The M(r) 43K major capsid protein of rice ragged stunt oryzavirus is a post-translationally processed product of a M(r) 67 348 polypeptide encoded by genome segment 8

The nucleotide sequence of DNA complementary to rice ragged stunt oryzavirus (RRSV) genome segment 8 (S8) of an isolate from Thailand was determined. RRSV S8 is 1 914 bp in size and contains a single large open reading frame (ORF) spanning nucleotides 23 to 1 810 which is capable of encoding a protein of M(r) 67 348. The N-terminal amino acid sequence of a ~43K virion polypeptide matched to that inferred for an internal region of the S8 coding sequence. These data suggest that the 43K protein is encoded by S8 and is derived by a proteolytic cleavage. Predicted polypeptide sizes from this possible cleavage of S8 protein are 26K and 42K. Polyclonal antibodies raised against a maltose binding protein (MBP)-S8 fusion polypeptide (expressed in Escherichia coli) recognised four RRSV particle associated polypeptides of M(r) 67K, 46K, 43K and 26K and all except the 26K polypeptide were also highly immunoreactive to polyclonal antibodies raised against purified RRSV particles. Cleavage of the MBP-S8 fusion polypeptide with protease Factor X produced the expected 40K MBP and two polypeptides of apparent M(r) 46K and 26K. Antibodies to purified RRSV particles reacted strongly with the intact fusion protein and the 46K cleavage product but weakly to the 26K product. Furthermore, in vitro transcription and translation of the S8 coding region revealed a post-translational self cleavage of the 67K polypeptide to 46K and 26K products. These data indicate that S8 encodes a structural polypeptide, the majority of which is auto- catalytically cleaved to 26K and 46K proteins. The data also suggest that the 26K protein is the self cleaving protease and that the 46K product is further processed or undergoes stable conformational changes to a ~43K major capsid protein.

Genome segment 5 of rice ragged stunt virus encodes a virion protein

The complete nucleotide sequence of the genome segment 5 (S5) of a Thai isolate of rice ragged stunt virus (RRSV) was determined. The 2682 nucleotide sequence contains a single long open reading frame capable of encoding a polypeptide with a molecular mass of ~91 kDa. Polypeptides encoded by various truncated cDNAs of S5 were expressed using the pGEX fusion protein vector and the highest level of fusion protein was obtained from a construct encoding a hydrophilic region of S5 protein. Antibodies raised against this fusion protein recognized a minor polypeptide, with a molecular mass of ~ 91 kDa, that was present in purified preparations of RRSV particles, infected insect vectors and infected rice plants. This indicates that RRSV S5 encodes a minor structural protein. Comparing the RRSV S5 sequence with sequences of other reo-viruses did not reveal any significant sequence similarities.

Physiological basis of salt stress tolerance in rice expressing the antiapoptotic gene SfIAP

Programmed cell death-associated genes, especially antiapoptosis-related genes have been reported to confer tolerance to a wide range of biotic and abiotic stresses in dicotyledonous plants such as tobacco (Nicotiana tabacum L.) and tomato (Solanum lycopersicum L.). This is the first time the antiapoptotic gene SfIAP was transformed into a monocotyledonous representative: rice (Oryza sativa L.). Transgenic rice strains expressing SfIAP were generated by the Agrobacterium-mediated transformation method and rice embryogenic calli, and assessed for their ability to confer tolerance to salt stress at both the seedling and reproductive stages using a combination of molecular, agronomical, physiological and biochemical techniques. The results show that plants expressing SfIAP have higher salt tolerance levels in comparison to the wild-type and vector controls. By preventing cell death at the onset of salt stress and maintaining the cell membrane’s integrity, SfIAP transgenic rice plants can retain plant water status, ion homeostasis, photosynthetic efficiency and growth to combat salinity successfully.

Modeling nitrous oxide emissions from irrigated agriculture : testing DayCent with high-frequency measurements

A unique high temporal frequency dataset from an irrigated cotton-wheat rotation was used to test the agroecosystem model DayCent to simulate daily N2O emissions from sub-tropical vertisols under different irrigation intensities. DayCent was able to simulate the effect of different irrigation intensities on N2O fluxes and yield, although it tended to overestimate seasonal fluxes during the cotton season. DayCent accurately predicted soil moisture dynamics and the timing and magnitude of high fluxes associated with fertilizer additions and irrigation events. At the daily scale we found a good correlation of predicted vs. measured N2O fluxes (r2 = 0.52), confirming that DayCent can be used to test agricultural practices for mitigating N2O emission from irrigated cropping systems. A 25 year scenario analysis indicated that N2O losses from irrigated cotton-wheat rotations on black vertisols in Australia can be substantially reduced by an optimized fertilizer and irrigation management system (i.e. frequent irrigation, avoidance of excessive fertiliser application), while sustaining maximum yield potentials.

Engineering salinity tolerance in rice by exogenous expression of cell death regulators

Rice, an important crop that feeds more than half of the world's population is very sensitive to salinity stress – a growing problem affecting crop production globally. This PhD study addressed this problem by manipulating the programmed cell death pathways in rice resulting in significant enhancement of salinity stress tolerance. The impact of this work is that farmers would be in a position to grow rice containing such a trait in environments where salinisation of the soil exists, thereby addressing food security needs.

The relationship between N2O, NO, and N2 fluxes from fertilized and irrigated dryland soils of the Aral Sea Basin, Uzbekistan

Microbial respiratory reduction of nitrous oxide (N2O) to dinitrogen (N2) via denitrification plays a key role within the global N-cycle since it is the most important process for converting reactive nitrogen back into inert molecular N2. However, due to methodological constraints, we still lack a comprehensive, quantitative understanding of denitrification rates and controlling factors across various ecosystems. We investigated N2, N2O and NO emissions from irrigated cotton fields within the Aral Sera Basin using the He/O2 atmosphere gas flow soil core technique and an incubation assay. NH4NO3 fertilizer, equivalent to 75 kg ha−1 and irrigation water, adjusting the water holding capacity to 70, 100 and 130% were applied to the incubation vessels to assess its influence on gaseous N emissions. Under soil conditions as they are naturally found after concomitant irrigation and fertilization, denitrification was the dominant process and N2 the main end product of denitrification. The mean ratios of N2/N2O emissions increased with increasing soil moisture content. N2 emissions exceeded N2O emissions by a factor of 5 ± 2 at 70% soil water holding capacity (WHC) and a factor of 55 ± 27 at 130% WHC. The mean ratios of N2O/NO emissions varied between 1.5 ± 0.4 (70% WHC) and 644 ± 108 (130% WHC). The magnitude of N2 emissions for irrigated cotton was estimated to be in the range of 24 ± 9 to 175 ± 65 kg-N ha−1season−1, while emissions of NO were only of minor importance (between 0.1 to 0.7 kg-N ha−1 season−1). The findings demonstrate that for irrigated dryland soils in the Aral Sera Basin, denitrification is a major pathway of N-loss and that substantial amounts of N-fertilizer are lost as N2 to the atmosphere for irrigated dryland soils.

Nitrous oxide emissions from fertilized, irrigated cotton (Gossypium hirsutum L.) in the Aral Sea Basin, Uzbekistan : influence of nitrogen applications and irrigation practices

Nitrous oxide emissions were monitored at three sites over a 2-year period in irrigated cotton fields in Khorezm, Uzbekistan, a region located in the arid deserts of the Aral Sea Basin. The fields were managed using different fertilizer management strategies and irrigation water regimes. N2O emissions varied widely between years, within 1 year throughout the vegetation season, and between the sites. The amount of irrigation water applied, the amount and type of N fertilizer used, and topsoil temperature had the greatest effect on these emissions. Very high N2O emissions of up to 3000 μg N2O-N m−2 h−1 were measured in periods following N-fertilizer application in combination with irrigation events. These “emission pulses” accounted for 80–95% of the total N2O emissions between April and September and varied from 0.9 to 6.5 kg N2O-N ha−1.. Emission factors (EF), uncorrected for background emission, ranged from 0.4% to 2.6% of total N applied, corresponding to an average EF of 1.48% of applied N fertilizer lost as N2O-N. This is in line with the default global average value of 1.25% of applied N used in calculations of N2O emissions by the Intergovernmental Panel on Climate Change. During the emission pulses, which were triggered by high soil moisture and high availability of mineral N, a clear diurnal pattern of N2O emissions was observed, driven by daily changes in topsoil temperature. For these periods, air sampling from 8:00 to 10:00 and from 18:00 to 20:00 was found to best represent the mean daily N2O flux rates. The wet topsoil conditions caused by irrigation favored the production of N2O from NO3− fertilizers, but not from NH4+ fertilizers, thus indicating that denitrification was the main process causing N2O emissions. It is therefore argued that there is scope for reducing N2O emission from irrigated cotton production; i.e. through the exclusive use of NH4+ fertilizers. Advanced application and irrigation techniques such as subsurface fertilizer application, drip irrigation and fertigation may also minimize N2O emission from this regionally dominant agro-ecosystem.

Biolistic transformation of elite indica rice (Oryza sativa L.) cultivars through semi-solid and liquid medium selection systems

Following microprojectile mediated delivery of a plasmid construct (pAHC-25) encoding bar (bialophos resistance) gene into five-day-old scutellar calli derived from mature embryos, the effectiveness of selection procedure for bar-gene expressing tissue was compared for two indica rice cultivars (IR-64 and Karnal Local). While IR-64 transformants could be selected through the generally used semi-solid selection medium, the same procedure was not effective in the basmati cultivar Karnal Local. In the latter case, while lower concentrations (2–4 mg 1−1) of the selective agent phosphinothricin (PPT) yielded only escapes, higher concentrations (6–8 mg l−1) inhibited proliferation of transformed as well as untransformed sectors. For Karnal Local, a liquid medium based selection system was successfully utilized for recovering transformed sectors and, eventually, regenerants. The study demonstrates the generation of transformants of two elite indica cultivars using the environment-independent system of mature embryos from seeds.

The effect of incentive reforms upon productivity : evidence from the Vietnamese rice industry

In this study we use region-level panel data on rice production in Vietnam to investigate total factor productivity (TFP) growth in the period since reunification in 1975. Two significant reforms were introduced during this period, one in 1981 allowing farmers to keep part of their produce, and another in 1987 providing improved land tenure. We measure TFP growth using two modified forms of the standard Malmquist data envelopment analysis (DEA) method, which we have named the Three-year-window (TYW) and the Full Cumulative (FC) methods. We have developed these methods to deal with degrees of freedom limitations. Our empirical results indicate strong average TFP growth of between 3.3 and 3.5 per cent per annum, with the fastest growth observed in the period following the first reform. Our results support the assertion that incentive related issues have played a large role in the decline and subsequent resurgence of Vietnamese agriculture.

Potential climate effect on Japanese rice productivity

Adaptation to climate change has become an important policy question in recent years. Agriculture is an economic activity that is most sensitive to climate change. We evaluate the dynamic effects of productivity change and individual efforts to adapt to climate change. Adaptation actions in agriculture are evaluated to determine how the climate affects production efficiency. In this paper, we use the bi-directional distance function method to measure Japanese rice production loss due to climate. We find that (1) accumulated precipitation has the greatest effect on rice production efficiency and (2) the climate effect on rice production efficiency decreases over time. Our results empirically support the benefit of the adaptation approach.

Japonica rice: Intellectual property, scientific publishing and data-sharing

This article examines a series of controversies within the life sciences over data sharing. Part 1 focuses upon the agricultural biotechnology firm Syngenta publishing data on the rice genome in the journal Science, and considers proposals to reform scientific publishing and funding to encourage data sharing. Part 2 examines the relationship between intellectual property rights and scientific publishing, in particular copyright protection of databases, and evaluates the declaration of the Human Genome Organisation that genomic databases should be global public goods. Part 3 looks at varying opinions on the information function of patent law, and then considers the proposals of Patrinos and Drell to provide incentives for private corporations to release data into the public domain.

Behavior of simetryn and thiobencarb in the plough zone of rice fields

The behavior of simetryn and thiobencarb in flooded rice soil was investigated in a 2-year study. The concentrations of simetryn and thiobencarb were in the hundreds of μg kg^-1 in the top soil layer (0-5 cm) and became significantly lower in tens of μg kg^-1 in the deeper soil layers (5-10 and 10-15 cm). The half-lives of the two herbicides were also shorter (36 and 17 days for simetryn and thiobencarb, respectively) in the top soil layer, as they were most affected by environmental conditions, compared with corresponding values of 82 and 69 days in the 5-10 cm soil layer. Simetryn concentration was stable, while thiobencarb's half-life was 165 days in the 10-15 cm layer. About 35% of the applied mass of simetryn and thiobencarb were found in the rice soil compartment.

Simulated rainfall removal of tricyclazole sprayed on rice foliage

Two rainfall simulations of 30 mm h^-1, with 48-h interval between two simulations, were performed on rice lysimeters at 24, 48, and 72 h after being sprayed with tricyclazole. In the first simulated rainfall, wash-off concentration of tricyclazole was significant irrespective of the interval between the spray time and the rainfall simulation. And from 20.5% to 24.2% of tricyclazole deposited on leaves was removed from the rice foliage. In the second simulated rainfall, concentration of tricyclazole in wash-off water was significantly lower and less than 3.6% of the deposited tricyclazole was lost. © 2008 Springer Science+Business Media, LLC.

Behavior of sprayed tricyclazole in rice paddy lysimeters

The behavior of sprayed tricyclazole in rice paddy lysimeters was studied. Tricyclazole residues were measured from rice leaves and paddy water after tricyclazole spraying in paddy lysimeters. The rate of photolysis and hydrolysis of tricyclazole on the surface of rice leaves was also determined in a laboratory experiment. Tricyclazole was extracted from leaf and water samples and determined by liquid chromatography with UV or mass spectrometry. The hydrolysis half-lives of tricyclazole on rice leaves were 11.9 and 5.1 d for the formulated product and standard, respectively. The photolysis half-lives were longer, 16.4 d for the formulated product and 20.9 d for the standard. In the paddy lysimeter, tricyclazole dissipation on leaves involved either biphasic first-order kinetics or single-phase first-order kinetics, depending on the rainfall pattern. Half-lives of tricyclazole on lysimeter rice leaves were from 3.0 to 5.7 d. The dissipation of tricyclazole in paddy water followed single-phase first-order kinetics with half-lives ranging from 2.1 to 5.0 d.