Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa

A long non-coding RNA associated with H3K7me3 methylation negatively regulates OsZIP16 transcription under cadmium stress

Cadmium (Cd) is a toxic environmental pollutant, posing a high risk to crop production and human health. However, the genetic mechanisms for regulation of Cd accumulation in crops are poorly understood. In this study, we functionally identified a novel long non-coding RNA (lncRNA, TCONS_00502780) that repressed a locus encoding an uncharacterized metal transporter ZIP16 (ZRT/IRT-like Protein) in rice. LncRNA-OsZIP16 (L16) is resident in the antisense strand of OsZIP16. Both L16 and OsZIP16 were transcriptionally expressed during the life cycle, but under Cd stress the L16 transcription was repressed, whereas the OsZIP16 expression was upregulated. OsZIP16 is localized to the endoplasmic reticulum. Knocking out OsZIP16 by CRISPR-Cas9 (C16) resulted in Cd sensitivity, manifested by reduced plant growth and intense cellular damage with a slightly higher Cd translocation from roots to shoots, suggesting that OsZIP16 expression is required for rice growth and development under Cd stress. Conversely, OsZIP16 constitutive overexpression (OE16) lines displayed a growth phenotype compatible to the wide-type with lower Cd translocation ratio from roots to shoots. L16 knock-down lines by RNA interference (L16-R) showed a similar phenotype to the OE16 lines, while the L16 overexpression (L16-OE) lines were phenotypically similar to the C16 lines. The OsZIP16 transcription was upregulated in the L16-R lines but downregulated in the L16-OE lines. Using an antibody against the trimethylation of histone H3 lysine 27 (H3K27me3) followed by chromatin immunoprecipitation (ChIP), we found the reduced H3K27me3 methylation marks surrounding the OsZIP16 gene under Cd stress. Further examination of H3K27me3 in the L16-R lines revealed that the methylation levels were also significantly lower than those in WT. Taken together, these data suggest that the L16 could negatively regulate the OsZIP16 transcriptional expression through an epigenetic mechanism for rice adaption to Cd stress.

Transcriptomic and physiological analyses of Trichoderma citrinoviride HT-1 assisted phytoremediation of Cd contaminated water by Phragmites australis

Plant growth promoting microbe assisted phytoremediation is considered a more effective approach to rehabilitation than the single use of plants, but underlying mechanism is still unclear. In this study, we combined transcriptomic and physiological methods to explore the mechanism of plant growth promoting microbe Trichoderma citrinoviride HT-1 assisted phytoremediation of Cd contaminated water by Phragmites australis. The results show that the strain HT-1 significantly promoted P. australis growth, increased the photosynthetic rate, enhanced antioxidant enzyme activities. The chlorophyll content and the activity of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) were increased by 83.78%, 23.17%, 47.60%, 97.14% and 12.23% on average, and decreased the content of malondialdehyde (MDA) by 31.10%. At the same time, strain HT-1 improved the absorption and transport of Cd in P. australis, and the removal rate of Cd was increased by 7.56% on average. Transcriptome analysis showed that strain HT-1 induced significant up-regulated the expression of genes related to oxidative phosphorylation and ribosome pathways, and these upregulated genes promoted P. australis remediation efficiency and resistance to Cd stress. Our results provide a mechanistic understanding of plant growth promoting microbe assisted phytoremediation under Cd stress.

Integrated physio-biochemical and RNA sequencing analysis revealed mechanisms of long non-coding RNA-mediated response to cadmium toxicity in wheat

The yield and quality of wheat (Triticum aestivum L.) is seriously affected by soil cadmium (Cd), a hazardous material to plant and human health. Long non-coding RNAs (lncRNAs) of plants are shown actively involved in response to various biotic and abiotic stresses by mediating the gene regulatory networks. However, the functions of lncRNAs in wheat against Cd stress are still obscure. Using deep strand-specific RNA sequencing, 10,044 confident novel lncRNAs in wheat roots response to Cd stress were identified. It was found that 69 lncRNA-target pairs referred to cis-acting regulation and impacted the expressions of their neighboring genes involving in Cd transport and detoxification, photosynthesis, and antioxidant defense. These findings were positively corelated with the physio-biochemical results, i.e. Cd stress affected Cd accumulation, photosynthesis system and ROS in wheat. Overexpression of lncRNA37228 (targeted to a photosystem II protein D1 coding gene), resulted in enhancing Arabidopsis thaliana resistance against Cd stress. By genome-wide identification and characterization, the possible functions of photosystem II protein gene family in wheat under Cd condition were illustrated. Our findings provide novel knowledge into the molecular mechanisms of lncRNAs-regulated wheat tolerance to Cd toxicity and lay foundations for the further studies concerning lncRNAs in food safety production.

Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Integrated transcriptomics and metabolomics reveal key metabolic pathway responses in Pistia stratiotes under Cd stress

Cadmium (Cd) can interfere with plant gene expression, change the content of metabolites and affect plant growth. In this study, untargeted metabolomics (LC-MS) and RNA-Seq sequencing were performed on root tissues of Pistia stratiotes exposed to Cd stress. The results showed that cadmium stress affected the accumulation and transport of cadmium in plants and increased the content of soluble sugar, the activities of ascorbate peroxidase (APX), and peroxidase (POD) by 34.89%, 41.45%, and 6.71% on average, and decreased the activity of superoxide dismutase (SOD) by 51.51% on average. At the same time, the contents of carotenoid, chlorophyll a, and chlorophyll b decreased by 29.52%, 20.11%, and 13.14%, respectively, Thus affecting the growth and development of plants. Metabolomic analysis showed that Cd stress affected eight metabolic pathways, involving 27 differentially expressed metabolites, mainly including unsaturated fatty acids, amino acids (phenylalanine), nucleotides, sulfur compounds, and flavonoids. By transcriptome analysis, a total of 3107 differentially expressed genes (DEGs, 2666 up-regulated genes, and 441 down-regulated genes) were identified, which were mainly involved in four pathways, among which glutathione metabolism and lignin biosynthesis were the key metabolic pathways. In conclusion, this study reveals the metabolic and transcriptional response mechanisms of P. stratiotes to Cd stress through multi-omics, providing the theoretical basis for the phytoremediation of water contaminated by Cd.

Genome-wide identification and characterization of long non-coding RNA in barley roots in response to Piriformospora indica colonization

Currently, there is very limited information about long noncoding RNAs (lncRNAs) found in barley. It remains unclear whether barley lncRNAs are responsive to Piriformospora indica (P. indica) colonization.We found that barley roots exhibited fast development and that large roots branched after P. indica colonization. Genome-wide high-throughput RNA-seq and bioinformatic analysis showed that 4356 and 5154 differentially expressed LncRNAs (DELs) were found in response to P. indica at 3 and 7 days after colonization (dai), respectively, and 2456 DELs were found at 7 dai compared to 3 dai. Based on the coexpression correlation of lncRNAmRNA, we found that 98.6% of lncRNAs were positively correlated with 3430 mRNAs at 3 dai and 7 dai. Further GO analysis showed that 30 lncRNAs might be involved in the regulation of gene transcription; 23 lncRNAs might participate in cell cycle regulation. Moreover, the metabolite analysis indicated that chlorophyll a, sucrose, protein, gibberellin, and auxin were in accordance with the results of the transcriptome, and the respective lncRNAs were positively correlated with these target RNAs. Gene silencing suggested that lncRNA TCONS_00262342 is probably a key regulator of GA₃ synthesis pathway, which participates in P. indica and barley interactions. We concluded that acting as a molecular material basis and resource, lncRNAs respond to P. indica colonization by regulating metabolite content in barley and coordinate the complex regulatory process of higher life by constructing highly positive correlations with their target mRNAs.

ASLncR: a novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants

Abiotic stresses are detrimental to plant growth and development and have a major negative impact on crop yields. A growing body of evidence indicates that a large number of long non-coding RNAs (lncRNAs) are key to many abiotic stress responses. Thus, identifying abiotic stress-responsive lncRNAs is essential in crop breeding programs in order to develop crop cultivars resistant to abiotic stresses. In this study, we have developed the first machine learning-based computational model for predicting abiotic stress-responsive lncRNAs. The lncRNA sequences which were responsive and non-responsive to abiotic stresses served as the two classes of the dataset for binary classification using the machine learning algorithms. The training dataset was created using 263 stress-responsive and 263 non-stress-responsive sequences, whereas the independent test set consists of 101 sequences from both classes. As the machine learning model can adopt only the numeric data, the Kmer features ranging from sizes 1 to 6 were utilized to represent lncRNAs in numeric form. To select important features, four different feature selection strategies were utilized. Among the seven learning algorithms, the support vector machine (SVM) achieved the highest cross-validation accuracy with the selected feature sets. The observed 5-fold cross-validation accuracy, AU-ROC, and AU-PRC were found to be 68.84, 72.78, and 75.86%, respectively. Furthermore, the robustness of the developed model (SVM with the selected feature) was evaluated using an independent test dataset, where the overall accuracy, AU-ROC, and AU-PRC were found to be 76.23, 87.71, and 88.49%, respectively. The developed computational approach was also implemented in an online prediction tool ASLncR accessible at https://iasri-sg.icar.gov.in/aslncr/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for the identification of abiotic stress-responsive lncRNAs in plants.

Research progress on the roles of lncRNAs in plant development and stress responses

Long non-coding RNAs (lncRNAs) are RNAs of more than 200 nucleotides in length that are not (or very rarely) translated into proteins. In eukaryotes, lncRNAs regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. lncRNAs are categorized according to their genomic position and molecular mechanism. This review summarized the characteristics and mechanisms of plant lncRNAs involved in vegetative growth, reproduction, and stress responses. Our discussion and model provide a theoretical basis for further studies of lncRNAs in plant breeding.

Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption

Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.

Integration of transcriptome and metabolome analyses reveals sorghum roots responding to cadmium stress through regulation of the flavonoid biosynthesis pathway

Cadmium (Cd) pollution is a serious threat to plant growth and human health. Although the mechanisms controlling the Cd response have been elucidated in other species, they remain unknown in Sorghum (Sorghum bicolor (L.) Moench), an important C₄ cereal crop. Here, one-week-old sorghum seedlings were exposed to different concentrations (0, 10, 20, 50, 100, and 150 μM) of CdCl₂ and the effects of these different concentrations on morphological responses were evaluated. Cd stress significantly decreased the activities of the enzymes peroxidase (POD), superoxide dismutase (SOD), glutathione S-transferase (GST) and catalase (CAT), and increased malondialdehyde (MDA) levels, leading to inhibition of plant height, decreases in lateral root density and plant biomass production. Based on these results, 10 μM Cd concentration was chosen for further transcription and metabolic analyses. A total of 2683 genes and 160 metabolites were found to have significant differential abundances between the control and Cd-treated groups. Multi-omics integrative analysis revealed that the flavonoid biosynthesis pathway plays a critical role in regulating Cd stress responses in sorghum. These results provide new insights into the mechanism underlying the response of sorghum to Cd.

Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra

Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.

Novel control strategies for the endocrine-disrupting effect of PAEs to pregnant women in traffic system

Traffic-related air pollution has become a global issue, and scientific regulation measures are urgently needed to reduce traffic pollution. Phthalates (PAEs) have been widely detected in the traffic environment; thus, they were chosen as target pollutants because of their endocrine-disrupting effects. The pathways of action and mechanisms of PAEs' endocrine-disrupting effects in pregnant women through inhalation were deduced. A novel whole-process 1C + 3D + 5R regulation system was developed to control the endocrine-disrupting effect of PAEs on pregnant women based on the cleaning production concept. (1) For source reduction, the 2D-QSAR model of endocrine-disrupting effects of PAEs in pregnant women was constructed to screen out the key influencing factors as hydrogen bond interaction and hydrophobic interaction. Based on this, a designed PAE substitute molecule with low volatility and endocrine-disrupting effects and no developmental toxicity was screened. The substitute molecule could reduce the volatilization amount of PAEs at the source by 41.76 %; (2) For process interception, selecting C-band UV light to eliminate PAEs molecules in the traffic environment can slow down 19.99 % of the endocrine-disrupting effect of PAEs molecules. The homology modeling method was used to design four kinds of green belt plant proteins with high PAEs absorption efficiency to absorb PAEs molecules in the traffic environment. Compared with the original green belt plant proteins, the absorption amount of PAEs increased by up to 96.08 %, and (3) For terminal prevention, dietary food schemes were designed to regulate PAEs' endocrine-disrupting effect on pregnant women. The optimal dietary food scheme was the simultaneous intake of glutamate, catechin and folic acid, which could reduce the adverse effect of PAEs on maternal and infants by 32.51 %. This study presents theoretical support for regulating PAE exposure to specific populations in the traffic environment and treating other pollutants in the future.

LncRNA PMAT-PtoMYB46 module represses PtoMATE and PtoARF2 promoting Pb2+ uptake and plant growth in poplar

Lead (Pb²⁺) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb²⁺ uptake in woody plants remains unclear. Here, we identified 226 Pb²⁺-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb²⁺-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb²⁺ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT-PtoMYB46-PtoMATE-PtoARF2 regulatory module control Pb²⁺ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb²⁺ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.

Nitric oxide enhances resistance of Pleurotus eryngii to cadmium stress by alleviating oxidative damage and regulating of short-chain dehydrogenase/reductase family

The function and mechanism of nitric oxide (NO) in regulating Pleurotus eryngii biological response to cadmium (Cd) stress was evaluated by using anti-oxidation and short-chain dehydrogenase/reductase (SDR) family analysis. The fresh biomass of P. eryngii mycelia sharply decreased after treatment with 50 µM Cd; the lipid peroxidation and H₂O₂ accumulation in P. eryngii were found responsible for it. Proper exogenous supply of NO (150 µM SNP) alleviated the oxidative damage induced by Cd stress in P. eryngii, which reduced the accumulation of thiobarbituric acid reactive substances (TBARS) and H₂O₂. The activities of antioxidant enzymes (superoxide dismutase, peroxidase) were significantly increased to deal with Cd stress when treated with SNP (150 µM), and the content of proline was also closely related to NO-mediated reduction of Cd toxicity. Moreover, SDR family members were widely involved in the response to Cd stress, especially PleSCH70 gene was observed for the first time in participating in NO-mediated enhancement of Cd tolerance in P. eryngii. Taken together, this study provides new insights in understanding the tolerance mechanisms of P. eryngii to heavy metal and lays a foundation for molecular breeding of P. eryngii to improve its tolerance to environmental stress.

Temporal and tissue-specific transcriptome analyses reveal mechanistic insights into the Solidago canadensis response to cadmium contamination

Understanding the cellular mechanisms mediating invasive plant adaptation to excessive cadmium (Cd) in environments is crucial for designing phytoremediation strategies for Cd-contaminated soils. Here we performed RNA sequencing on the root and leaf tissues of Solidago canadensis stressed by Cd for 0, 12, 24, and 48 h. Tissue-specific gene expression was notably significant, i.e., 76% (1667) of differentially expressed unigenes in the root and 78% (1856) in the leaf were exclusive to each tissue. Distinctive enrichment of gene functions was further observed in each tissue's response. In detail, adaptation of the root to Cd stress involved the up-regulation of genes encoding molecular chaperones (mainly heat shock proteins) and induction of some antioxidants, which may help cells scavenge reactive oxygen species (ROS). In comparison, leaf exposure to Cd ramped up the expression of genes associated with secondary metabolism, comprised mainly of cytochrome P450, but slowed down its photosynthetic functions, which seems to conserve energy for survival. Moreover, we highlighted candidate gene modules that are highly linked to physiological traits. Collectively, these observations suggest that S. canadensis may adopt a multipronged approach to actively cope with Cd stress, with both management of ROS accumulation and metabolic adjustment to optimize energy metabolism.

Biologia Futura: progress and future perspectives of long non-coding RNAs in forest trees

Forest trees are affected by climate change, anthropogenic pressure, as well as abiotic and biotic stresses. Conventional tree breeding has so far been limited to enhance overall productivity, and our understanding of the genetic basis of quantitative traits is still inadequate. Quantum leaps in next-generation sequencing technologies and bioinformatics have permitted the exploration and identification of various non-coding regions of the genome other than protein coding genes. These genomic regions produce various types of non-coding RNAs and regulate myriads of biological functions at epigenetic, transcriptional and translational levels. Recently, long non-coding RNAs (lncRNAs) which act as molecular switch have been identified to be pivotal molecules in forest trees. This review focuses on progress made in regulatory mechanisms in various developmental phases like wood formation, adventitious rooting and flowering and stress responses. It was predicted that complex regulatory interactions among lncRNA, miRNA and gene exist. LncRNAs can function as a sponge for miRNAs, reducing the suppressive effect of miRNAs on target mRNAs and perhaps adding a new layer of regulatory interactions among non-coding RNA classes in trees. Furthermore, network analysis revealed the interactions of lncRNA and genes during the expression of several important genes. The insights generated about lncRNAs in forest trees would enable improvement of economically important traits including the devastating abiotic and biotic stresses. In addition, solid understanding on the wide range of regulatory functions of lncRNAs on traits influencing biomass productivity and adaptation would aid the applications of biotechnology in genetic improvement of forest trees.