Epigenetic responses to drought stress in rice (Oryza sativa L.)

Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F₁ hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. The cytosine methylation polymorphism in genomic DNA was quantified under both the conditions at the reproductive stage of the plant using the Methylation Sensitive Amplified Polymorphism (MSAP) technique devised by Xiong et al. (261:439–446, 1999). The results depicted that under drought condition, hyper-methylation was predominant in the drought susceptible genotypes while drought tolerant genotypes presented hypo-methylation behavior. While imposing drought, spikelet sterility per cent was positively correlated to percentage of methylation whereas, panicle length, number of seed per panicle, panicle weight, 100 seed weight, and yield/plant were negatively correlated indicating the role of epigenetic regulation in yield attributing traits in response to drought. Thus, methylation can be considered as an important epigenetic regulatory mechanism in rice plants to adapt drought situation. From this study, we speculate that the hyper- methylation may be an indicator of drought susceptibility and the hypo-methylation for drought tolerance and this methylation polymorphism can be effectively used in drought screening program.     

Hydrogen peroxide is involved in the regulation of rice (Oryza sativa L.) tolerance to salt stress

In the present study, we investigated the salt tolerance mechanism of two rice cultivars (Zhenghan-2 and Yujing-6), which show different tolerance to drought and disease. NaCl induced higher extent of lipid peroxide and ion leakage in Yujing-6 roots than those in Zhenghan-2 roots. H₂O₂ accumulation in Zhenghan-2 roots was lower than that in Yujing-6 roots under salt stress. Comparatively, NaCl treatment did not increase O₂ ^? contents in both rice roots, however, O₂ ^? level in Yujing-6 roots was higher than that in Zhenghan-2 roots under both control and salt stress conditions. Ascorbate peroxidases (APX) activity increased more significantly in Zhenghan-2 roots than that in Yujing-6 roots. The activity of catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and glucose-6-phosphate dehydrogenase (G6PDH) was similarly enhanced in both rice roots under salt stress; however, they showed higher levels in Zhenghan-2 roots than in Yujing-6 roots. Exogenous H₂O₂ could enhance APX, CAT, POD, SOD and G6PDH activities in a concentration-dependent manner in both rice roots. Diphenylene iodonium (DPI), a plasma membrane (PM) NADPH oxidase inhibitor, which counteracted the NaCl-induced H₂O₂ accumulation, markedly decreased the activity of above enzymes. Moreover, ion leakage increased dramatically in Zhenghan-2 roots and reached to the similar level of Yujing-6 roots under NaCl+DPI treatment. Taken together, H₂O₂, which is mainly generated from PM NADPH oxidase, is involved in Zhenghan-2 rice tolerance to salt stress by enhancing the cellular antioxidant level.     

Low irradiance stress tolerance in rice (Oryza sativa L.)

The effect of low irradiance on three rice cultivars (shade tolerant cvs. Swarnaprabha and CO 43 and shade susceptible cv. IR 20) was studied. The large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase with molecular mass of 55 kDa was reduced in cv. IR 20 grown under low irradiance (LI). Native protein profile studied showed, under LI, reduction in the contents of proteins with RF values 0.03, 0.11 and 0.37. Analysis of chloroplast polypeptides revealed an induction of light-harvesting chlorphyll-protein 2 (LHCP2) under shade. The induction was more expressed in cv. CO 43 than in cv. IR 20. Under LI, in vivo labelled protein bands in the molecular range of 26 - 27 kDa were induced. These proteins were highly turned over in the LI-grown plants of cv. CO 43 than in cv. IR 20. A signal for rbcL gene sequences in EcoRI digested lanes was also found. Isozyme analysis of peroxidase showed an induction of a new band with RF 0.43 in cv. IR 20 subjected to LI. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phosphorylation upon cold stress in rice (Oryza sativa L.) seedlings

The response of plants to cold stress is not well understood at the biochemical level, although it has been studied extensively at the ecological level. To investigate whether protein phosphorylation may play an important role in cold stress, we exposed rice seedlings to low temperatures, prepared protein extracts from the leaves and incubated these in the presence of [γ-³²P]ATP. The proteins were then separated by two-dimensional polyacrylamide gel electrophoresis. While several proteins were found to be phosphorylated upon cold stress one protein, pp35, which has an isoelectric point of 8.0, was more phosphorylated than the others. The pp35 protein was found to be phosphorylated when rice seedlings were incubated for 6 h at 5°C before the leaf protein extract was prepared and radioactive labeling was performed. The pp35 was, however, significantly more phosphorylated in cold-tolerant rice varieties. Antibodies were raised against purified pp35 in adult rabbits. Using this pp35 antibody, which can recognize the RuBisCO large-chain subunit (LSU), and from amino acid sequencing of pp35, we were able to identify and confirm the pp35 protein as the fragment of RuBisCO LSU (EC 4.1.1.39). Phosphorylation of the RuBisCO LSU may be important in cold tolerance. Received: 7 July 1998 / Accepted: 19 December 1998     

Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

A total of ten rare indigenous rice landraces of West Bengal were screened for germination potential and seedling growth under varying concentrations of sodium chloride (NaCl) and polyethylene glycol (PEG) solutions as osmotic stress inducing agents. Among the studied rice landraces Kelas and Bhut Moori showed highest degree of tolerance to induced osmotic stresses. Proline content of the studied lines was also determined. Genetic relationship among the studied rice landraces was assessed with 22 previously reported osmotic stress tolerance linked Simple Sequence Repeat (SSR) markers. The identified allelic variants in form of amplified products size (molecular weight) for each SSR marker were documented to find out allele mining set for the linked markers of the studied genotypes in relation to osmotic stress tolerance. A Microsatellite Panel was constructed for the different allelic forms (size of amplified products) of each used marker. Among 22 SSR markers, ten showed unique alleles in form of single specific amplified product for the studied four genotypes which can be used for varietal identification. Genetic relationship among the studied rice lines was determined and a dendrogram was constructed to reveal their genetic inter-relationship. Polymorphism Information Content (PIC) for each used marker was also calculated for the studied rice lines.     

Water-use efficiency in rice (Oryza sativa L.) in relation to resistance to salinity

Abstract The effects of sodium chloride on water-use efficiency of a number of varieties of rice have been investigated. Sensitivity to salinity in rice arises in large part from excessive rates of sodium ion transport to the shoot consequent upon high rates of transpirational water loss. Varietal differences in water-use efficiency were found: these were greater when measured for whole shoots over a period of one week, than when made as instantaneous measurements on individual leaves. Salinity had rather little effect on water use efficiency but overall resistance of seedlings to salt was, in general, greater the greater the water-use efficiency. The reasons for the differences between varieties are discussed in terms of differences in growth pattern: among the seven varieties investigated, water-use efficiency and salt-resistance were lower in dwarfed as opposed to non-dwarfed varieties.     

Cadmium stress-induced oxidative stress and role of nitric oxide in rice (Oryza sativa L.)

Cadmium (Cd) is a potential environmental phytotoxicant. The generation of reactive oxygen species (ROS) due to Cd stress is responsible for the induction of oxidative stress in plants. On the other hand, SNP, a NO donor is known to have effect on Cd-induced oxidative stress in plants. We evaluated the effect of NO on the regulation of Cd stress in the rice (Oryza sativa L.) variety MSE-9. Cd treatment was given in the form of 50, 100 and 200 ??M, whereas for interaction study, 100 ??M of Cd and 100 ??M of SNP were used. The result showed that Cd-induced oxidative stress in MSE-9 by generating ROS. However, when SNP was given with Cd stress, it was seen that SNP treatment regulated the stress metabolism in rice seedlings under Cd toxicity by generating NO. It can be said that the SNP in combination with Cd treatment might possess the way to protect rice seedlings under Cd stress.     

Heterosis breeding in rice (Oryza sativa L.)

Summary Studies conducted at the International Rice Research Institute (IRRI) during 1980 and 1981 have shown up to 73% heterosis, 59% heterobeltiosis and 34% standard heterosis for yield in rice. The latter was estimated in comparison to commercial varieties: IR36 and IR42 (yield 4–5 t/ha in wet season trials and 7–8 t/ha in dry season trials). Generally speaking, absolute yield was lower and extent of standard heterosis was higher in wet season than in dry season with some exception. Yields up to 5.9 t/ha (22% standard heterosis) in the wet season and 10.4 t/ha (34% standard heterosis) in the dry season were obtained. Most of the hybrids performed better in some season while some performed better in both seasons. Hybrids showed better lodging resistance although they were 5–10 cm taller. F₁ hybrids had significant positive correlations with the parental traits viz., yield (r = 0.446), tillering (r = 0.746), height (r = 0.810) and flowering (r = 0.843). Selection of parents among elite breeding lines on the basis of their per se yield performance, diverse origin and resistance to insects and diseases should give heterotic combination. Yield advantage of hybrids was due primarily to increase in number of spikelets per unit area even though tiller number was reduced. Grain weight was either the same or slightly higher. High yielding hybrids also showed significant heterosis and heterobeltiosis for total dry matter and harvest index. For commercial utilization of heterosis in rice, effective male sterility and fertility restoration systems are available and up to 45% natural outcrossing on male sterile lines has been observed. Consequently, F₁ rice hybrid have been successfully developed and used in China. Prospects of developing hybrid rice varieties elsewhere appear bright especially in countries that have organized seed production, certification and distribution programs and where hybrid seed can be produced at a reasonable cost.     

High temperature stress and spikelet fertility in rice (Oryza sativa L.)

In future climates, greater heat tolerance at anthesis will be required in rice. The effect of high temperature at anthesis on spikelet fertility was studied on IR64 (lowland indica) and Azucena (upland japonica) at 29.6 degrees C (control), 33.7 degrees C, and 36.2 degrees C tissue temperatures. The objectives of the study were to: (i) determine the effect of temperature on flowering pattern; (ii) examine the effect of time of day of spikelet anthesis relative to a high temperature episode on spikelet fertility; and (iii) study the interactions between duration of exposure and temperature on spikelet fertility. Plants were grown at 30/24 degrees C day/night temperature in a greenhouse and transferred to growth cabinets for the temperature treatments. Individual spikelets were marked with paint to relate fertility to the time of exposure to different temperatures and durations. In both genotypes the pattern of flowering was similar, and peak anthesis occurred between 10.30 h and 11.30 h at 29.2 degrees C, and about 45 min earlier at 36.2 degrees C. In IR64, high temperature increased the number of spikelets reaching anthesis, whereas in Azucena numbers were reduced. In both genotypesor=33.7 degrees C at anthesis caused sterility. In IR64, there was no interaction between temperature and duration of exposure, and spikelet fertility was reduced by about 7% per degrees C>29.6 degrees C. In Azucena there was a significant interaction and spikelet fertility was reduced by 2.4% degrees Cd-1 above a threshold of 33 degrees C. Marking individual spikelets is an effective method to phenotype genotypes and lines for heat tolerance that removes any apparent tolerance due to temporal escape.     

Arsenic toxicity to rice (Oryza sativa L.) in Bangladesh

Natural contamination of groundwater with arsenic (As) occurs around the world but is most widespread in the river basin deltas of South and Southeast Asia. Shallow groundwater is extensively used in the Bengal basin for irrigation of rice in the dry winter season, leading to the possibility of As accumulation in soils, toxicity to rice and increased levels of As in rice grain and straw. The impact of As contaminated irrigation water on soil-As content and rice productivity was studied over two winter-season rice crops in the command area of a single tubewell in Faridpur district, Bangladesh. After 16–17 years of use of the tubewell, a spatially variable build up of As and other chemical constituents of the water (Fe, Mn and P) was observed over the command area, with soil-As levels ranging from about 10 to 70 mg kg^?1. A simple mass balance calculation using the current water As level of 0.13 mg As L^?1 suggested that 96% of the added arsenic was retained in the soil. When BRRI dhan 29 rice was grown in two successive years across this soil-As gradient, yield declined progressively from 7–9 to 2–3 t ha^?1 with increasing soil-As concentration. The average yield loss over the 8 ha command area was estimated to be 16%. Rice-straw As content increased with increasing soil-As concentration; however, the toxicity of As to rice resulted in reduced grain-As concentrations in one of the 2 years. The likelihood of As-induced yield reductions and As accumulation in straw and grain has implications to agricultural sustainability, food quality and food security in As-affected regions throughout South and Southeast Asia.     

The role of lateral roots in bypass flow in rice (Oryza sativa L.)

Although an apoplastic pathway (the so‐called bypass flow) is implicated in the uptake of Na⁺ by rice growing in saline conditions, the point of entry of this flow into roots remains to be elucidated. We investigated the role of lateral roots in bypass flow using the tracer trisodium‐8‐hydroxy‐1,3,6‐pyrenetrisulphonic acid (PTS) and the rice cv. IR36. PTS was identified in the vascular tissue of lateral roots using both epifluorescence microscopy and confocal laser scanning microscopy. Cryo‐scanning electron microscopy and epifluorescence microscopy of sections stained with berberine‐aniline blue revealed that the exodermis is absent in the lateral roots. We conclude that PTS can move freely through the cortical layers of lateral roots, enter the stele and be transported to the shoot via the transpiration stream.     

Spectral response of rice (Oryza sativa L.) leaves to Fe2+ stress

In the management of lake eutrophication, the regulation effect of Fe is considered, in addition to the controlling nitrogen- and phosphorus input. Based on the “Fe hypothesis”, this paper tentatively ap-plied plant spectral response to the remote sensing early-warning mechanism of lake eutrophication. A laboratory water culture experiment with rice (Oryza sativa L.) was conducted to study Fe uptake by plants and the chlorophyll concentration and visible-near infrared spectrum of vegetable leaves as well as their interrelations under Fe²⁺ stress. Three spectral indices, i.e., A₁ (integral value of the changes of spectral reflectivity in the range 460―670 nm under Fe²⁺ stress), A₂ (integral value of the changes of spectral reflectivity in the range of 760―1000 nm under Fe²⁺ stress) and S (blue-shift range of red edge curve under Fe²⁺ stress), were used to establish quantitative models about the relationships between the rice leaf spectrum and Fe²⁺ stress. With the increase of Fe²⁺ in a culture solution, the Fe content in rice plants increased, while the chlorophyll concentration in vegetative leaves decreased. The spectral reflectivity of vegetable leaves increased in the visible light band but decreased in the near infrared band, and the blue-shift range of the red edge curve increased. The indices _A1, A₂ and S all had sig-nificant correlations with the Fe content in rice leaves, the correlation coefficient being respectively 0.951 (P < 0.01), −0.988 (P < 0.01) and 0.851 (P < 0.01), and simulated (multiple correlation coefficients R² > 0.96) and predict the Fe level in rice leaves.     

The extent of linkage disequilibrium in rice (Oryza sativa L.)

Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (approximately 150 kb) and indica (approximately 75 kb). LD extends over a shorter distance in O. rufipogon (<40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.     

Zinc ameliorates copper-induced oxidative stress in developing rice (Oryza sativa L.) seedlings

Rice (Oryza sativa L.) seedlings were treated with different concentrations of copper (Cu) either in presence or absence of zinc (Zn), and different events were investigated to evaluate the ameliorative effect of Zn on Cu stress. In presence of high Cu concentration, growth of both root and shoots were considerably reduced. Decline in elongation and fresh mass was observed in root and shoot. Zn alone did not show any considerable difference as compared to control, but when supplemented along with high concentration Cu, it prompted the growth of both root and shoot. After 7 days, root growth was 9.36 and 9.59 cm, respectively, at 200 and 500 μM of Cu alone as compared to 10.59 and 12.26 cm at similar Cu concentrations, respectively, in presence of Zn. Cu accumulation was considerably high after 7 days of treatment. In absence of Zn, significant accumulation of Cu was observed. Zn supplementation ameliorated the toxic impact of Cu and minimized its accumulation. Cu treatment for 1 and 7 days resulted in a dose-dependent increase in hydrogen peroxide (H₂O₂). When Cu was added in presence of Zn, the H₂O₂ production in root and shoot was reduced significantly. The increase in H₂O₂ production under Cu stress was accompanied by augmentation of lipid peroxidation. In absence of Zn, Cu alone enhanced the malondialdehyde (MDA) production in both root and shoot after 1 and 7 days of treatment. The MDA content drastically reduced in root and shoot as when Zn was added during Cu treatment. The activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), and guaiacol peroxidase (GPX) were elevated under Cu stress both in root and shoot. Addition of Zn further stimulated the activities of these enzymes. Both ascorbate (AsA) and glutathione (GSH) contents were high under Cu stress either in presence or absence of Zn. The results suggests that Zn supplementation improves plant survival capacity under high Cu stress by modulating oxidative stress through stimulation of antioxidant mechanisms and restricts the accumulation of toxic concentrations of Cu.     

低钾胁迫对水稻(Oryza sativa L.)化感潜力变化的影响

研究以国际公认的化感水稻P1312777和非化感水稻Lemont为供体,稗草（Echinochloa cru-galli L.）为受体,采用稻／稗共培体系,研究低钾胁迫对水稻化感潜力变化的影响及其机制。受体稗草的形态指标分析结果表明,低钾胁迫促使化感水稻P1312777对共培稗草的根长、株高和干重的抑制率均升高,增幅远大于非化感水稻Lemont。受体稗草生理生化指标分析结果表明,低钾胁迫下化感与非化感水稻对受体稗草保护酶系（SOD、POD、CAT）及根系活力的抑制作用增强,但化感水稻P1312777比非化感水稻Lemont的抑制程度大,且达极显著差异。实时荧光定量PCR分析结果表明,低钾胁迫下,化感水稻P1312777根部与叶部中酚类代谢的关键酶——苯丙氨酸解氨酶、肉桂酸-4-羟化酶、羟化酶、O-甲基转移酶的基因均上调表达,而非化感水稻根部相应酶均下调表达,叶部除苯丙氨酸解氨酶上调,其余酶也下调表达。而萜类代谢途径关键酶——HMG—CoA还原酶、角鲨烯合酶、单萜烯环化酶、倍半萜烯环化酶、二萜烯环化酶的基因,在两种水稻根部中呈现出相同或相似的表达方式（上调或下调）,即HMG—CoA还原酶上调表达,角鲨烯合酶、单萜烯环化酶、倍半萜烯环化酶、二萜烯环化酶下调表达;而在水稻叶部,非化感水稻Lmont相应酶基因表达方式仍然不变,化感水稻P1312777除了角鲨烯合酶下调表达,其余4个酶均上调表达。水稻根系分泌物中酚类物质的HPLC分析结果表明,低钾胁迫下,化感水稻P1312777根系分泌物中,所检出的酚酸类物质总量是正常营养条件下的2．30倍,而非化感水稻Lemont则是正常营养条件下的0．91倍。综合分析认为低钾胁迫下,化感水稻P1312777抑草能力增强主要是由于酚类代谢途径关键酶基因表达上调,导致酚类代谢途径旺盛,分泌出更多的酚类物质,进而破坏受体稗草保护酶系统,抑制了稗草的正常生长。     

RNAi-directed down-regulation of RSV results in increased resistance in rice (Oryza sativa L.)

Rice stripe disease (RSD), caused by rice stripe virus (RSV), is a serious disease in temperate rice-growing areas. We have created an RNAi construct containing coat protein gene (CP) and disease specific protein gene (SP) sequences from RSV. The RNAi construct was transformed into two susceptible japonica varieties, Suyunuo and Guanglingxiangjing, to develop resistance against RSD. The homozygous progeny of rice plants in the T(5) and T(7) generations containing RNAi constructs, after self-fertilization were strongly resistant to viral infection. RT-PCR indicated that viral replication of SP and CP in the transgenic plants was significantly inhibited. There were no obvious morphological or developmental differences between the transgenic and wild-type plants from seedling stage to maturity. The excellent agronomic traits of these two varieties, such as high yield and good quality were maintained. Suppression of virus genes using RNAi is therefore a practical and effective strategy for controlling viral infection in crops.