Rice-arsenate interactions in hydroponics:whole genome transcriptional analysis

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

Rice-arsenate interactions in hydroponics: a three-gene model for tolerance

In this study, the genetic mapping of the tolerance of root growth to 13.3 muM arsenate [As(V)] using the BalaxAzucena population is improved, and candidate genes for further study are identified. A remarkable three-gene model of tolerance is advanced, which appears to involve epistatic interaction between three major genes, two on chromosome 6 and one on chromosome 10. Any combination of two of these genes inherited from the tolerant parent leads to the plant having tolerance. Lists of potential positional candidate genes are presented. These are then refined using whole genome transcriptomics data and bioinformatics. Physiological evidence is also provided that genes related to phosphate transport are unlikely to be behind the genetic loci conferring tolerance. These results offer testable hypotheses for genes related to As(V) tolerance that might offer strategies for mitigating arsenic (As) accumulation in consumed rice.

Arsenic contamination of Bangladesh paddy field soils:implications for rice contribution to arsenic consumption

Arsenic contaminated groundwater is used extensively in Bangladesh to irrigate the staple food of the region, paddy rice (Oryza sativa L.). To determine if this irrigation has led to a buildup of arsenic levels in paddy fields, and the consequences for arsenic exposure through rice ingestion, a survey of arsenic levels in paddy soils and rice grain was undertaken. Survey of paddy soils throughout Bangladesh showed that arsenic levels were elevated in zones where arsenic in groundwater used for irrigation was high, and where these tube-wells have been in operation for the longest period of time. Regression of soil arsenic levels with tube-well age was significant. Arsenic levels reached 46 microg g(-1) dry weight in the most affected zone, compared to levels below l0 microg g(-1) in areas with low levels of arsenic in the groundwater. Arsenic levels in rice grain from an area of Bangladesh with low levels of arsenic in groundwaters and in paddy soils showed that levels were typical of other regions of the world. Modeling determined, even these typical grain arsenic levels contributed considerably to arsenic ingestion when drinking water contained the elevated quantity of 0.1 mg L(-1). Arsenic levels in rice can be further elevated in rice growing on arsenic contaminated soils, potentially greatly increasing arsenic exposure of the Bangladesh population. Rice grain grown in the regions where arsenic is building up in the soil had high arsenic concentrations, with three rice grain samples having levels above 1.7 microg g(-1).

Uptake kinetics of arsenic species in rice plants

Arsenic (As) finds its way into soils used for rice (Oryza sativa) cultivation through polluted irrigation water, and through historic contamination with As-based pesticides. As is known to be present as a number of chemical species in such soils, so we wished to investigate how these species were accumulated by rice. As species found in soil solution from a greenhouse experiment where rice was irrigated with arsenate contaminated water were arsenite, arsenate, dimethylarsinic acid, and monomethylarsonic acid. The short-term uptake kinetics for these four As species were determined in 7-d-old excised rice roots. High-affinity uptake (0-0.0532 mM) for arsenite and arsenate with eight rice varieties, covering two growing seasons, rice var. Boro (dry season) and rice var. Aman (wet season), showed that uptake of both arsenite and arsenate by Boro varieties was less than that of Aman varieties. Arsenite uptake was active, and was taken up at approximately the same rate as arsenate. Greater uptake of arsenite, compared with arsenate, was found at higher substrate concentration (low-affinity uptake system). Competitive inhibition of uptake with phosphate showed that arsenite and arsenate were taken up by different uptake systems because arsenate uptake was strongly suppressed in the presence of phosphate, whereas arsenite transport was not affected by phosphate. At a slow rate, there was a hyperbolic uptake of monomethylarsonic acid, and limited uptake of dimethylarsinic acid.

Effect of organic matter amendment, arsenic amendment and water management regime on rice grain arsenic species

Arsenic accumulation in rice grain has been identified as a major problem in some regions of Asia. A study was conducted to investigate the effect of increased organic matter in the soil on the release of arsenic into soil pore water and accumulation of arsenic species within rice grain. It was observed that high concentrations of soil arsenic and organic matter caused a reduction in plant growth and delayed flowering time. Total grain arsenic accumulation was higher in the plants grown in high soil arsenic in combination with high organic matter, with an increase in the percentage of organic arsenic species observed. The results indicate that the application of organic matter should be done with caution in paddy soils which have high soil arsenic, as this may lead to an increase in accumulation of arsenic within rice grains. Results also confirm that flooding conditions substantially increase grain arsenic. (c) 2013 Elsevier Ltd. All rights reserved.

Profiling the ionome of rice and its use in discriminating geographical origins at the regional scale, China

Element profile was investigated for their use to trace the geographical origin of rice (Oryza sativa L.) samples. The concentrations of 13 elements (calcium (Ca), potassium (K), magnesium (Mg), phosphorus (P), boron (B), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), arsenic (As), selenium (Se), molybdenum (Mo), and cadmium (Cd)) were determined in the rice samples by inductively coupled plasma optical emission and mass spectrometry. Most of the essential elements for human health in rice were within normal ranges except for Mo and Se. Mo concentrations were twice as high as those in rice from Vietnam and Spain. Meanwhile, Se concentrations were three times lower in the whole province compared to the Chinese average level of 0.088 mg/kg. About 12% of the rice samples failed the Chinese national food safety standard of 0.2 mg/kg for Cd. Combined with the multi-elemental profile in rice, the principal component analysis (PCA), discriminant function analysis (DFA) and Fibonacci index analysis (FIA) were applied to discriminate geographical origins of the samples. Results indicated that the FIA method could achieve a more effective geographical origin classification compared with PCA and DFA, due to its efficiency in making the grouping even when the elemental variability was so high that PCA and DFA showed little discriminatory power. Furthermore, some elements were identified as the most powerful indicators of geographical origin: Ca, Ni, Fe and Cd. This suggests that the newly established methodology of FIA based on the ionome profile can be applied to determine the geographical origin of rice.

Spatial distribution of arsenic and temporal variation of its concentration in rice

P>In order to gain insights into the transport and distribution of arsenic (As) in intact rice (Oryza sativa) plants and its unloading into the rice grain, we investigated the spatial distribution of As and the temporal variation of As concentration in whole rice plants at different growth stages. To the best of our knowledge, this is the first time that such a study has been performed.

Inductively coupled plasma mass spectroscopy (ICP-MS) and high-performance liquid chromatography (HPLC)-ICP-MS were used to analyze total As concentration and speciation. Moreover, synchrotron-based X-ray fluorescence (SXRF) was used to investigate in situ As distribution in the leaf, internode, node and grain.

Total As concentrations of vegetative tissues increased during the 2 wk after flowering. The concentration of dimethylarsinic acid (DMA) in the caryopsis decreased progressively with its development, whereas inorganic As concentration remained stable. The ratios of As content between neighboring leaves or between neighboring internodes were c. 0.6. SXRF revealed As accumulation in the center of the caryopsis during its early development and then in the ovular vascular trace.

These results indicate that there are different controls on the unloading of inorganic As and DMA; the latter accumulated mainly in the caryopsis before flowering, whereas inorganic As was mainly transported into the caryopsis during grain filling. Moreover, nodes appeared to serve as a check-point in As distribution in rice shoots.

Influences of phosphorus starvation on OsACR2.1 expression and arsenic metabolism in rice seedlings

The effects of phosphorus (P) status on arsenate reductase gene (OsACR2.1) expression, arsenate reductase activity, hydrogen peroxide (H(2)O(2)) content, and arsenic (As) species in rice seedlings which were exposed to arsenate after -P or +P pretreatments were investigated in a series of hydroponic experiments. OsACR2.1 expression increased significantly with decreasing internal P concentrations; more than 2-fold and 10-fold increases were found after P starvation for 30 h and 14 days, respectively. OsACR2.1 expression exhibited a significant positive correlation with internal root H(2)O(2) accumulation, which increased upon P starvation or exposure to H(2)O(2) without P starvation. Characterization of internal and effluxed As species showed the predominant form of As was arsenate in P-starved rice root, which contrasted with the +P pretreated plants. Additionally, more As was effluxed from P-starved rice roots than from non-starved roots. In summary, an interesting relationship was observed between P-starvation induced H(2)O(2) and OsACR2.1 gene expression. However, the up-regulation of OsACR2.1 did not increase arsenate reduction in P-starved rice seedlings when exposed to arsenate.

The C-Terminal Variable Region Specifies the Dynamic Properties of Arabidopsis Microtubule-Associated Protein MAP65 Isotypes

The microtubule-associated protein, MAP65, is a member of a family of divergent microtubule-associated proteins from different organisms generally involved in maintaining the integrity of the central spindle in mitosis. The dicotyledon Arabidopsis thaliana and the monocotyledon rice (Oryza sativa) genomes contain 9 and 11 MAP65 genes, respectively. In this work, we show that the majority of these proteins fall into five phylogenetic clades, with the greatest variation between clades being in the C-terminal random coil domain. At least one Arabidopsis and one rice isotype is within each clade, indicating a functional specification for the C terminus. In At MAP65-1, the C-terminal domain is a microtubule binding region (MTB2) harboring the phosphorylation sites that control its activity. The At MAP65 isotypes show differential localization to microtubule arrays and promote microtubule polymerization with variable efficiency in a MTB2-dependent manner. In vivo studies demonstrate that the dynamics of the association and dissociation of different MAP65 isotypes with microtubules can vary up to 10-fold and that this correlates with their ability to promote microtubule polymerization. Our data demonstrate that the C-terminal variable region, MTB2, determines the dynamic properties of individual isotypes and suggest that slower turnover is conditional for more efficient microtubule polymerization.

A PCR-based method to distinguish fungi of the rice sheath-blight complex, Rhizoctonia solani, R. oryzae and R. oryzae-sativae

Identification of Rhizoctonia solani, R. oryzae and R. oryzae-sativae, components of the rice sheath disease complex, is extremely difficult and often inaccurate and as a result may hinder the success of extensive breeding programmes throughout Asia. In this study, primers designed from unique regions within the rDNA internal transcribed spacers have been used to develop a rapid PCR-based diagnostic test to provide an accurate identification of the species on rice. Tests on the specificity of the primers concerned showed that they provide the means for accurate identification of the Rhizoctonia species responsible for sheath diseases in rice.

Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

Rice (Oryza sativa) cultivar Azucena--belonging to the Japonica subspecies--exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a low-tillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci--qSLB1.1--for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes--SLB1 and SLB2--with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2'-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice.

Sprinkler irrigation of rice fields reduces grain arsenic but enhances cadmium

Previous studies have demonstrated that rice cultivated under flooded conditions has higher concentrations of arsenic (As) but lower cadmium (Cd) compared to rice grown in unsaturated soils. To validate such effects over long terms under Mediterranean conditions a field experiment, conducted over 7 successive years was established in SW Spain. The impact of water management on rice production and grain arsenic (As) and cadmium (Cd) was measured, and As speciation was determined to inform toxicity evaluation. Sprinkler irrigation was compared to traditional flooding.

Both irrigation techniques resulted in similar grain yields (similar to 3000 kg grain ha(-1)). Successive sprinkler irrigation over 7 years decreased grain total As to one-sixth its initial concentration in the flooded system (0.55 to 0.09 mg As kg(-1)), while one cycle of sprinkler irrigation also reduced grain total As by one-third (0.20 mg kg(-1)). Grain inorganic As concentration increased up to 2 folds under flooded conditions compared to sprinkler irrigated fields while organic As was also lower in sprinkler system treatments, but to a lesser extent. This suggests that methylation is favored under water logging. However, sprinkler irrigation increased Cd transfer to grain by a factor of 10, reaching 0.05 mg Cd kg(-1) in 7 years. Sprinlder systems in paddy fields seem particularly suited for Mediterranean climates and are able to mitigate against excessive As accumulation, but our evidence shows that an increased Cd load in rice grain may result.

Methylated Arsenic Species in Rice:Geographical Variation, Origin, and Uptake Mechanisms

Rice is a major source of inorganic arsenic (iAs) in the human diet because paddy rice. efficient at accumulating As Rice As speciation is dominated by iAs and dimethylarsinic acid (DMA). Here we review the global pattern in rice As speciation and the factors causing the variation. Rice produced in Asia shows a strong linear relationship between iAs and total As concentration with a slope of 0.78. Rice produced in Europe and the United States shows a more variable, but generally hyperbolic relationship with DMA being predominant in U.S. rice. Although there is significant genotypic variation in grain As speciation, the regional Variations are primarily attributed to environmental factors. Emerging evidence also indicates that methylated. As species in rice are derived from the soil, while rice plants lack the As methylation ability. Soil flooding and additions of organic matter increase microbial methylation of As, although the microbial community responsible for methylafion is poorly understood. Compared with iAs, methylated As species are taken up by rice roots less efficiently but are transported to the grain much, more efficiently, which may be an important factor responsible for the spikelet sterility disorder (straight head disease) in rice. DMA is a weak carcinogen, but the level of ingestion from rice consumption is much lower than that of concern. Questions that require further investigations are identified.

Identification of quantitative trait loci for rice grain element composition on an arsenic impacted soil:Influence of flowering time on genetic loci

Elements in grain crops such as iron, zinc and selenium are essential in the human diet, whereas elements such as arsenic are potentially toxic to humans. This study aims to identify quantitative trait loci (QTLs) for trace elements in rice grain. A field experiment was conducted in an arsenic enriched field site in Qiyang, China using the Bala x Azucena mapping population grown under standard field conditions. Grains were subjected to elemental analysis by inductively coupled plasma mass spectroscopy. QTLs were detected for the elemental composition within the rice grains, including for iron and selenium, which have previously been detected in this population grown at another location, indicating the stability of these QTLs. A correlation was observed between flowering time and a number of the element concentrations in grains, which was also revealed as co-localisation between flowering time QTLs and grain element QTLs. Unravelling the environmental conditions that influence the grain ionome appears to be complex, but from the results in this study one of the major factors which controls the accumulation of elements within the grain is flowering time.

Effects of arsenic-contaminated irrigation water on growth, yield, and nutrient concentration in rice

A study was undertaken to determine the effects of different concentrations of arsenic (As) in irrigation water on Boro (dry-season) rice (Oryza sativa) and their residual effects on the following Aman (wet-season) rice. There were six treatments, with 0, 0.1, 0.25, 0.5, 1, and 2 mg As L-1 applied as disodium hydrogen arsenate. All the growth and yield parameters of Boro rice responded positively at lower concentrations of up to 0.25 mg As L-1 in irrigation water but decreased sharply at concentrations more than 0.5 mg As L-1. Arsenic concentrations in grain and straw of Boro rice increased significantly with increasing concentration of As in irrigation water. The grain As concentration was in the range of 0.25 to 0.97 μg g-1 and its concentration in rice straw varied from 2.4 to 9.6 μg g-1 over the treatments. Residual As from previous Boro rice showed a very similar pattern in the following Aman rice, although As concentration in Aman rice grain and straw over the treatments was almost half of the As levels in Boro rice grain. Arsenic concentrations in both grain and straw of Boro and Aman rice were found to correlate with iron and be antagonistic with phosphorus. Copyright © Taylor & Francis Group, LLC.