CAB International and IRRI: Wallingford, UK)
Dobermann A, Cassman KG, Mamaril CP and Sheehy JE (1998) Management of phosphorus, potassium, and sulfur in intensive, irrigated lowland rice. Field Crops Research. March 56, 113-138.
Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K and Yamaguchi-Shinozaki K (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant Journal 33, 751-763.
Ella E, Kawano N, Yamauchi Y, Tanaka K and Ismail A (2003) Blocking ethylene perception enhances flooding tolerance in rice. Functional Plant Biology 30, 813-819.
Fageria N, Morais O, Baligar V and Wright R (1988) Response of rice cultivars to phosphorus supply on an oxisol. Fertilizer Research 16, 195-206.
Fischer K, Lafitte H, Fukai S, Atlin G and Hardy B (2003) 'Breeding rice for drought-prone environments.' (International Rice Research Institute: Los Banos, Philippines)
Flowers T and Yeo A (1981) Variability in the resistance of sodium chloride salinity within rice (Oryza sativa L.) varieties. New Phytologist 88, 363-373.
Forno D, Yoshida S and Asher C (1975) Zinc deficiency in rice. I. Soil factors associated with the deficiency. Plant and Soil 42, 537-550.
Gale MD and Devos KM (2001) Comparative genetics and cereal evolution. Israel Journal of Plant Sciences 49, S19-S23.
Gao XH, Ren ZH, Zhao YX and Zhang H (2003) Overexpression of SOD2 increases salt tolerance of arabidopsis. Plant Physiology 133, 1873-1881.
Garg AK, Kim J-K, Owens TG, Ranwala AP, Choi YD, Kochian LV and Wu RJ (2002) Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. PNAS 99, 15898-15903.
Ge L, Chen H, Jiang JF, Zhao Y, Xu ML, Xu YY, Tan KH, Xu ZH and Chong K (2004) Overexpression of OsRAA1 causes pleiotropic phenotypes in transgenic rice plants, including altered leaf, flower, and root development and root response to gravity. Plant Physiology 135, 1502-1513.
Glazier AM, Nadeau JH and Aitman TJ (2002) Finding Genes That Underlie Complex Traits. Science 298, 2345-2349.
Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchinson D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong JP, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu YS, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A and Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296, 92-100.
Hedley M, Kirk G and Santos M (1994) Phosphorus efficiency and the forms of soil phosphorus utilized by upland rice cultivars. Plant and Soil 158, 53-62.
HilleRisLambers D and Vergara B (1982) Summary results of an international collaboration on screening methods for flood tolerance. In 'Proceedings of the 1981 International Deepwater Rice Workshop' pp. 347-353. (International Rice Research Institute: Los Baños, Philippines)
Huke R and Huke E (1997) 'Rice area by type of culture: South, Southeast and East Asia. A revised and updated database.' (International Rice Research Institute: Manila, Philippines)
Ishimaru K, Ono K and Kashiwagi T (2004) Identification of a new gene controlling plant height in rice using the candidate-gene strategy. Planta 218, 388-395.
Jackson MB and Ram PC (2003) Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence. Annals of Botany 91, 227-241.
Jang IC, Oh SJ, Seo JS, Choi WB, Song SI, Kim CH, Kim YS, Seo HS, Do Choi Y, Nahm BH and Kim JK (2003) Expression of a bifunctional fusion of the Escherichia coli genes for trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in transgenic rice plants increases trehalose accumulation and abiotic stress tolerance without stunting growth. Plant Physiology 131, 516-524.
Javot H and Maurel C (2002) The role of aquaporins in root water uptake. Annals of Botany 90, 301-313.
Kaminaka H, Morita S, Nakajima M, Masumura T and Tanaka K (1998) Gene cloning and expression of cytosolic glutathione reductase in rice (Oryza sativa L.). Plant and Cell Physiology. Dec. 39, 1269-1280.
Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sarkarung S and Nguyen HT (2002) Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theoretical and Applied Genetics 104, 880-893.
Kathiresan A, Lafitte H, Chen J and Bennet J (2004) Expression Microarrays and their Application in Drought Stress Research. Field Crops Research in press.
Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D and Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13, 889-905
Kirk G and Bajita J (1995) Root-induced iron oxidation, pH changes and zinc solubilization in the rhizosphere of lowland rice. New Phytologist 131, 129-137.
Kirk G and Du L (1997) Changes in rice root architecture, porosity, and oxygen and proton release under phosphorus deficiency. New Phytologist 135, 191-200.
Kirk G, Santos E and Santos M (1999) Phosphate solubilization by organic anion excretion from rice growing in aerobic soil: rates of excretion and decomposition, effects on rhizosphere pH and effects on phosphate solubility and uptake. New Phytologist 142, 185-200.
Koag MC, Fenton RD, Wilkens S and Close TJ (2003) The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity. Plant Physiology 131, 309-316.
Koller A, Washburn MP, Lange BM, Andon NL, Deciu C, Haynes PA, Hays L, Schieltz D, Ulaszek R, Wei J, Wolters D and Yates JR, III (2002) From the Cover: Proteomic survey of metabolic pathways in rice. PNAS 99, 11969-11974.
Koyama M, Levesley A, Koebner R, Flowers T and Yeo A (2001) Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiology 125, 406-422.
Lafitte H, Price A and Courtois B (2004) Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers. Theoretical and Applied Genetics efirst 28 July 2004.
Lafitte HR and Courtois B (2002) Interpreting cultivar x environment interactions for yield in upland rice: Assigning value to drought-adaptive traits. Crop Science 42, 1409-1420.
Lanceras JC, Pantuwan G, Jongdee B and Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiology 135, 384-399.
Lee SB, Kwon HB, Kwon SJ, Park SC, Jeong MJ, Han SE, Byun MO and Daniell H (2003) Accumulation of trehalose within transgenic chloroplasts confers drought tolerance. Molecular Breeding 11, 1-13.
Li Y, Jones L and McQueen-Mason S (2003a) Expansins and cell growth. Current Opinion in Plant Biology 6, 603-610.
Li Zi Y and Chen Shou Y (1999) Inducible expression of translation elongation factor 1A gene in rice seedlings in response to environmental stresses. Acta Botanica Sinica. Aug., 1999; 41, 800-806.
Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CHM, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S and Khush GS (2003b) QTL x environment interactions in rice. I. Heading date and plant height. Theoretical and Applied Genetics 108, 141-153.
Lian HL, Yu X, Ye Q, Ding XS, Kitagawa Y, Kwak SS, Su WA and Tang ZC (2004) The role of aquaporin RWC3 in drought avoidance in rice. Plant and Cell Physiology 45, 481-489.
Lilley JM and Fukai S (1994) Effect of timing and severity of water deficit on four diverse rice cultivars: II. Pathological responses to soil water deficit. Field Crops Research 37, 215-223
Lilley JM and Ludlow MM (1996) Expression of osmotic adjustment and dehydration tolerance in diverse rice lines. Field Crops Research 48, 185-197.
Lilley JM, Ludlow MM, McCouch SR and O'Toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. Journal of Experimental Botany 47, 1427-1436.
Lin HX, Zhu MZ, Yano M, Gao JP, Liang ZW, Su WA, Hu XH, Ren ZH and Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theoretical and Applied Genetics 108, 253-260.
Liu JX, Liao DQ, Oane R, Estanor L, Yang XE, Li ZC, Bennett J (2004a) Genetic variation in the sensitivity of anther dehiscence to drought stress in rice. Field Crops Res in press
Liu L, Lafitte HR and Guan D (2004b) Wild Oryza species as potential sources of drought-adaptive traits. Euphytica in press.
Liu W, Xu ZH, Luo D and Xue HW (2003) Roles of OsCKI1, a rice casein kinase I, in root development and plant hormone sensitivity. Plant Journal 36, 189-202.
Maathuis FJM, Filatov V, Herzyk P, Krijger GC, Axelsen KB, Chen SX, Green BJ, Li Y, Madagan KL, Sanchez-Fernandez R, Forde BG, Palmgren MG, Rea PA, Williams LE, Sanders D and Amtmann A (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. Plant Journal 35, 675-692.
Mackill D, Amante M, Vergara B and Sarkarung S (1993) Improved semidwarf rice lines with tolerance to submergence of seedlings. Crop Science 33, 749-753.
Mackill D, Coffman W and Garrity D (1996) 'Rainfed Lowland Rice Improvement.' (International Rice Research Institute: Manila, Philippines)
Mackill D and Xu K (1996) Genetics of seedling-stage submergence tolerance in rice. In 'Rice Genetics III'. (Ed. G Khush) pp. 607-612. (International Rice Research Institute: Manila, Philippines)
Mackill J (1986) Rainfed lowland rice improvement in South and Southeast Asia: results of a survey. In 'Progress in Rainfed Lowland Rice' pp. 115-144. (International Rice Research Institute: Los Baños, Philippines)
Mallik S, Kundu C, Banerji C, Nayak D, Chatterjee S, Nada K, Ingram K and Setter T (1995) Rice germplasm evaluation and improvement for stagnant flooding. In 'Rainfed lowland rice - Agricultural research for high risk environments'. (Ed. K Ingram) pp. 97-109. (International Rice Research Institute: Manila, Philippines)
Martre P, Morillon R, Barrieu F, North GB, Nobel PS and Chrispeels MJ (2002) Plasma membrane Aquaporins play a significant role during recovery from water deficit. Plant Physiology 130, 2101-2110.
McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D and Stein L (2003) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research 9, 199-207.
Mitchell JH, Siamhan, D., Wamala, M.H., Risimeri, J.B., Chinyamakobvu, E., Henderson, S.A., Fukai, S. (1998) The use of seedling leaf death score for evaluation of drought resistance of rice. Field Crops Res 55, 129-139.
Moradi F, Ismail A, Gregorio G and Egdane J (2003) Salinity tolerance of rice during reproductive development and association with tolerance at the seedling stage. Indian Journal Plant Physiology 8, 105-116.
Nandi S, Subudhi P, Senadhira D, Manigbas N, Sen-Mandi S and Huang N (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Molecular Genetics, 1-8.
Narciso J and Hossain M (2002) World Rice Statistics. In. (IRRI)
Neue H (1994) Variability in rice to chemical stresses of problem soils and their method of identification. In 'Rice and Problem Soils in South and Southeast Asia'. (Ed. D Senadhira) pp. 115-144. (International Rice Research Institute: Manile, Philippines)
Nguyen HT, Babu RC and Blum A (1997) Breeding for drought resistance in rice: Physiology and molecular genetic considerations. Crop Science 37, 1426-1434.
Otani T and Ae N (1996) Sensitivity of phosphorus uptake to changes in root length and soil volume. Agronomy Journal 88, 371-375.
O'Toole JC (1982) Adaptation of rice to drought-prone environments. In 'in Drought Resistance in Crops, with Emphasis on Rice' pp. 195-213. (International Rice Research Institute, P.O. Box933, Manila, Philippines)
Pantuwan G, Fukai S, Cooper M, Rajatasereekul S and O'Toole JC (2002) Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 3. Plant factors contributing to drought resistance. Field Crops Research 73, 181-200.
Pinheiro B (2003) Integrating selection for drought tolerance into a breeding program: the Brazilian experience. In 'Breeding rice for drought-prone environments'. (Eds KS Fisher, HR Lafitte, S Fukai, B Hardy and G Atlin) pp. 81-92. (IRRI: Manila, Philippines)
Prasad S, Bagali P, Hittalmani S and Shashidhar H (2000) Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). Current Science 78, 162-164.
Price AH, Steele KA, Moore BJ and Jones RGW (2002a) Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes II. Mapping quantitative trait loci for root morphology and distribution. Field Crops Research 76, 25-43.
Price AH, Townend J, Jones MP, Audebert A and Courtois B (2002b) Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa. Plant Molecular Biology 48, 683-695.
Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K and Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA get-blot analyses. Plant Physiology 133, 1755-1767.
Ram P, Singh B, Singh A, Ram P, Singh P, Singh H, Boamfa I, Harren Santosa F, Jackson M, Setter T, Reuss J, Wade L, Singh V and Singh R (2002) Submergence tolerance in rainfed lowland rice: physiological basis and prospects for cultivar improvement through marker-aided breeding. Field Crops Research, 131-152.
Ramalingam J, Cruz CMV, Kukreja K, Chittoor JM, Wu JL, Lee SW, Baraoidan M, George ML, Cohen MB, Hulbert SH, Leach JE and Leung H (2003) Candidate Defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice. Molecular Plant-Microbe Interactions 16, 14-24.
Rausch C and Bucher M (2002) Molecular mechanisms of phosphate transport in plants. Planta 216, 23-37.
Ray JD, Yu L, McCouch SR, Champoux MC, Wang G and Nguyen HT (1996) Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.). Theoretical and Applied Genetics 92, 627-636.
Robin S, Pathan MS, Courtois B, Lafitte R, Carandang S, Lanceras S, Amante M, Nguyen HT and Li Z (2003) Mapping osmotic adjustment in an advanced back-cross inbred population of rice. Theoretical and Applied Genetics 107, 1288-1296.
Rohila JS, Jain RK and Wu R (2002) Genetic improvement of Basmati rice for salt and drought tolerance by regulated expression of a barley Hva1 cDNA. Plant Science 163, 525-532.
Saijo Y, Hata S, Kyozuka J, Shimamoto K and Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant Journal 23, 319-327.
Saijo Y, Kinoshita N, Ishiyama K, Hata S, Kyozuka J, Hayakawa T, Nakamura T, Shimamoto K, Yamaya T and Izui K (2001) A Ca2+-dependent protein kinase that endows rice plants with cold- and salt-stress tolerance functions in vascular bundles. Plant and Cell Physiology 42, 1228-1233.
Saleque M and Kirk G (1995) Root-induced solubilization of phosphate in the rhizosphere of lowland rice. New Phytologist 129, 325-336.
Setter T, Ella E and Valdez A (1994) Relationship between coleoptile elongation and alcoholic fermentation in rice exposed to anoxia. II. Cultivar differences. Annals Botany 74, 273-279.
Setter T, Ellis M, Laureles E, Ella E, Senadhira D, Mishra S, Sarkarung S and Datta S (1997) Physiology and genetics of submergence tolerance in rice. Annals Botany 79, 67-77.
Singh R and Dwivedi J (1996) Rice improvement for rainfed lowland ecosystem: breeding methods and practices in Eastern India. In 'Breeding strategies for rainfed lowland rice in drought-prone environments, Proc. Intl. Workshop 5-8 Nov. 1996'. (Eds S Fukai, M Cooper and J Salisbury) pp. 50-57. (ACIAR: Canberra)
Singh S, Singh O and Singh R (1998) A shuttle breeding approach to rice improvement for rainfed lowland ecosystem in eastern India. In 'Sustainable agriculture for food, energy and industry' pp. 105-115. (James & James (Science Publishers) Ltd.)
Smith F (2002) The phosphate uptake mechanism. Plant and Soil 245, 105-114.
Sripongpangkul K, Posa G, Senadhira D, Brar D, Huang N, Khush G and Li Z (2000) Genes/QTLs affecting flood tolerance in rice. Theoretical Applied Genetics 101, 1074-1081.
Stiller V, Lafitte RandSperry J (2003) Hydraulic properties of rice and the response of gas exchange to water stress. Plant Physiology 132, 1698-1706.
Suprihatno BandCoffman W (1981) Inheritance of submergence tolerance in rice (Oryza sativa L.). SABRAO Journal 13, 98-108.
Thorup TA, Tanyolac B, Livingstone KD, Popovsky S, Paran I and Jahn M (2000) Candidate gene analysis of organ pigmentation loci in the Solanaceae. PNAS 97, 11192-11197.
Tripathy JN, Zhang J, Robin S, Nguyen TT and Nguyen HT (2000) QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theoretical and Applied Genetics 100, 1197-1202.
Van der Straeten D, Zhou ZY, Prinsen E, Van Onckelen HA and Van Montagu MC (2001) A comparative molecular-physiological study of submergence response in lowland and deepwater rice. Plant Physiology 125, 955-968.
van Dijken AJH, Schluepmann H and Smeekens SCM (2004) Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering. Plant Physiology 135, 969-977.
Venuprasad R, Shashidhar HE, Hittalmani S and Hemamalini GS (2002) Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica 128, 293-300.
Ware DH, Jaiswal PJ, Ni JJ, Yap I, Pan XK, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD and McCouch SR (2002) Gramene, a tool for grass Genomics. Plant Physiology 130, 1606-1613.
Wayne M and McIntyre L (2002) Combining mapping and arraying: An approach to candidate gene identification. PNAS 99, 14903-14906.
White J and Zasoski R (1999) Mapping soil micronutrients. Field Crops Research 60, 11-26.
Wissuwa M (2003) How do plants achieve tolerance to phosphorus deficiency - small causes with big effects. Plant Physiology 133, 1947-1958.
Wissuwa M and Ae N (1999) Molecular markers associated with phosphorus uptake and internal phosphorus-use efficiency in rice. In 'Plant Nutrition - Molecular Biology and Genetics'. (Eds G Gissel-Nielsen and A Jensen) pp. 433-439)
Wissuwa M and Ae N (2001a) Further characterization of two QTLs that increase phosphorus uptake of rice (Oryza sativa L.) under phosphorus deficiency. Plant and Soil 237, 275-286.
Wissuwa M and Ae N (2001b) Genotypic variation for tolerance to phosphorus deficiency in rice and the potential for its exploitation in rice improvement. Plant Breeding 120, 43-48.
Wissuwa M, Yano M and Ae N (1998) Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.). Theoretical Applied Genetics 97, 777-783.
Xiong LZ and Yang YN (2003) Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell 15, 745-759.
Xu D, Duan X, Wang B, Hong B, Ho T-H and Wu R (1996) Expression of a late embryogenesis abundant (LEA) protein gene, HvA1, from barley confers tolerance to drought and salinity in transgenic rice. Plant Physiology 110, 249-257.
Xu K and Mackill D (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Molecular Breeding 2, 219-224.
Xu K, Xu X, Ronalds P and Mackill D (2000) A high-resolution linkage map in the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet 263, 681-689.
Yang X, Romheld V and Marschner H (1994) Uptake of iron, zinc, manganese, and copper by seedlings of hybrid and traditional rice cultivars from different soil types. Journal Plant Nutrition 17, 319-331.
Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y and Kikuchi S (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics 17, 87-100.
Yeo A and Flowers T (1986) Salinity resistance in rice (Oryza sativa L.) and a pyramiding approach to breeding varieties for saline soils. Australian Journal Plant Physiology 13, 161-173.
Yoshida S, Ahn J and Forno D (1973) Occurrence, diagnosis and correction of zinc deficiency of lowland rice. Soil Science Plant Nutrition 19, 83-93.
Yu LX and Setter TL (2003) Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiology 131, 568-582.
Zhang G, Guo Y, Chen S and Chen S (1995) RFLP tagging of a salt-tolerance gene in rice. Plant Science 110, 227-234.
Zhang H and Blumwald E (2001) Transgenic salt tolerant tomato plants accumulate salt in foliage but not in fruit. Nature Biotechnology 19, 765-768.
Zhang H-X, Hodson J, Williams J and Blumwald E (2001) Engineering salt-tolerant Brassica plants: Characterization of yield and seed oil quality in transgenic plants with increased vacuolar sodium accumulation. Proc. Nat. Acad. Sci. 98, 12832-12836.
Zhang J, Xie C, Li Z and Chen S (1999) Expression of the plasma membrane H+ATPase gene in response to salt stress in rice salt-tolerant mutant and its original variety. Theoretical Applied Genetics 99, 1006-1011.
Zheng BS, Yang L, Zhang WP, Mao CZ, Wu YR, Yi KK, Liu FY and Wu P (2003) Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theoretical and Applied Genetics 107, 1505-1515.
Zheng HG, Babu RC, Pathan MS, Ali L, Huang N, Courtois B and Nguyen HT (2000) Quantitative trait loci for root-penetration ability and root thickness in rice: Comparison of genetic backgrounds. Genome 43, 53-61.
Zinselmeier C, Sun YJ, Helentjaris T, Beatty M, Yang S, Smith H and Habben J (2002) The use of gene expression profiling to dissect the stress sensitivity of reproductive development in maize. Field Crops Research 75, 111-121.