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1.
Emerging concepts of potassium homeostasis in plants.
Srivastava, AK, Shankar, A, Nalini Chandran, AK, Sharma, M, Jung, KH, Suprasanna, P, Pandey, GK
Journal of experimental botany. 2020;(2):608-619
Abstract
Potassium (K+) is an essential cation in all organisms that influences crop production and ecosystem stability. Although most soils are rich in K minerals, relatively little K+ is present in forms that are available to plants. Moreover, leaching and run-off from the upper soil layers contribute to K+ deficiencies in agricultural soils. Hence, the demand for K fertilizer is increasing worldwide. K+ regulates multiple processes in cells and organs, with K+ deficiency resulting in decreased plant growth and productivity. Here, we discuss the complexity of the reactive oxygen species-calcium-hormone signalling network that is responsible for the sensing of K+ deficiency in plants, together with genetic approaches using K+ transporters that have been used to increase K+ use efficiency (KUE) in plants, particularly under environmental stress conditions such as salinity and heavy metal contamination. Publicly available rice transcriptome data are used to demonstrate the two-way relationship between K+ and nitrogen nutrition, highlighting how each nutrient can regulate the uptake and root to shoot translocation of the other. Future research directions are discussed in terms of this relationship, as well as prospects for molecular approaches for the generation of improved varieties and the implementation of new agronomic practices. An increased knowledge of the systems that sense and take up K+, and their regulation, will not only improve current understanding of plant K+ homeostasis but also facilitate new research and the implementation of measures to improve plant KUE for sustainable food production.
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2.
The STEME system: a novel tool for directed evolution in vivo.
Hu, FY, Wang, KJ
Yi chuan = Hereditas. 2020;(3):231-235
Abstract
Directed evolution can be rapidly applied for engineering proteins, studying gene functions, and obtaining mutants with important agronomic traits. Recently, Caixia Gao and Jiayang Li's team from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, worked together to engineer novel saturated targeted endogenous mutagenesis editors (STEMEs), realizing in vivo directed evolution and function selection in plants. This system integrated the existing two single-base editing techniques, successfully induced C:G>T:A and A:T>G:C double-base editing in plants, and artificially evolved into herbicide-resistant rice through targeting the OsACC carboxyltransferase domain coding sequence. This new method of gene directed evolution in vivo displays great application potential in important agronomic trait screening and plant functional gene researches. Here we introduce the composition, editing efficiency, and application principle of the STEME system, and compare it with the existing directed evolution methods, so as to provide a reference for accelerating the innovation of crop germplasm resources.
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3.
Nitrogen-phosphorus interplay: old story with molecular tale.
Hu, B, Chu, C
The New phytologist. 2020;(4):1455-1460
Abstract
Nitrogen (N) and phosphorus (P) are the two most abundant mineral nutrients used by plants, and are also the mostly widely used fertilizer elements driving crop yield improvement in agricultural production. The coordinated utilization of N and P is essential to maintain optimal plant growth and achieve maximal crop yield. The signaling pathways of N and P are generally studied separately, so our understanding of N-P interactions is very limited. A series of recent studies have revealed the critical components regulating N-P interactions in both Arabidopsis thaliana and rice (Oryza sativa), and have shed light on our in-depth understanding of the network integrating N and P signaling pathways. Here, we summarize recent progress on N-P interaction and propose possible working mechanisms integrating these N-P interactive regulation pathways. We further discuss future work that might reveal the N-P interactive regulation network in plants.
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4.
Gluconate enhanced the water uptake and improved the growth of rice seedlings under PEG-induced osmotic stress.
Li, P, Chen, B, Ding, F
Plant physiology and biochemistry : PPB. 2020;:514-523
Abstract
Low-molecular-weight organic acid not only serves as a nutrient of plants or as a source of energy metabolism but also a bioactive molecule, which can be linked with hormones, nitrogen (N), and other signals to participate in regulating gene expression, stress response, growth, and development of plants via mechanisms that remain poorly understood. We investigated how the supply of gluconate and sulfate affects rice plant growth and water absorption at the same N supply under osmotic stress. Using a greenhouse hydroponic experimental approach, we assessed the physiology of rice seedlings supplied with C6H11O7NH4 (AG) and (NH4)2SO4 (AS) over multiple weeks. The root xylem sap rate in rice roots treated with AG increased significantly compared with AS treatment and the control under osmotic stress. The length of roots between 0.5 and 1.5 mm in diameter was obtained after treatment with polyethylene glycol (PEG) solutions containing AG, which was lower than those treated with PEG alone and PEG solutions containing AS. Compared with PEG alone and PEG solutions containing AS, AG induced a significant increase in root lignin under PEG-induced osmotic stress. However, relative to AS supply characteristics, the markedly reduced aerenchyma and porosity of roots, as well as higher root activity, increased fine root tips and length, and higher aquaporins and glutamate synthase (GS) activity in AG supply resulted in increased water uptake under osmotic stress. In addition, AG supply markedly increased leaf area and chlorophyll content. These results suggested that gluconate can enhance the water absorption capacity of the root system by promoting the growth and development of the root system, increasing the activity of aquaporin and GS and reducing the aeration tissue and porosity of the root system under osmotic stress.
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5.
Uptake and transformation of decabromodiphenyl ether in different rice cultivars: Evidence from a carbon-14 study.
Zhao, P, Ye, Q, Yu, K, Whalen, JK, Rajesh Kumar, R, Cheng, X, Delgado-Moreno, L, Wang, W
The Science of the total environment. 2020;:135398
Abstract
The differences of PBDE absorption, accumulation, and metabolism in different cultivars of the same crop are rarely explored. This study used 14C tracing to fully demonstrate the uptake and transformation of soil-borne BDE209 in three rice cultivars, including two indica (HHZ and YD1) and one japonica cultivars (NJ3). Results showed that about 6.9, 17.2, and 17.4% of the applied 14C-BDE209 were transformed to 14C-metabolites in soils planted with HHZ, YD1, and NJ3, respectively. The 14C-BDE209 and its 14C-metabolites in soil could be absorbed by the rice and gradually transported to its root, stem, leaf, and grain, with the total whole-plant uptake of 8.52, 4.55 and 3.43 nmol for HHZ, YD1, and NJ3, respectively. The cultivar of HHZ had the greatest whole-plant 14C absorption but the lowest ΣPBDEs residues in its grain, with the ΣPBDEs of 421.8, 454.2 and 967.0 ng g-1 for HHZ, YD1, and NJ3, respectively. BDE-209 accounted for 90%, 31% and 50% of the ΣPBDEs in the grain from HHZ, YD1, and NJ3, respectively. The estimated daily intake (EDI) amounts of ΣPBDEs were 928, 1056, and 2675 ng kg-1 bw d-1 via consuming rice grains from HHZ, YD1, and NJ3, respectively, which were below the safe threshold limits for human consumption. This study proved the different BDE-209 absorption, accumulation and transformation in different rice cultivars, which potentially suggests the need of considering cultivar differences in assessing the dietary risks of PBDEs.
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6.
Inversion modeling of japonica rice canopy chlorophyll content with UAV hyperspectral remote sensing.
Cao, Y, Jiang, K, Wu, J, Yu, F, Du, W, Xu, T
PloS one. 2020;(9):e0238530
Abstract
Chlorophyll content is an important indicator of the growth status of japonica rice. The objective of this paper is to develop an inversion model that can predict japonica rice chlorophyll content by using hyperspectral image of rice canopy collected with unmanned aerial vehicle (UAV). UAV-based hyperspectral remote sensing can provide timely and cost-effective monitoring of chlorophyll content over a large region. The study was based on hyperspectral data collected at the Shenyang Agricultural College Academician Japonica Rice Experimental Base in 2018 and 2019. In order to extract the salient information embedded in the high-dimensional hyperspectral data, we first perform dimension reduction by using a successive projection algorithm (SPA). The SPA extracts the characteristic hyperspectral bands that are used as input to the inversion model. The characteristic bands extracted by SPA are 410 nm, 481 nm, 533 nm, 702 nm, and 798 nm, respectively. The inversion model is developed by using an extreme learning machine (ELM), the parameters of which are optimized by using particle swarm optimization (PSO). The PSO-ELM algorithm can accurately model the nonlinear relationship between hyperspectral data and chlorophyll content. The model achieves a coefficient of determination R2 = 0.791 and a root mean square error of RMSE = 8.215 mg/L. The model exhibits good predictive ability and can provide data support and model reference for research on nutrient diagnosis of japonica rice.
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7.
Gracilibacillus oryzae sp. nov., isolated from rice seeds.
He, SW, Wang, X, Guo, HB, Han, JG, Thin, KK, Gao, JS, Ma, LA, Zhang, XX
International journal of systematic and evolutionary microbiology. 2020;(10):5467-5472
Abstract
A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).
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8.
Review: Crucial role of inorganic pyrophosphate in integrating carbon metabolism from sucrose breakdown to starch synthesis in rice endosperm.
Lee, SK, Jeon, JS
Plant science : an international journal of experimental plant biology. 2020;:110572
Abstract
The endosperm is a primary constituent of mature seeds in rice as well as in other cereal crops, serving as the major storage reserve of starch. Observations indicate that the central part of the endosperm is subject to hypoxic conditions, which require a switch of energy metabolism owing to limited mitochondrial respiration. Uniquely, this endosperm generates a large source of inorganic pyrophosphate (PPi) as a byproduct of the reaction of ADP glucose pyrophosphorylase in the cytosol. Recent results derived from examination of the mutants of cereal crops, especially rice, for PPi-utilizing enzymes clearly suggest an important role of PPi as an alternative energy currency for integrating carbon metabolism from sucrose breakdown to starch synthesis in the endosperm. Thus, the present review provides an outline of the interlaced PPi-dependent metabolic pathways, which are critical for starch synthesis in the endosperm in terms of energy metabolism, along with its application to enhance yield potential.
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9.
Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods.
Liu, S, Zhong, H, Meng, X, Sun, T, Li, Y, Pinson, SRM, Chang, SKC, Peng, Z
BMC plant biology. 2020;(1):441
Abstract
BACKGROUND Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. RESULTS To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. CONCLUSIONS While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.
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10.
Methylene blue adsorption on magnetic alginate/rice husk bio-composite.
Alver, E, Metin, AÜ, Brouers, F
International journal of biological macromolecules. 2020;:104-113
Abstract
Magnetic alginate/rice husk (m-ALG/RH) bio-composite beads prepared with ionotropic gelation method and used for methylene blue (MB) removal. Structural analysis of magnetic alginate/rice husk composite beads was performed using FTIR, SEM-EDS and TGA techniques. The accomplishment of magnetic alginate/rice husk composite beads as an adsorbent for the removal methylene blue was investigated from aqueous solution. Maximum experimental adsorption capacity of the bio-composite beads was calculated as 274.9 mg/g. The various process parameters such as pH, temperature and initial MB concentration optimized. It was determined that pH no significant effect on dye removal efficiency of beads while temperature and ionic strength caused a decrease on removal efficiency. The various isotherm models were applied for determine the adsorption mechanism and Freundlich isotherm model is more compatible with the experimental data. The kinetic studies showed that the adsorption of methylene blue can be well described by the fractal Brouers-Sotolongo kinetic model. The thermodynamic calculations indicated that methylene blue adsorption was a spontaneous and exothermic nature. The results showed that the magnetic alginate/rice husk bio-composite as low-cost and eco-friendly adsorbent can be effectively used for cationic dye removal steps in the environmental engineering applications.