Physiological responses and transcriptome analyses of upland rice following exposure to arsenite and arsenate

Di, Xuerong; Feng, Zijian; Norton, Gareth J.; Beesley, Luke; Zhang, Zulin; Lin, Hui; Zhi, Suli; Liu, Xuncheng; Ding, Yongzhen

doi:10.1016/j.envexpbot.2020.104366

Cited by 35 publications

(11 citation statements)

References 58 publications

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“…Arsenic treatment resulted in unique transcriptome profiles changes, and a novel set of typical response genes were found. The antioxidant enzyme activities were consistent with the antioxidant enzyme-related genes expression, and several transports and defense enzyme-related pathways were identified ( Di et al, 2021 ). Shukla T. et al (2018) studied the response of Arabidopsis accessions under As(V) toxicity.…”

Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 64%

“…Moreover, nine genes that played a major role in regulating these metabolic pathways were found to be differentially expressed in response to stress conditions ( Yadav et al, 2019 ). Recently, Di et al (2021) studied the stress-responsive genes of upland rice exposed to As(III) and As(V). Under metals toxicity, many genes were down-regulated compared to those that were up-regulated.…”

Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 99%

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Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

et al. 2022

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Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

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Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 64%

Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 99%

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

et al. 2022

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“…OsNAC15 was previously reported to be mainly induced by abiotic stress treatments (cold, drought, salt, submergence, laid-down submergence and ABA) and biotic stress (rice blast) [ 63 , 64 , 65 , 66 ]. OsNAC15 was also strongly induced by As (III) treatment after 12 h and 24 h in shoots of upland rice [ 67 ]. We found that OsNAC15 was repressed by Zn deficiency and toxicity and induced by Cd stress ( Figure 1 A,B).…”

Section: Discussionmentioning

confidence: 99%

OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice

Zhan

Zou

et al. 2022

IJMS

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Zinc (Zn) deficiency and cadmium (Cd) stress are severe threats to the growth and development of plants. Increasing Zn content and/or decreasing Cd content in grain are also important objectives of rice breeding. However, the molecular mechanisms of Zn deficiency tolerance (ZDT) and Cd stress tolerance (CDT) are largely unknown in rice. Here, we report that a NAM/CUC2-like transcription factor, OsNAC15, contributes to ZDT and CDT in rice. Knockout of OsNAC15 reduced ZDT and CDT at the vegetative stage. OsNAC15 expresses in all tissues of different developmental stages, and is repressed by Zn deficiency and induced by Cd stress. OsNAC15 is a functional transcription factor with transactivation and DNA binding activities. Expression analysis of rice ZIP family genes suggested that the knockout of OsNAC15 activates or inhibits their transcriptions under Zn deficiency or Cd stress conditions. The yeast one-hybrid assay, transient transcriptional activity assay using the dual-luciferase reporter system and electrophoretic mobility shift assay demonstrated that OsNAC15 directly binds to the zinc deficiency-responsive element motifs in the promoters of OsZIP7 and OsZIP10 to repress their transcriptions. The OsNAC15–OsZIP7/10 module is an essential foundation for further study on the regulatory mechanisms of ZDT and CDT in rice.

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“…The antioxidant system was differentially induced in dry rice in response to oxidative stress under different inorganic arsenic As (III) and As (V) stresses. The oxidoreductase gene (Os04g0339400) was sequentially induced (Di et al 2021), and in ceRNA analysis, Os04g0339400 competed with LNC3807 for target binding to Novel.44 (Fig. 8A).…”

Section: ; Hwang Et Al 2005)mentioning

confidence: 99%

Genome-wide identification and functional prediction of long non-coding RNAs associated with cold tolerance in japonica rice

Wang

Jia

Bai

et al. 2023

Preprint

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Background Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, ceRNA mechanism in rice at low temperatures has not been reported. Therefore, to establish the ceRNA network and elucidate the transcriptional regulatory network and physiological mechanism of rice leaves in response to low-temperature stress, experiments were conducted using two rice (Oryza sativa. L) varieties with significantly different cold tolerances. Results The cold-tolerant variety has prolonged and relatively stable regulation of antioxidant enzymes (superoxide dismutase [SOD] and peroxidase [POD] catalase [CAT], and total antioxidant capacity) and osmotic substances (Proline [PRO], Soluble sugars [SS], and Soluble protein [SP]), which can remove harmful substances to maintain plant cell stability. Further screening based on VIP (variable importance in the projection) identified SOD and POD as two of the most essential antioxidant phenotypes. Furthermore, by combining antioxidant physiological indices with whole transcriptome data through weighted gene co-expression network analysis (WGCNA), the highly correlated modules were black and green, significantly associated with critical antioxidant indices (SOD and POD). Enrichment analysis revealed that black module genes were significantly enriched in the redox pathway. This module hub gene included UDP-glucosyltransferase family protein (Os05g0527000), sesquiterpene synthase (Os08g0167800), indole-3-glycerophosphatase gene (Os03g0797500), encoding oxidoreductase gene (Os04g0339400), and unknown genes (Os05g0212900). The green module genes were significantly enriched in the linoleic acid metabolic pathway. This module hub gene included WRKY transcription factor (Os11g0685700),abscisic acid (ABA) signal transduction pathway-related gene plasma membrane hydrogen-ATPase (Os02g0825600), Beta-Ig-containing H3 structural domain protein leucine-rich repeat-like receptor kinase (Os02g0615800), and two unknown genes (Os03g0103950 and Os08g0288050). Therefore, we selected module hub and significantly enriched pathway genes to construct key competing endogenous ceRNA networks. Both modules’ networks were integrated to obtain the ceRNA network of six lncRNAs regulating three co-expressed mRNAs through four miRNAs and six lncRNAs regulating two co-expressed mRNAs through four miRNAs. Finally, we performed preliminary gene sequence difference analysis, subcellular localization, and phenotypic validation of mutants for the putative glutamate protein OsGLR1.2 (Os02g0787600), which was previously thought to be associated with Ca2+ transport. Conclusions The results of this study reveal the characteristics of the response of rice to low temperature and provide insight into the mechanisms of regulation of rice to low temperature.

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Physiological responses and transcriptome analyses of upland rice following exposure to arsenite and arsenate

Cited by 35 publications

References 58 publications

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice

Genome-wide identification and functional prediction of long non-coding RNAs associated with cold tolerance in japonica rice

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