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1.  Evidence for separate translocation pathways in determining cadmium accumulation in grain and aerial plant parts in rice 
BMC Plant Biology  2009;9:8.
Background
Cadmium (Cd) translocation and accumulation in the grain and aerial plant parts of rice (Oryza sativa L.) is an important aspect of food safety and phytoextraction in areas with contaminated soil. Because control of Cd translocation and accumulation is likely to be determined by the plants genetics, the Cd contents of grain and the aerial parts of rice may be manipulated to improve food safety and for phytoextraction ability. This study studied Cd translocation and accumulation and their genetic control in aerial parts of rice to provide a starting point for improving food safety and phytoextraction in Cd-contaminated soils.
Results
In the japonica rice cultivar "Nipponbare", Cd accumulated in leaves and culms until heading, and in culms and ears after heading. Two quantitative trait loci (QTLs) from indica cv. "Kasalath", qcd4-1 and qcd4-2, affect Cd concentrations in upper plant parts just before heading. Three near-isogenic lines (NILs) with qcd4-1 and qcd4-2 were selected from the "Nipponbare" background, and were analyzed for the effects of each QTL, and for interactions between the two QTLs. From the results compared between "Nipponbare" and each NIL, neither QTL influenced total Cd accumulation in aerial parts at 5 days after heading, but the interaction between two QTLs increased Cd accumulation. At 35 days after heading, qcd4-2 had increased Cd accumulation in the aerial plant parts and decreased translocation from leaves other than flag leaf, but interaction between the two QTLs increased translocation from leaves. NILqcd4-1,2 accumulated higher concentrations of Cd in brown rice than "Nipponbare".
Conclusion
Three types of Cd translocation and accumulation patterns demonstrated by NILs suggested that the accumulation of Cd in leaves and culms before heading, and translocation from them after heading are responsible for Cd accumulation in grain. Cd translocation from roots to culms and ears after heading may direct Cd to the aerial organs without influencing brown rice accumulation.
doi:10.1186/1471-2229-9-8
PMCID: PMC2632998  PMID: 19154618
2.  Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics 
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism.
doi:10.3390/ijms13077994
PMCID: PMC3430217  PMID: 22942686
glutamine synthetase; Lotus japonicus; functional genomics; nitrogen metabolism
3.  Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice 
Comparisons of the activities and diversities of ammonia-oxidizing bacteria (AOB) in the root environment of different cultivars of rice (Oryza sativa L.) indicated marked differences despite identical environmental conditions during growth. Gross nitrification rates obtained by the 15N dilution technique were significantly higher in a modern variety, IR63087-1-17, than in two traditional varieties. Phylogenetic analysis based on the ammonium monooxygenase gene (amoA) identified strains related to Nitrosospira multiformis and Nitrosomonas europaea as the predominant AOB in our experimental rice system. A method was developed to determine the abundance of AOB on root biofilm samples using fluorescently tagged oligonucleotide probes targeting 16S rRNA. The levels of abundance detected suggested an enrichment of AOB on rice roots. We identified 40 to 69% of AOB on roots of IR63087-1-17 as Nitrosomonas spp., while this subpopulation constituted 7 to 23% of AOB on roots of the other cultivars. These results were generally supported by denaturing gradient gel electrophoresis of the amoA gene and analysis of libraries of cloned amoA. In hydroponic culture, oxygen concentration profiles around secondary roots differed significantly among the tested rice varieties, of which IR63087-1-17 showed maximum leakage of oxygen. The results suggest that varietal differences in the composition and activity of root-associated AOB populations may result from microscale differences in O2 availability.
doi:10.1128/AEM.68.6.3067-3075.2002
PMCID: PMC123923  PMID: 12039768
4.  Examination of two lowland rice cultivars reveals that gibberellin-dependent early response to submergence is not necessarily mediated by ethylene 
Plant Signaling & Behavior  2011;6(1):134-136.
Using two lowland rice (Oryza sativa L.) cultivars we found that in both cases submerged-induced elongation early after germination depends on gibberellins (GAs). Submergence increases the content of the active GA1 by enhancing the expression of GA biosynthesis genes, thus facilitating the seedlings to escape from the water and preventing asphyxiation. However, the two cultivars differ in their response to ethylene. The cultivar Senia (short), by contrast to cultivar Bomba (tall), does not elongate after ethylene application, and submerged-induced elongation is not negated by an inhibitor of ethylene perception. Also, while ethylene emanation in Senia is not altered by submergence, Bomba seedlings emanate more ethylene upon desubmergence, associated with enhanced expression of the ethylene biosynthesis gene OsACS5. The cultivar Senia thus allows the possibility of clarifying the role of ethylene and other factors as triggers of GA biosynthesis enhancement in rice seedlings under submergence.
doi:10.4161/psb.6.1.14268
PMCID: PMC3122026  PMID: 21224726
gibberellins; ethylene; submergence; lowland rice; Oryza sativa
5.  Identification of Differential Expression Genes in Leaves of Rice (Oryza sativa L.) in Response to Heat Stress by cDNA-AFLP Analysis 
BioMed Research International  2013;2013:576189.
High temperature impedes the growth and productivity of various crop species. To date, rice (Oryza sativa L.) has not been exploited to understand the molecular basis of its abnormally high level of temperature tolerance. To identify transcripts induced by heat stress, twenty-day-old rice seedlings of different rice cultivars suffering from heat stress were treated at different times, and differential gene expression analyses in leaves were performed by cDNA-AFLP and further verified by real-time RT-PCR. In aggregate, more than three thousand different fragments were indentified, and 49 fragments were selected for the sequence and differential expressed genes were classified functionally into different groups. 6 of 49 fragments were measured by real-time RT-PCR. In addition, the variations of three different polyamine contents in response to heat stress through high-performance liquid chromatography (HPLC) analysis were also performed. The results and their direct and indirect relationships to heat stress tolerance mechanism were discussed.
doi:10.1155/2013/576189
PMCID: PMC3590577  PMID: 23509744
6.  The Arabidopsis thaliana MYB60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells 
Journal of Experimental Botany  2013;64(11):3361-3371.
Plants have evolved different strategies to resist drought, of which the best understood is the abscisic acid (ABA)-induced closure of stomatal pores to reduce water loss by transpiration. The availability of useful promoters that allow for precise spatial and temporal control of gene expression in stomata is essential both for investigating stomatal regulation in model systems and for biotechnological applications in field crops. Previous work indicated that the regulatory region of the transcription factor AtMYB60 specifically drives gene expression in guard cells of Arabidopsis, although its activity is rapidly down-regulated by ABA. Here, the activity of the full-length and minimal AtMYB60 promoters is reported in rice (Oryza sativa), tobacco (Nicotiana tabacum), and tomato (Solanum lycopersicum), using a reporter gene approach. In rice, the activity of both promoters was completely abolished, whereas it was spatially restricted to guard cells in tobacco and tomato. To overcome the negative effect of ABA on the AtMYB60 promoter, a chimeric inducible system was developed, which combined the cellular specificity of the AtMYB60 minimal promoter with the positive responsiveness to dehydration and ABA of the rd29A promoter. Remarkably, the synthetic module specifically up-regulated gene expression in guard cells of Arabidopsis, tobacco, and tomato in response to dehydration or ABA. The comparative analysis of different native and synthetic regulatory modules derived from the AtMYB60 promoter offers new insights into the functional conservation of the cis-mechanisms that mediate gene expression in guard cells in distantly related dicotyledonous species and provides novel tools for modulating stomatal activity in plants.
doi:10.1093/jxb/ert180
PMCID: PMC3733157  PMID: 23828545
ABA; dehydration; guard cell-specific promoters; inducible promoters; stomata; synthetic regulatory modules.
7.  Photorespiration 
Photorespiration is initiated by the oxygenase activity of ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCO), the same enzyme that is also responsible for CO2 fixation in almost all photosynthetic organisms. Phosphoglycolate formed by oxygen fixation is recycled to the Calvin cycle intermediate phosphoglycerate in the photorespiratory pathway. This reaction cascade consumes energy and reducing equivalents and part of the afore fixed carbon is again released as CO2. Because of this, photorespiration was often viewed as a wasteful process. Here, we review the current knowledge on the components of the photorespiratory pathway that has been mainly achieved through genetic and biochemical studies in Arabidopsis. Based on this knowledge, the energy costs of photorespiration are calculated, but the numerous positive aspects that challenge the traditional view of photorespiration as a wasteful pathway are also discussed. An outline of possible alternative pathways beside the major pathway is provided. We summarize recent results about photorespiration in photosynthetic organisms expressing a carbon concentrating mechanism and the implications of these results for understanding Arabidopsis photorespiration. Finally, metabolic engineering approaches aiming to improve plant productivity by reducing photorespiratory losses are evaluated.
doi:10.1199/tab.0130
PMCID: PMC3244903  PMID: 22303256
8.  Microsatellite markers reveal multiple origins for Italian weedy rice 
Ecology and Evolution  2013;3(14):4786-4798.
Weedy rice (Oryza sativa L.) is one of the major issues of rice cultivation worldwide. In Italy, it infests about 70% of the total rice area. Different Weedy Rice populations can be distinguished based on variable morphological and physiological traits; however, little is known about genetic differentiation and origin of Italian weedy rice populations. The objective of this study was to genetically and morphologically characterize and compare different Italian weedy rice populations selected on the basis of different phenotypes. The main Italian rice territory was divided into 10 geographical areas in which 40 weedy rice populations were collected and grouped according to the awn traits. All the individuals of the populations were morphologically characterized according to plant and seed traits. Genetic characterization was performed using 19 SSR markers on all the collected accessions, and several rice cultivars, including some very old (late 19th century), nowadays are no longer cultivated. ANOVA showed that morphological plant and seed traits were significantly affected by the collection area and awnedness group. The importance of the awn morphology was also reflected in the Bayesian clustering where, despite a relatively low genetic diversity, the clusters displayed different awn types. An UPGMA dendrogram confirmed the clusters detected in STRUCTURE analysis and also revealed a grouping of certain old cultivars with the weedy rice, suggesting a common origin.
doi:10.1002/ece3.848
PMCID: PMC3867911  PMID: 24363904
Awn; plant morphology; population genetics; SSRs; weedy rice
9.  The 3′ untranslated region of a soybean cytosolic glutamine synthetase (GS1) affects transcript stability and protein accumulation in transgenic alfalfa 
The Plant journal : for cell and molecular biology  2006;45(5):10.1111/j.1365-313X.2005.02644.x.
Summary
Higher plants assimilate nitrogen in the form of ammonia through the concerted activity of glutamine synthetase (GS) and glutamate synthase (GOGAT). The GS enzyme is either located in the cytoplasm (GS1) or in the chloroplast (GS2). Glutamine synthetase 1 is regulated in different plants at the transcriptional level and there are some reports of regulation at the level of protein stability. Here we present data that clearly establish that GS1 in plants is also regulated at the level of transcript turnover and at the translational level. Using a Glycine max (soybean) GS1 transgene, with and without its 3′ untranslated region (UTR), driven by the constitutive CaMV 35S promoter in Medicago sativa (alfalfa) and Nicotiana tabacum (tobacco), we show that the 3′ UTR plays a major role in both transcript turnover and translation repression in both the leaves and the nodules. Our data suggest that the 3′ UTR mediated turnover of the transcript is regulated by a nitrogen metabolite or carbon/nitrogen ratios. We also show that the 3′ UTR of the gene for the soybean GS1 confers post-transcriptional regulation on a reporter gene. Our dissection of post-transcriptional and translational levels of regulation of GS in plants shows that the situation in plants strongly resembles that in other organisms where GS is regulated at almost all levels. Multistep regulation of GS shows the high priority given by organisms to regulating and ensuring optimal control of nitrogen substrates and preventing overproduction of glutamine and drainage of the glutamate pool.
doi:10.1111/j.1365-313X.2005.02644.x
PMCID: PMC3881554  PMID: 16460515
Glutamine synthetase; 3′ untranslated region; post-transcriptional regulation; transgenic alfalfa; nitrogen assimilation
10.  Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice 
In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93–11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93–11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity.
doi:10.1007/s00122-008-0780-9
PMCID: PMC2470208  PMID: 18491070
11.  C4 photosynthesis and water stress 
Annals of Botany  2008;103(4):635-644.
Background
In contrast to C3 photosynthesis, the response of C4 photosynthesis to water stress has been less-well studied in spite of the significant contribution of C4 plants to the global carbon budget and food security. The key feature of C4 photosynthesis is the operation of a CO2-concentrating mechanism in the leaves, which serves to saturate photosynthesis and suppress photorespiration in normal air. This article reviews the current state of understanding about the response of C4 photosynthesis to water stress, including the interaction with elevated CO2 concentration. Major gaps in our knowledge in this area are identified and further required research is suggested.
Scope
Evidence indicates that C4 photosynthesis is highly sensitive to water stress. With declining leaf water status, CO2 assimilation rate and stomatal conductance decrease rapidly and photosynthesis goes through three successive phases. The initial, mainly stomatal phase, may or may not be detected as a decline in assimilation rates depending on environmental conditions. This is because the CO2-concentrating mechanism is capable of saturating C4 photosynthesis under relatively low intercellular CO2 concentrations. In addition, photorespired CO2 is likely to be refixed before escaping the bundle sheath. This is followed by a mixed stomatal and non-stomatal phase and, finally, a mainly non-stomatal phase. The main non-stomatal factors include reduced activity of photosynthetic enzymes; inhibition of nitrate assimilation, induction of early senescence, and changes to the leaf anatomy and ultrastructure. Results from the literature about CO2 enrichment indicate that when C4 plants experience drought in their natural environment, elevated CO2 concentration alleviates the effect of water stress on plant productivity indirectly via improved soil moisture and plant water status as a result of decreased stomatal conductance and reduced leaf transpiration.
Conclusions
It is suggested that there is a limited capacity for photorespiration or the Mehler reaction to act as significant alternative electron sinks under water stress in C4 photosynthesis. This may explain why C4 photosynthesis is equally or even more sensitive to water stress than its C3 counterpart in spite of the greater capacity and water use efficiency of the C4 photosynthetic pathway.
doi:10.1093/aob/mcn093
PMCID: PMC2707343  PMID: 18552367
C3 and C4 photosynthesis; stomatal and non-stomatal limitation; high CO2; water stress
12.  Development of casparian strip in rice cultivars 
Plant Signaling & Behavior  2011;6(1):59-65.
The development of Casparian strips (CSs) on the endo- and exodermis and their chemical components in roots of three cultivars of rice (Oryza sativa) with different salt tolerance were compared using histochemistry and Fourier transform infrared (FTIR) spectroscopy. The development and deposition of suberin lamellae of CSs on the endo- and exodermis in the salt-tolerant cultivar Liaohan 109 was earlier than in the moderately tolerant cultivar Tianfeng 202 and the sensitive cultivar Nipponbare. The detection of chemical components indicated major contributions to the structure of the outer part from aliphatic suberin, lignin and cell wall proteins and carbohydrates to the rhizodermis, exodermis, sclerenchyma and one layer of cortical cells in series (OPR) and the endodermal Casparian strip. Moreover, the amounts of these major chemical components in the outer part of the Liaohan 109 root were higher than in Tianfeng 202 and Nipponbare, but there was no distinct difference in endodermal CSs among the three rice cultivars. The results suggest that the exodermis of the salt-tolerant cultivar Liaohan 109 functions as a barrier for resisting salt stress.
doi:10.4161/psb.6.1.13545
PMCID: PMC3122007  PMID: 21248477
casparian strip; chemical components; development; rice; root
13.  The effects of water regime on phosphorus responses of rainfed lowland rice cultivars 
Annals of Botany  2008;103(2):211-220.
Background and Aims
Soil phosphorus (P) solubility declines sharply when a flooded soil drains, and an important component of rice (Oryza sativa) adaptation to rainfed lowland environments is the ability to absorb and utilize P under such conditions. The aim of this study was to test the hypothesis that rice cultivars differ in their P responses between water regimes because P uptake mechanisms differ.
Methods
Six lowland rice cultivars (three considered tolerant of low P soils, three sensitive) were grown in a factorial experiment with three water regimes (flooded, moist and flooded-then-moist) and four soil P levels, and growth and P uptake were measured. Small volumes of soil were used to maximize inter-root competition and uptake per unit root surface. The results were compared with the predictions of a model allowing for the effects of water regime on P solubility and diffusion.
Key Results
The plants were P stressed but not water stressed in all the water regimes at all P levels except the higher P additions in the flooded soil. The cultivar rankings scarcely differed between the water regimes and P additions. In all the treatments, the soil P concentrations required to explain the measured uptake were several times the concentration of freely available P in the soil.
Conclusions
The cultivar rankings were driven more by differences in growth habit than specific P uptake mechanisms, so the hypothesis cannot be corroborated with these data. Evidently all the plants could tap sparingly soluble forms of P by releasing a solubilizing agent or producing a greater root length than measured, or both. However, any cultivar differences in this were not apparent in greater net P uptake, possibly because the restricted rooting volume meant that additional P uptake could not be converted into new root growth to explore new soil volumes.
doi:10.1093/aob/mcn199
PMCID: PMC2707314  PMID: 18945744
Oryza sativa; rainfed lowland; phosphorus efficiency; root morphology; solubilization; rice cultivar
14.  Aluminium tolerance in rice is antagonistic with nitrate preference and synergistic with ammonium preference 
Annals of Botany  2012;111(1):69-77.
Background and Aims
Acidic soils are dominated chemically by more ammonium and more available, so more potentially toxic, aluminium compared with neutral to calcareous soils, which are characterized by more nitrate and less available, so less toxic, aluminium. However, it is not known whether aluminium tolerance and nitrogen source preference are linked in plants.
Methods
This question was investigated by comparing the responses of 30 rice (Oryza sativa) varieties (15 subsp. japonica cultivars and 15 subsp. indica cultivars) to aluminium, various ammonium/nitrate ratios and their combinations under acidic solution conditions.
Key Results
indica rice plants were generally found to be aluminium-sensitive and nitrate-preferring, while japonica cultivars were aluminium-tolerant and relatively ammonium-preferring. Aluminium tolerance of different rice varieties was significantly negatively correlated with their nitrate preference. Furthermore, aluminium enhanced ammonium-fed rice growth but inhibited nitrate-fed rice growth.
Conclusions
The results suggest that aluminium tolerance in rice is antagonistic with nitrate preference and synergistic with ammonium preference under acidic solution conditions. A schematic diagram summarizing the interactions of aluminium and nitrogen in soil–plant ecosystems is presented and provides a new basis for the integrated management of acidic soils.
doi:10.1093/aob/mcs234
PMCID: PMC3523647  PMID: 23118122
Aluminium; ammonium; correlation; Indica; Japonica; nitrate; rice
15.  Seasonal Changes in Temperature Dependence of Photosynthetic Rate in Rice Under a Free-air CO2 Enrichment 
Annals of Botany  2006;97(4):549-557.
• Background and Aims Influences of rising global CO2 concentration and temperature on plant growth and ecosystem function have become major concerns, but how photosynthesis changes with CO2 and temperature in the field is poorly understood. Therefore, studies were made of the effect of elevated CO2 on temperature dependence of photosynthetic rates in rice (Oryza sativa) grown in a paddy field, in relation to seasons in two years.
• Methods Photosynthetic rates were determined monthly for rice grown under free-air CO2 enrichment (FACE) compared to the normal atmosphere (570 vs 370 µmol mol−1). Temperature dependence of the maximum rate of RuBP (ribulose-1,5-bisphosphate) carboxylation (Vcmax) and the maximum rate of electron transport (Jmax) were analysed with the Arrhenius equation. The photosynthesis–temperature response was reconstructed to determine the optimal temperature (Topt) that maximizes the photosynthetic rate.
• Key Results and Conclusions There was both an increase in the absolute value of the light-saturated photosynthetic rate at growth CO2 (Pgrowth) and an increase in Topt for Pgrowth caused by elevated CO2 in FACE conditions. Seasonal decrease in Pgrowth was associated with a decrease in nitrogen content per unit leaf area (Narea) and thus in the maximum rate of electron transport (Jmax) and the maximum rate of RuBP carboxylation (Vcmax). At ambient CO2, Topt increased with increasing growth temperature due mainly to increasing activation energy of Vcmax. At elevated CO2, Topt did not show a clear seasonal trend. Temperature dependence of photosynthesis was changed by seasonal climate and plant nitrogen status, which differed between ambient and elevated CO2.
doi:10.1093/aob/mcl001
PMCID: PMC2803663  PMID: 16399793
Temperature dependence; photosynthesis; optimal temperature; activation energy; limiting step; temperature acclimation; free-air CO2 enrichment (FACE); seasonal change; rice; Oryza sativa
16.  Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions  
Journal of Experimental Botany  2012;63(14):5137-5153.
To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background.
doi:10.1093/jxb/ers170
PMCID: PMC3430991  PMID: 22888131
drought; genetic variation; mesophyll conductance; modelling; Oryza sativa L.; photosynthesis; rice; stomatal conductance
17.  Putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance 
Journal of Experimental Botany  2010;61(10):2719-2733.
Effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (Oryza sativa L.) cultivars [I Kong Pao (IKP), salt sensitive; and Pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mM) and 0, 50, and 100 mM NaCl. The salt-sensitive (IKP) and salt-resistant (Pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stressed tissues. Salt stress increased the proportion of conjugated putrescine in salt-resistant Pokkali and decreased it in the salt-sensitive IKP, suggesting a possible protective function in response to NaCl. Activities of the enzymes ornithine decarboxylase (ODC; EC 4.1.1.17) and arginine decarboxylase (ADC; EC 4.1.1.19) involved in putrescine synthesis were higher in salt-resistant Pokkali than in salt-sensitive IKP. Both enzymes were involved in the response to salt stress. Salt stress also increased diamine oxidase (DAO; 1.4.3.6) and polyamine oxidase (PAO EC 1.5.3.11) activities in the roots of salt-resistant Pokkali and in the shoots of salt-sensitive IKP. Gene expression followed by reverse transcription-PCR suggested that putrescine could have a post-translational impact on genes coding for ADC (ADCa) and ODC (ODCa and ODCb) but could induce a transcriptional activation of genes coding for PAO (PAOb) mainly in the shoot of salt-stressed plants. The salt-resistant cultivar Pokkali produced higher amounts of ethylene than the salt-sensitive cultivar IKP, and exogenous putrescine increased ethylene synthesis in both cultivars, suggesting no direct antagonism between polyamine and ethylene pathways in rice.
doi:10.1093/jxb/erq118
PMCID: PMC2882274  PMID: 20472577
Ethylene; Oryza sativa; polyamine; putrescine; rice; salinity; salt resistance
18.  Involvement of S-adenosylmethionine-dependent halide/thiol methyltransferase (HTMT) in methyl halide emissions from agricultural plants: isolation and characterization of an HTMT-coding gene from Raphanus sativus (daikon radish) 
BMC Plant Biology  2009;9:116.
Background
Biogenic emissions of methyl halides (CH3Cl, CH3Br and CH3I) are the major source of these compounds in the atmosphere; however, there are few reports about the halide profiles and strengths of these emissions. Halide ion methyltransferase (HMT) and halide/thiol methyltransferase (HTMT) enzymes concerning these emissions have been purified and characterized from several organisms including marine algae, fungi, and higher plants; however, the correlation between emission profiles of methyl halides and the enzymatic properties of HMT/HTMT, and their role in vivo remains unclear.
Results
Thirty-five higher plant species were screened, and high CH3I emissions and HMT/HTMT activities were found in higher plants belonging to the Poaceae family, including wheat (Triticum aestivum L.) and paddy rice (Oryza sativa L.), as well as the Brassicaceae family, including daikon radish (Raphanus sativus). The in vivo emission of CH3I clearly correlated with HMT/HTMT activity. The emission of CH3I from the sprouting leaves of R. sativus, T. aestivum and O. sativa grown hydroponically increased with increasing concentrations of supplied iodide. A gene encoding an S-adenosylmethionine halide/thiol methyltransferase (HTMT) was cloned from R. sativus and expressed in Escherichia coli as a soluble protein. The recombinant R. sativus HTMT (RsHTMT) was revealed to possess high specificity for iodide (I-), bisulfide ([SH]-), and thiocyanate ([SCN]-) ions.
Conclusion
The present findings suggest that HMT/HTMT activity is present in several families of higher plants including Poaceae and Brassicaceae, and is involved in the formation of methyl halides. Moreover, it was found that the emission of methyl iodide from plants was affected by the iodide concentration in the cultures. The recombinant RsHTMT demonstrated enzymatic properties similar to those of Brassica oleracea HTMT, especially in terms of its high specificity for iodide, bisulfide, and thiocyanate ions. A survey of biogenic emissions of methyl halides strongly suggests that the HTM/HTMT reaction is the key to understanding the biogenesis of methyl halides and methylated sulfur compounds in nature.
doi:10.1186/1471-2229-9-116
PMCID: PMC2752461  PMID: 19723322
19.  A Model Explaining Genotypic and Ontogenetic Variation of Leaf Photosynthetic Rate in Rice (Oryza sativa) Based on Leaf Nitrogen Content and Stomatal Conductance 
Annals of Botany  2007;99(2):265-273.
Backgrounds and Aims
Identification of physiological traits associated with leaf photosynthetic rate (Pn) is important for improving potential productivity of rice (Oryza sativa). The objectives of this study were to develop a model which can explain genotypic variation and ontogenetic change of Pn in rice under optimal conditions as a function of leaf nitrogen content per unit area (N) and stomatal conductance (gs), and to quantify the effects of interaction between N and gs on the variation of Pn.
Methods
Pn, N and gs were measured at different developmental stages for the topmost fully expanded leaves in ten rice genotypes with diverse backgrounds grown in pots (2002) and in the field (2001 and 2002). A model of Pn that accounts for carboxylation and CO2 diffusion processes, and assumes that the ratio of internal conductance to gs is constant, was constructed, and its goodness of fit was examined.
Key Results
Considerable genotypic differences in Pn were evident for rice throughout development in both the pot and field experiments. The genotypic variation of Pn was correlated with that of gs at a given stage, and the change of Pn with plant development was closely related to the change of N. The variation of gs among genotypes was independent of that of N. The model explained well the variation in Pn of the ten genotypes grown under different conditions at different developmental stages.
Conclusions
The response of Pn to increased N differs with gs, and the increase in Pn of genotypes with low gs is smaller than that of genotypes with high gs. Therefore, simultaneous improvements of these two traits are essential for an effective breeding of rice genotypes with increased Pn.
doi:10.1093/aob/mcl253
PMCID: PMC2802993  PMID: 17204541
Model; leaf photosynthesis; genotypic and ontogenetic variation; rice (Oryza sativa); leaf nitrogen content; stomatal conductance; internal conductance
20.  Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves 
PLoS ONE  2011;6(3):e17613.
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
doi:10.1371/journal.pone.0017613
PMCID: PMC3047585  PMID: 21407816
21.  Root morphology, hydraulic conductivity and plant water relations of high-yielding rice grown under aerobic conditions 
Annals of Botany  2011;108(3):575-583.
Background and Aims
Increasing physical water scarcity is a major constraint for irrigated rice (Oryza sativa) production. ‘Aerobic rice culture’ aims to maximize yield per unit water input by growing plants in aerobic soil without flooding or puddling. The objective was to determine (a) the effect of water management on root morphology and hydraulic conductance, and (b) their roles in plant–water relationships and stomatal conductance in aerobic culture.
Methods
Root system development, stomatal conductance (gs) and leaf water potential (Ψleaf) were monitored in a high-yielding rice cultivar (‘Takanari’) under flooded and aerobic conditions at two soil moisture levels [nearly saturated (> –10 kPa) and mildly dry (> –30 kPa)] over 2 years. In an ancillary pot experiment, whole-plant hydraulic conductivity (soil-leaf hydraulic conductance; Kpa) was measured under flooded and aerobic conditions.
Key Results
Adventitious root emergence and lateral root proliferation were restricted even under nearly saturated conditions, resulting in a 72–85 % reduction in total root length under aerobic culture conditions. Because of their reduced rooting size, plants grown under aerobic conditions tended to have lower Kpa than plants grown under flooded conditions. Ψleaf was always significantly lower in aerobic culture than in flooded culture, while gs was unchanged when the soil moisture was at around field capacity. gs was inevitably reduced when the soil water potential at 20-cm depth reached –20 kPa.
Conclusions
Unstable performance of rice in water-saving cultivations is often associated with reduction in Ψleaf. Ψleaf may reduce even if Kpa is not significantly changed, but the lower Ψleaf would certainly occur in case Kpa reduces as a result of lower water-uptake capacity under aerobic conditions. Rice performance in aerobic culture might be improved through genetic manipulation that promotes lateral root branching and rhizogenesis as well as deep rooting.
doi:10.1093/aob/mcr184
PMCID: PMC3158697  PMID: 21807692
Aerobic rice; leaf water potential; Oryza sativa; root system architecture; stomatal conductance; water-saving technology
22.  Ascorbate biosynthesis and function in photoprotection. 
Ascorbate (vitamin C) can reach very high concentrations in chloroplasts (20-300 mM). The pool size in leaves and chloroplasts increases during acclimation to high light intensity and the highest concentrations recorded are in high alpine plants. Multiple functions for ascorbate in photosynthesis have been proposed, including scavenging of active oxygen species generated by oxygen photoreduction and photorespiration, regeneration of alpha-tocopherol from alpha-tocopheryl radicals, cofactor for violaxanthin de-epoxidase and donation of electrons to photosystem II. Hydrogen peroxide scavenging is catalysed by ascorbate peroxidase (Mehler peroxidase reaction) and the subsequent regeneration of ascorbate by reductant derived from photosystem I allows electron flow in addition to that used for CO2 assimilation. Ascorbate is synthesized from guanosine diphosphate-mannose via L-galactose and L-galactono-1,4-lactone. The last step, catalysed by L-galactono-1,4-lactone dehydrogenase, is located on the inner mitochondrial membrane and uses cytochrome c as electron acceptor. L-galactono-1,4-lactone oxidation to ascorbate by intact leaves is faster in high-light acclimated leaves and is also enhanced by high light, suggesting that this step contributes to the control of pool size by light. Ascorbate-deficient Arabidopsis thaliana vtc mutants are hypersensitive to a number of oxidative stresses including ozone and ultraviolet B radiation. Further investigation of these mutants shows that they have reduced zeaxanthin-dependent non-photochemical quenching, confirming that ascorbate is the cofactor for violaxanthin de-epoxidase and that availability of thylakoid lumen ascorbate could limit this reaction. The vtc mutants are also more sensitive to photo-oxidation imposed by combined high light and salt treatments.
PMCID: PMC1692873  PMID: 11127999
23.  Identification of Two Novel hrp-Associated Genes in the hrp Gene Cluster of Xanthomonas oryzae pv. oryzae† 
Journal of Bacteriology  2000;182(7):1844-1853.
We have cloned a hrp gene cluster from Xanthomonas oryzae pv. oryzae. Bacteria with mutations in the hrp region have reduced growth in rice leaves and lose the ability to elicit a hypersensitive response (HR) on the appropriate resistant cultivars of rice and the nonhost plant tomato. A 12,165-bp portion of nucleotide sequence from the presumed left end and extending through the hrpB operon was determined. The region was most similar to hrp genes from Xanthomonas campestris pv. vesicatoria and Ralstonia solanacearum. Two new hrp-associated loci, named hpa1 and hpa2, were located beyond the hrpA operon. The hpa1 gene encoded a 13-kDa glycine-rich protein with a composition similar to those of harpins and PopA. The product of hpa2 was similar to lysozyme-like proteins. Perfect PIP boxes were present in the hrpB and hpa1 operons, while a variant PIP box was located upstream of hpa2. A strain with a deletion encompassing hpa1 and hpa2 had reduced pathogenicity and elicited a weak HR on nonhost and resistant host plants. Experiments using single mutations in hpa1 and hpa2 indicated that the loss of hpa1 was the principal cause of the reduced pathogenicity of the deletion strain. A 1,519-bp insertion element was located immediately downstream of hpa2. Hybridization with hpa2 indicated that the gene was present in all of the strains of Xanthomonas examined. Hybridization experiments with hpa1 and IS1114 indicated that these sequences were detectable in all strains of X. oryzae pv. oryzae and some other Xanthomonas species.
PMCID: PMC101866  PMID: 10714988
24.  Increased leaf photosynthesis caused by elevated stomatal conductance in a rice mutant deficient in SLAC1, a guard cell anion channel protein 
Journal of Experimental Botany  2012;63(15):5635-5644.
In rice (Oryza sativa L.), leaf photosynthesis is known to be highly correlated with stomatal conductance; however, it remains unclear whether stomatal conductance dominantly limits the photosynthetic rate. SLAC1 is a stomatal anion channel protein controlling stomatal closure in response to environmental [CO2]. In order to examine stomatal limitations to photosynthesis, a SLAC1-deficient mutant of rice was isolated and characterized. A TILLING screen of N-methyl-N-nitrosourea-derived mutant lines was conducted for the rice SLAC1 orthologue gene Os04g0674700, and four mutant lines containing mutations within the open reading frame were obtained. A second screen using an infrared thermography camera revealed that one of the mutants, named slac1, had a constitutive low leaf temperature phenotype. Measurement of leaf gas exchange showed that slac1 plants grown in the greenhouse had significantly higher stomatal conductance (g s), rates of photosynthesis (A), and ratios of internal [CO2] to ambient [CO2] (C i/C a) compared with wild-type plants, whereas there was no significant difference in the response of photosynthesis to internal [CO2] (A/C i curves). These observations demonstrate that in well-watered conditions, stomatal conductance is a major determinant of photosynthetic rate in rice.
doi:10.1093/jxb/ers216
PMCID: PMC3444276  PMID: 22915747
Anion channel; carbon dioxide; mutant; Oryza sativa; photosynthesis; SLAC1; stomatal conductance
25.  Evaluation of Pseudomonas fluorescens for Suppression of Sheath Rot Disease and for Enhancement of Grain Yields in Rice (Oryza sativa L.) 
Pseudomonas fluorescens strains antagonistic to Sarocladium oryzae, the sheath rot (Sh-R) pathogen of rice (Oryza sativa L.), were evaluated in greenhouse and field tests for suppression of Sh-R severity and enhancement of grain yields of rice. Imprints of rice seedlings and a direct-observation technique of staining roots with fluorochromes confirmed the association of P. fluorescens with roots and the ability of the strain to move along shoot tips. In greenhouse tests, P. fluorescens-treated rice plants (cv. IR 20) showed a 54% reduction in the length of Sh-R lesions. In three field tests, treatment with P. fluorescens reduced the severity of Sh-R by 20 to 42% in five rice cultivars. Bacterization of rice cultivars with P. fluorescens enhanced plant height, number of tillers, and grain yields from 3 to 160%.
Images
PMCID: PMC204057  PMID: 16347428

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