Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants

Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.

Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties

Introduction

Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined.

Methods

We conducted RNA sequencing on two japonica rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress.

Results

We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). WRKY family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, Os03g0152000 in the antioxidant system, as well as Os12g0491800 and Os05g0381400, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of Os11g0685700 (OsWRKY61) within the WRKY family suggested its potential role in regulating cold tolerance in rice.

Discussion and conclusion

We identified Os11g0685700 (OsWRKY61) as a promising candidate gene for enhancing cold tolerance in japonica rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.

Potential functions of engineered nanomaterials in cadmium remediation in soil-plant system: A review

Soil cadmium (Cd) contamination is a global environmental issue facing agriculture. Under certain conditions, the stable Cd that bound to soil particles tend to be remobilized and absorbed into plants, which is seriously toxic to plant growth and threat food safety. Engineering nanomaterials (ENMs) has attracted increasing attentions in the remediation of Cd pollution in soil-plant system due to their excellent properties with nano-scale size. Herein, this article firstly systematically summarized Cd transformation in soil, transport in soil-plant system, and the toxic effects in plants, following which the functions of ENMs in these processes to remediate Cd pollution are comprehensively reviewed, including immobilization of Cd in soil, inhibition in Cd uptake, transport, and accumulation, as well as physiological detoxication to Cd stress. Finally, some issues to be further studied were raised to promote nano-remediation technology in the environment. This review provides a significant reference for the practical application of ENMs in remediation of Cd pollution in soil, and contributes to sustainable development of agriculture.

Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants

The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.

miRNAs for crop improvement

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Silicon inhibits the upward transport of Cd in the first internode of different rice varieties in a Cd stressed farm land

Silicon spraying on leaves can reduce the accumulation of cadmium (Cd) in rice grain. However, it has been found that not all rice varieties decrease in Cd content after silicon (Si) application. A field study was conducted to check the performance of Si on the accumulation and transport of Cd in four rice varieties. TY390 and YXY2, having 51.5%- 60.6% Cd content of grain was inhibited by foliar Si, were classified as CRS varieties; BXY9978 and YXYLS, having Cd content of grain is nonresponsive with Si, were classified as CNS varieties. The Cd contents were mainly accumulated in stem, especially in the first stem node. While foliar Si reported no changes in the Cd content of first node in four different rice varieties. Comparing the correlation between Si and Cd contents in the above part of the first internode of CRS and CNS, as well as the relative expression of Cd transport genes in the first internode suggested that first internode was the key site to effect Cd transport through Si application, and OsZIP7 is a key Cd transporter protein responsive to Si, leading to different response of Cd transport and accmulation between the CRS and the CNS varieties of rice.

Nodes play a major role in cadmium (Cd) storage and redistribution in low-Cd-accumulating rice (Oryza sativa L.) cultivars

Rice cadmium (Cd) contamination is one of the critical agricultural issues. Breeding of low-Cd-accumulating cultivar is an effective approach to reduce Cd bioaccumulation in rice. To investigate the molecular mechanism underlying Cd transport in rice, the functions of nodes in Cd transport are explored. The results show that different nodes have different functions of Cd transport in the rice plant and the physiological structure of the first node under panicle (N1) determine the Cd accumulation in the brown rice. The upper nodes can redistribute the Cd transport in aboveground tissues. The expressions of Cd-efflux transporter genes (OsLCT1 and OsHMA2) located on the plasma-membrane are the main factors affecting the Cd transport form node to brown rice, which are more depended on the node functions but not the node Cd concentrations. Lower expressions of OsLCT1 and OsHMA2 in N1 result in lower Cd transport from node to brown rice. The size of vascular-bundle (VB) areas in the junctional node with the flag leaf can determine the expression of OsHMA2 and the expression of OsLCT1 positively correlated with the Cd transport ability of first node (N1). The expressions of OsVIT2 and OsABCC1 cannot allow Cd to be immobilized into the vacuoles in node. The VB structure and Cd transporter gene expression level of N1 proved that the Cd concentration of N1 can be used as an important indicator for screening low-Cd-accumulating cultivars. The major implication is that selecting or breeding cultivars with lower Cd accumulations in N1 could be an effective strategy to reduce Cd accumulation in rice grains.

WGCNA Analysis Revealed the Hub Genes Related to Soil Cadmium Stress in Maize Kernel (Zea mays L.)

Soil contamination by heavy metals has become a prevalent topic due to their widespread release from industry, agriculture, and other human activities. Great progress has been made in elucidating the uptake and translocation of cadmium (Cd) accumulation in rice. However, there is still little known about corresponding progress in maize. In the current study, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) of maize immature kernel related to Cd stress. In total, 55, 92, 22, and 542 DEGs responsive to high cadmium concentration soil were identified between XNY22-CHS-8 vs. XNY22-YA-8, XNY22-CHS-24 vs. XNY22-YA-24, XNY27-CHS-8 vs. XNY27-YA-8, and XNY27-CHS-24 vs. XNY27-YA-24, respectively. The weighted gene co-expression network analysis (WGCNA) categorized the 9599 Cd stress-responsive hub genes into 37 different gene network modules. Combining the hub genes and DEGs, we obtained 71 candidate genes. Gene Ontology (GO) enrichment analysis of genes in the greenyellow module in XNY27-YA-24 and connectivity genes of these 71 candidate hub genes showed that the responses to metal ion, inorganic substance, abiotic stimulus, hydrogen peroxide, oxidative stress, stimulus, and other processes were enrichment. Moreover, five candidate genes that were responsive to Cd stress in maize kernel were detected. These results provided the putative key genes and pathways to response to Cd stress in maize kernel, and a useful dataset for unraveling the underlying mechanism of Cd accumulation in maize kernel.

Heat Shock 70 kDa Protein Cognate 3 of Brown Planthopper Is Required for Survival and Suppresses Immune Response in Plants

The brown planthopper (Nilaparvata lugens) is a monophagous pest of rice (Oryza sativa), which threatens food security around the world. Insect Heat shock proteins 70 kDa (Hsp70s) play a key role in insect growth and development, however, if they also modulate the plant physiological processes is still unclear. In this study, we identified the Heat shock 70 kDa protein cognate 3 (NlHSC70-3) of BPH from compared protein profiles of Nipponbare tissues after BPH infestation via LC/MS. NlHSC70-3 has a predicted signal peptide and displays high transcription levels in the salivary glands, which further supported that it is secreted into plants by BPH during the feeding process. Using RNA interference (RNAi), we showed that NlHSC70-3 is indispensable for the survival of BPH on rice. Most importantly, NlHSC70-3 mediates the plant immune responses including cell death, flg22-induced ROS burst and defense-related gene expression in N. benthamiana. These results demonstrate that NlHSC70-3 may function as an effector manipulating plant physiological processes to facilitate pest survival on rice, which provides a new potential target for future pest control.

Stress signaling convergence and nutrient crosstalk determine zinc-mediated amelioration against cadmium toxicity in rice

Consumption of rice (Oryza sativa L.) is one of the major pathways for heavy metal bioaccumulation in humans over time. Understanding the molecular responses of rice to heavy metal contamination in agriculture is useful for eco-toxicological assessment of cadmium (Cd) and its interaction with zinc (Zn). In certain crops, the impacts of Cd stress or Zn nutrition on the biophysical chemistry and gene expression have been widely investigated, but their molecular interactions at transcriptomic level, particularly in rice roots, are still elusive. Here, hydroponic investigations were carried out with two rice genotypes (Yinni-801 and Heizhan-43), varying in Cd contents in plant tissues to determine their transcriptomic responses upon Cd15 (15 µM) and Cd15+Zn50 (50 µM) treatments. High throughput RNA-sequencing analysis confirmed that 496 and 2407 DEGs were significantly affected by Cd15 and Cd15+Zn50, respectively, among which 1016 DEGs were commonly induced in both genotypes. Multitude of DEGs fell under the category of protein kinases, such as calmodulin (CaM) and calcineurin B-like protein-interacting protein kinases (CBL), indicating a dynamic shift in hormonal signal transduction and Ca2+ involvement with the onset of treatments. Both genotypes expressed a mutual regulation of transcription factors (TFs) such as WRKY, MYB, NAM, AP2, bHLH and ZFP families under both treatments, whereas genes econding ABC transporters (ABCs), high affinity K+ transporters (HAKs) and Glutathione-S-transferases (GSTs), were highly up-regulated under Cd15+Zn50 in both genotypes. Zinc addition triggered more signaling cascades and detoxification related genes in regulation of immunity along with the suppression of Cd-induced DEGs and restriction of Cd uptake. Conclusively, the effective integration of breeding techniques with candidate genes identified in this study as well as economically and technologically viable methods, such as Zn nutrient management, could pave the way for selecting cultivars with promising agronomic qualities and reduced Cd for sustainable rice production.

The Evolution and Functional Roles of miR408 and Its Targets in Plants

MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.

Role of phytomelatonin responsive to metal stresses: An omics perspective and future scenario

A pervasive melatonin (N-acetyl-5-methoxytryptamine) reveals a crucial role in stress tolerance and plant development. Melatonin (MT) is a unique molecule with multiple phenotypic expressions and numerous actions within the plants. It has been extensively studied in crop plants under different abiotic stresses such as drought, salinity, heat, cold, and heavy metals. Mainly, MT role is appraised as an antioxidant molecule that deals with oxidative stress by scavenging reactive oxygen species (ROS) and modulating stress related genes. It improves the contents of different antioxidant enzyme activities and thus, regulates the redox hemostasis in crop plants. In this comprehensive review, regulatory effects of melatonin in plants as melatonin biosynthesis, signaling pathway, modulation of stress related genes and physiological role of melatonin under different heavy metal stress have been reviewed in detail. Further, this review has discussed how MT regulates different genes/enzymes to mediate defense responses and overviewed the context of transcriptomics and phenomics followed by the metabolomics pathways in crop plants.

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

Comparative Transcriptomic Analysis of Root Cadmium Responses in Two Chinese Rice Cultivars Yuzhenxiang and Xiangwanxian 12

Cadmium (Cd) pollution in paddy soil is an increasingly serious issue in rice production. It has been reported that there is a higher or lower grain Cd accumulation in the rice cultivars Yuzhenxiang (YZX) or Xiangwanxian 12 (XWX), respectively. To better manage the Cd pollution problem, the genes that might play vital roles in governing the difference in root Cd responses between these two rice cultivars were examined. In this study, the results of RNA sequencing (RNA-seq) showed that there were 341 and 161 differentially expressed genes in the roots of YZX and XWX after Cd exposure, respectively. Among these genes, 7 genes, such as Os06g0196300 (OsJ_019618), Os07g0570700 (OsJ_24808), ADI1, GDCSH, HSFB2C, PEX11-4, and CLPB1, possessed higher degree nodes with each other, through interaction analysis by the STRING (search tool for the retrieval of interacting genes/proteins) software, suggesting that they might play vital roles in Cd response. Based on GO enrichment analysis, 41 differently expressed genes after Cd treatment in YZX or XWX were identified to be related to Cd response. Through comparative transcriptomic analysis, 257 genes might be associated with the root Cd response difference between YZX and XWX. Furthermore, we supposed that ADI1, CFBP1, PEX11-4, OsJ_019618, OsJ_24808, GDCSH, CLPB1, LAC6, and WNK3 might be implicated in Cd response based on the combined analysis of RT-qPCR, interaction, and GO annotation analysis. In conclusion, the numerous genes that might be related to Cd stress response and root Cd response difference between YZX and XWX at the booting stage may be of benefit for the development of rice varieties with low Cd consumption.

Molecular and biochemical mechanisms underlying boron-induced alleviation of cadmium toxicity in rice seedlings

Both cadmium (Cd) contamination and boron (B) deficiency in farmland soils pose a threat to the yield and quality of crops in Southern China. The present study investigated the mechanisms by which B reduces Cd accumulation in rice (Oryza sativa) seedlings. Boron supplementation partially restored the decline in shoot and root biomass caused by Cd treatment (26% and 33%, respectively), with no significant difference between the B+Cd and control groups. We also found that B significantly reduced shoot and root Cd concentrations (by 64% and 25%, respectively) but increased Cd concentration (by 43%) and proportion (from 38% to 55%) in root cell walls. Transcriptome analysis and biochemical tests suggested that B supplementation enhanced lignin and pectin biosynthesis, pectin demethylation, and sulfur and glutathione metabolism. Moreover, B decreased the expression of some Cd-induced transporter-related genes (i.e., HMA2, Nramp1, and several ABC genes). These results indicate that B relieved Cd toxicity and reduced Cd accumulation in rice seedlings by restraining Cd uptake and translocation from root to shoot by improving Cd tolerance and chelation ability. These novel findings would benefit further investigations into how B influences Cd uptake, translocation, detoxification, and accumulation in crops.

Factors influencing the effectiveness of liming on cadmium reduction in rice: A meta-analysis and decision tree analysis

Lime is widely applied as a soil amendment to reduce the grain cadmium (Cd) content in rice production. However, the effectiveness of liming on grain Cd reduction is inconsistent and often cannot meet the safety requirements established for rice production. To identify the factors causing the effectiveness of liming to vary, we collected data from peer-viewed articles regarding lime application in paddy soils that were published during the last ten years. The average Cd reduction rates in rice grains after liming were -44% across all the studies considered, which could be broken down into -48% for pot experiments only and -42% for field trials only. The results of a meta-analysis and decision tree analysis indicated that the experiment type (field or pot), lime dosage, lime type (CaCO₃, Ca(OH)₂, or CaO), soil environment factors (soil pH, soil available Cd content, soil total Cd, and Zn content), and rice cultivar all influenced the effectiveness of liming. Recommendations were made to guide future liming practice, e.g., (1) using a larger lime dosage when applied to soil with pH < 5.5, or soil with total Cd > 1 mg/kg or total Zn > 200 mg/kg; (2) using CaCO₃ when applied with large dosages; and (3) planting low-Cd accumulation rice cultivars while applying lime. CAPSULE: A meta-analysis showed that the effectiveness of liming on rice grain Cd reduction was affected by the experiment type (field or pot), lime dosage, lime type, soil pH, rice cultivar, and soil total Cd and Zn content.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.

Phytoremediation of Cadmium: Physiological, Biochemical, and Molecular Mechanisms

Cadmium (Cd) is one of the most toxic metals in the environment, and has noxious effects on plant growth and production. Cd-accumulating plants showed reduced growth and productivity. Therefore, remediation of this non-essential and toxic pollutant is a prerequisite. Plant-based phytoremediation methodology is considered as one a secure, environmentally friendly, and cost-effective approach for toxic metal remediation. Phytoremediating plants transport and accumulate Cd inside their roots, shoots, leaves, and vacuoles. Phytoremediation of Cd-contaminated sites through hyperaccumulator plants proves a ground-breaking and profitable choice to combat the contaminants. Moreover, the efficiency of Cd phytoremediation and Cd bioavailability can be improved by using plant growth-promoting bacteria (PGPB). Emerging modern molecular technologies have augmented our insight into the metabolic processes involved in Cd tolerance in regular cultivated crops and hyperaccumulator plants. Plants’ development via genetic engineering tools, like enhanced metal uptake, metal transport, Cd accumulation, and the overall Cd tolerance, unlocks new directions for phytoremediation. In this review, we outline the physiological, biochemical, and molecular mechanisms involved in Cd phytoremediation. Further, a focus on the potential of omics and genetic engineering strategies has been documented for the efficient remediation of a Cd-contaminated environment.