Search

SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1 , OsSPX2 , OsSPX4 , and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs , which is helpful for the gene-function research of DXWR and genetic improvements during breeding.

Background: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome., Results: Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots., Conclusion: We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract., (© 2022. The Author(s).)

Representing the staple crop for half of the world population, rice can accumulate high levels of cadmium (Cd) in its grain, posing concerns on food safety. Different soil amendments have been proposed to decrease Cd accumulation in rice grain by either decreasing soil Cd availability, introducing competitive ions on Cd uptake, or down-regulating the expression of transporters for Cd uptake. However, the effectiveness of soil amendments applied alone or in combinations needs to be tested under field conditions. Here, we present results of field trials with two rice cultivars differing in Cd accumulation grown at three field sites in southern China in two years, to investigate the effects of two Mn-containing soil amendments (MnO 2 , Mn-loaded biochar (MB)), Si fertilizer (Si), limestone, and K 2 SO 4 , as well as interactions among MnO 2 , Si, and limestone on decreasing Cd accumulation in rice grain. We found that single applications of MnO 2 or MB to acidic soils low in Mn decreased grain Cd concentrations by 44-53 % or 78-82 %, respectively, over two years without decrease in performance. These effects were comparable to or greater than those induced by limestone liming alone (45-62 %). Strong interactions between MnO 2 and limestone resulting from their influence on soil extractable Cd and Mn led to non-additive effects on lowering grain Cd. MB addition minimized grain Cd concentrations, primarily by increasing extractable and dissolved Mn concentrations, but also by decreasing Cd extractability in soil. In comparison, Si and K 2 SO 4 amendments affected grain Cd levels only weakly. We conclude that the amendments that decrease labile Cd and increase labile Mn in soils are most effective at reducing Cd accumulation in rice grain, thus contributing to food safety., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined., Results: In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together., Conclusions: This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Cadmium bioavailability in paddy soils is strongly affected by flooding-draining cycle. In this study, we used synchrotron-based X-ray absorption spectroscopy and a stirred-flow method to investigate the effects of flooding-draining and amendments of CaCO 3 and CaSO 4 on Cd speciation and release kinetics from a Cd-spiked paddy soil (total Cd concentration of 165 mg kg -1 ). Extended X-ray absorption fine structure analysis showed that Cd was predominantly bound to non-iron-clay minerals (e.g. Cd-kaolinite, Cd-illite, and Cd-montmorillonite, accounting for 60-100%) in the air-dried soil and 1- or 7-day flooded samples. After prolonged flooding (30 and 120 days), Cd-iron mineral complexes (e.g. Cd bound to ferrihydrite and goethite) became the predominant species (accounting for 52-100%). Stirred-flow kinetic analysis showed that both prolonged flooding and the amendments with CaCO 3 and CaSO 4 decreased the maximum amount and the rate coefficient of Cd release. However, the effect of prolonged flooding was reversed after a short period of draining, indicating that although Cd was immobilized during flooding, it became mobile rapidly after the soil was drained, possibly due to pH decrease and rapid oxidation of CdS. The effects of the amendments on Cd uptake in rice plants were tested in a pot experiment using the same paddy soil without Cd spiking (total Cd 2.1 mg kg -1 ). Amendment with CaCO 3 and, to a lesser extent, CaSO 4 , decreased the Cd accumulation in two cultivars of rice. The combination of CaCO 3 amendment and a low Cd accumulating cultivar was effective at limiting grain Cd concentration to below the 0.2 mg kg -1 limit., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Plastid-encoded genes are coordinately transcribed by the nucleus-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). Resulting primary transcripts are frequently subject to RNA editing by cytidine-to-uridine conversions at specific sites. The physiological role of many editing events is largely unknown. Here, we have used the CRISPR/Cas9 technique in rice to knock out a member of the PLS-DYW subfamily of pentatricopeptide repeat (PPR) proteins. We found that OsPPR16 is responsible for a single editing event at position 545 in the chloroplast rpoB messenger RNA (mRNA), resulting in an amino acid change from serine to leucine in the β-subunit of the PEP. In striking contrast to loss-of-function mutations of the putative orthologue in Arabidopsis, which were reported to have no visible phenotype, knockout of OsPPR16 leads to impaired accumulation of RpoB, reduced expression of PEP-dependent genes, and a pale phenotype during early plant development. Thus, by editing the rpoB mRNA, OsPPR16 is required for faithful plastid transcription, which in turn is required for Chl synthesis and efficient chloroplast development. Our results provide new insights into the interconnection of the finely tuned regulatory mechanisms that operate at the transcriptional and post-transcriptional levels of plastid gene expression., (©2020 The Authors. New Phytologist ©2020 New Phytologist Foundation.)

Rice is a major dietary source of the toxic trace metal Cd. Large variation in Cd concentration in rice grain was documented by global and regional surveys, with this variation difficult to predict from soil tests. Even within individual fields, a large spatial variation is often observed but the factors controlling this within-field spatial variation are still poorly understood. In the present study, we used field- and laboratory-based experiments to investigate the effects of a gentle slope gradient within paddy fields (a common farmers' practice to facilitate water flow from the inlet to the outlet) on Cd availability and grain Cd concentrations in unlimed and limed soils. In our field experiments, a gentle slope resulted in large spatial variations in soil redox potential (Eh) and pH upon soil drainage during rice grain filling. As a result of these variations in Eh and pH, there was a 6- to 7-fold spatial within-field variation in grain Cd concentrations, which were the highest in the irrigation inlet area associated with higher Eh values and the lowest in the outlet area with lower Eh values. Our results highlight that soil Eh, and more importantly, field-moist soil pH during grain filling determine grain Cd concentration and accordingly, incorporating measurements of soil redox status (or water content) and pH of field moist soils (rather than air-dried soils) during grain filling may improve the prediction of grain Cd concentrations. Delaying drainage during grain filling or increasing soil pH by liming is effective in reducing grain Cd accumulation., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The species of Oryza rufipogon. dw was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100.15 Gb raw data was obtained from seven pair-end libraries by Illumina Hiseq4000 platform. Subsequently, a draft assembly genome of O. rufipogon. dw was generated with a final size of 422.7 Mb with a contig N50 of 15 kb and a scaffold N50 of 296.2 bb. The assembly genome size was higher than the estimated genome size (413 Mb) based on k -mer analysis. The identified repeat sequences accounted for 40.09% of the entire genome, and 32,521 protein-coding genes with an average of 4.59 exons per gene was annotated in five databases. Phylogenetic analysis using 1460 single-copy gene, O. rufipogon. dw was close with O. rufipogon by Bayes method. The wild rice species of O. rufipogon. dw divergence was estimated at ∼0.3 million years ago (Mya) from O. rufipogon , and ∼0.6 Mya from the O. sativa. The draft genome of O. rufipogon. dw provided an essential resource for its origin and evolution study.

Rapid industrialization in China during the last three decades has resulted in widespread contamination of Cd in agricultural soils. A considerable proportion of the rice grain grown in some areas of southern China has Cd concentrations exceeding the Chinese food limit, raising widespread concern regarding food safety. In this review, we summarize rice grain Cd concentrations in national Chinese markets and in field surveys from contaminated areas, and analyze the potential health risk associated with increased dietary Cd intake. For subsistence rice farmers living in some contaminated areas of southern China who mainly consume locally-produced Cd-contaminated rice, their estimated dietary Cd intake is now comparable to that for the population in the region of Japan where the Itai-Itai disease was first reported. Interventions must be taken urgently to reduce Cd intake for these farmers. We also analyze i) the main reasons causing elevated grain Cd concentrations in southern China, ii) the dominant biogeochemical processes controlling the solubility of Cd in paddy soils, and iii) molecular mechanisms for the uptake and translocation of Cd in rice plants. Based on these analyses, we propose a number of countermeasures to address soil Cd contamination, including i) mitigation of Cd transfer from paddy soils to rice grain, and ii) intervention in those farmers who consume home-grown Cd-contaminated rice. Liming to increase soil pH to 6.5 and gene editing biotechnology are effective strategies to decrease Cd accumulation in rice grain. For these local farmers with high-Cd exposure risk, local governments should monitor the Cd concentration in their home-grown rice and exchange those high-Cd rice with low-Cd rice in order to reduce their dietary Cd intake., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Soil contamination in some areas of southern China has resulted in elevated dietary intake of cadmium (Cd), posing a potential risk to human health. A survey of paired soil-rice (n = 200) and soil-vegetable (n = 142) samples was conducted in Xiangtan county of Hunan province, southern China. The concentrations of Cd in all the samples were determined by inductively coupled plasma mass spectrometry. Dietary intakes of Cd from the consumption of locally produced rice and vegetables were estimated for different age groups. Among the 342 crop samples collected in the survey, 88% and 29% of rice grain and vegetable samples, respectively, exceeded the Chinese maximum permissible limit for Cd (0.2 mg dry weight kg -1 , 0.2 mg fresh weight kg -1 and 0.1 mg fresh weight kg -1 for rice, leafy vegetables and for rootstalk and legume vegetables, respectively). The median dietary Cd intake varied from 66.5 to 116 μg Cd kg -1 body weight (BW) month -1 , with children (4-11 years) exhibiting the highest intake. These values are 2.7-4.6 times the tolerable dietary intake of 25 μg kg -1  BW month -1 recommended by the Joint FAO/WHO Expert Committee on Food Additives. For the general population in Xiangtan county, rice contributed the majority (81%) of the Cd intake with vegetables contributing only 19%. The median hazard quotient calculated from dietary Cd intake was 2.4 times the permissible level, indicating a high risk to the local residents. This study highlights an urgent need to reduce the transfer of Cd from soil to the food chain in the investigated region., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Contamination of cadmium (Cd) in paddy soil is a serious environmental problem threatening food safety in some parts of southern China, where rice grain Cd concentration often exceeds the Chinese limit (0.2 mg kg -1 ). We tested the effect of CaCO 3 liming combined with growing low Cd cultivars on Cd accumulation in rice grain in 2-year field trials. A liming model was used to predict the doses of lime required. Lime (2.25-7.5 t ha -1 ) was applied in 2016 only and the effect monitored in both 2016 and 2017. Soil pH was increased from the initial 5.5 to the target value 6.5 by 7.5 t ha -1 CaCO 3 . Liming greatly reduced CaCl 2 -extractable Cd in the rhizospheric soil. Grain Cd concentration in the control exceeded the limit by 2-5 times. Liming at 7.5 t ha -1 decreased grain Cd concentration by 70-80% in both seasons without affecting grain yield. Grain Cd concentration was below the limit in the 7.5 t ha -1 liming treatment in both seasons. Grain Cd concentration correlated closely with CaCl 2 -extractable Cd in rhizospheric soil at the grain maturing stage. Seasonal difference in grain Cd concentration was attributed to the soil water status at the grain maturing stage. Liming had no significant effect on grain arsenic concentration or speciation. A single application of CaCO 3 to raise soil pH to 6.5, combined with low Cd cultivars and delayed drainage of paddy water during late grain filling stage, was highly effective at reducing Cd accumulation in rice grain., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Rapid industrialization in China in recent decades has resulted in soil contamination in some areas, raising the concern about food safety. Consumption of rice represents a major exposure route for the toxic elements cadmium (Cd) and arsenic (As). We collected 160 polished rice from local markets in 20 provinces in China and determined total Cd and As concentrations and As speciation. Total Cd concentration ranged from below the detection limit to 0.77 mg kg -1 , with 10% of the samples exceeding the Chinese limit (0.2 mg kg -1 ). Rice Cd concentration showed a distinct geographical pattern, increasing from low levels in the north to high levels in the south of China. Median daily Cd intake from rice varied from 0.01 μg kg -1 body weight in the north to 0.61 μg kg -1 body weight in the south of China, representing between 1% and 73% of the tolerable daily intake (TDI) recommended by FAO/WHO. The highest median Cd intake from rice was in Hunan province with 2 times TDI. Total As concentration ranged from 0.011 to 0.186 mg kg -1 , with inorganic As (iAs) and dimethylarsinic acid (DMAs) on average accounting for 69% and 31%, respectively. All samples were below the Chinese limit for iAs in rice (0.2 mg kg -1 ). There was no clear geographical pattern in rice total As concentration, but rice produced in northeastern China contained higher percentages of DMAs and lower percentages of iAs. This study highlights a high risk of Cd exposure from rice consumption for the population of southern China and suggested strategies for reducing Cd accumulation in rice crop., (Copyright © 2018 Elsevier Ltd. All rights reserved.)