Transcriptome profilings of two tall fescue (Festuca arundinacea) cultivars in response to lead (Pb) stress

Combined transcriptomics and metabolomics to analyse the response of Cuminum cyminum L. under Pb stress

Lead (Pb) can disrupt plant gene expression, modify metabolite contents, and influence the growth of plants. Cuminum cyminum L. is highly adaptable to adversity, but molecular mechanism by which it responds to Pb stress is unknown. For this study, transcriptomic and metabolomic sequencing was performed on root tissues of C. cyminum under Pb stress. Our results showed that high Pb stress increased the activity of peroxidase (POD), the contents of malondialdehyde (MDA) and proline by 80.03 %, 174.46 % and 71.24 %, respectively. Meanwhile, Pb stress decreased the activities of superoxide dismutase (SOD) and catalase (CAT) as well as contents of soluble sugars and GSH, which thus affected the growth of C. cyminum. In addition, Pb stress influenced the accumulation and transport of Pb in C. cyminum. Metabolomic results showed that Pb stress affected eight metabolic pathways involving 108 differentially expressed metabolites, primarily amino acids, organic acids, and carbohydrates. The differentially expressed genes identified through transcriptome analysis were mainly involved the oxidation reductase activity, transmembrane transport, phytohormone signaling, and MAPK signaling pathway. The results of this study will help to understand the molecular mechanisms of C. cyminum response to Pb stress, and provide a basis for screening seeds with strong resistance to heavy metals.

The metabolism and detoxification effects of lead exposure on Aleurolyphus ovatus (Acari: Acaridae) via transcriptome analysis

Aleurolyphus ovatus Troupeau is one of the most predominant species of the Acaridae family worldwide. Recent reports have demonstrated that the accumulation of lead in stored grains and dietary items exceeds the required standards. However, the molecular mechanism of heavy metal stress on mites has not been reported. To understand the mechanism underlying the heavy metal response of A. ovatus, comparative transcriptome analysis was performed in this study using an Illumina high throughput mRNA sequencing (RNA-seq) platform. A. ovatus was fed on artificial diets containing two different concentrations of lead, namely, a low concentration of 12.5 mg/kg (LAO) and a high concentration of 100 mg/kg (HAO), while the mites in the control (NAO) group were not exposed to lead. A total of 44,362 unigenes, with an average length of 1547 bp, were identified. Of these, 996 unigenes were successfully annotated in seven functional databases. The number of differentially expressed genes (DEGs) in A. ovatus under different lead concentrations was compared. In NAO versus LAO group, including 310 up-regulated and 1580 down-regulated DEGs. In NAO versus HAO group, including 3928 up-regulated and 1761 down-regulated DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that detoxification enzyme genes were significantly expressed in pathways, such as cytochrome P450 foreign body metabolism, glutathione metabolism and drug metabolism-cytochrome pathway. The results of gene annotation and quantitative real-time PCR showed that high concentration of lead significantly stimulated the expression of metabolic detoxification enzyme genes such as glutathione S transferase (GST) and superoxide dismutase (SOD), while low concentration inhibited their expression. This study will provide a basis for the molecular mechanism of A. ovatus in response to heavy metal lead stimulation in stored grain.

Yield and Rhizosphere Soil Environment of Greenhouse Zucchini in Response to Different Planting and Breeding Waste Composts

Composting, planting, and breeding waste for return to the field is the most crucial soil improvement method under the resource utilization of agricultural waste. However, how the vegetable yield and rhizosphere soil environment respond to different composts is still unknown. Therefore, eight formulations were designed for compost fermentation using agricultural waste [sheep manure (SM), tail vegetable (TV), cow manure (CM), mushroom residue (MR), and corn straw (CS)] without fertilizer (CK1) and local commercial organic fertilizer (CK2) as controls to study the yield and rhizosphere soil environment of greenhouse zucchini in response to different planting and breeding waste compost. Applying planting and breeding waste compost significantly increased the soil's organic matter and nutrient content. It inhibited soil acidification, which T4 (SM:TV:CS = 6:3:1) and T7 (SM:TV:MR:CS = 6:2:1:1) treatments affected significantly. Compared to CK2 treatment, T4 and T7 treatments showed a greater increase, with a significant increase of 14.69% and 11.01%, respectively. Therefore, T4, T7, and two control treatments were selected for high-throughput sequencing based on yield performance. Compared with the CK1 treatment, although multiple applications of chemical fertilizers led to a decrease in bacterial and fungal richness, planting and breeding waste compost maintained bacterial diversity and enhanced fungal diversity. Compared to CK2, the relative abundance increased in T7-treated Proteobacteria (Sphingomonas, Pseudomonas, and Lysobacter) and T4-treated Bacteroidetes (Flavobacterium) among bacteria. An increase in T4-treated Ascomycota (Zopfiella and Fusarium) and Basidiomycota among fungi and a decrease in T7-treated Mortierellomycota have been observed. Functional predictions of the bacterial Tax4Fun and fungal FUNGuild revealed that applying planting and breeding waste compost from the T4 treatment significantly increased the abundance of soil bacterial Metabolism of Cities, Genetic Information Processing, and Cellular Processes decreased the abundance of Pathotroph and Saprotroph-Symbiotroph fungi and increased the abundance of Saprotroph fungi. Overall, planting and breeding waste compost increased zucchini yield by improving soil fertility and microbial community structure. Among them, T4 treatment has the most significant effect, so T4 treatment can be selected as the optimized formulation of local commercial organic fertilizer. These findings have valuable implications for sustainable agricultural development.

Effects of mowing on Pb accumulation and transport in Cynodon dactylon (L.) Pers

Bermudagrass is a perennial herb with the potential to remediate Pb pollution in soils, and it has mechanical resistance to shearing. However, the effects of mowing on Pb absorption and accumulation in bermudagrass are still unclear. In this study, we investigated the effects of different quantities (0, 1, 2, 4 applications) of mowing treatments under 200 mg L^-1 Pb application on Pb accumulation and transport in bermudagrass and explored the related mechanisms. Compared to the Pb treatment, all of the mowing treatments greatly decreased root Pb concentration/accumulation, significantly enhanced Pb concentrations/accumulations in stubble stems and stubble leaves, and ultimately promoted Pb enrichment and transport. Of the treatments in this study, two applications of mowing best promoted Pb enrichment, and four applications of mowing best promoted Pb transport efficiency. Furthermore, mowing mediated the microdistribution and physiological patterns of Pb in bermudagrass and affected the Pb transport by changing the subcellar distribution patterns and chemical forms of Pb in various tissues. Additionally, mowing promoted the transport of all mineral elements and showed a synergistic relationship with Pb absorption and transport. The change in mineral element metabolism patterns may be an important reason why mowing promoted Pb accumulation in bermudagrass. Our study provides the first comprehensive evidence regarding mowing facilitating the absorption, accumulation and transport of Pb in bermudagrass. Moderate mowing may be an effective strategy to assist in soil Pb remediation using bermudagrass.

Transcriptomic mechanisms of reduced PM2.5-Pb retention in the leaves of the low-Pb-accumulation genotype of Chinese cabbage

Atmospheric fine particulate matter (PM_2.5) mainly contributes to Pb accumulation in the edible leaves of Chinese cabbage in North China. It was found that a low-Pb-accumulation (LPA) genotype of Chinese cabbage contained less Pb in leaves than high-Pb-accumulation (HPA) genotype exposed to PM_2.5-Pb. However, there are no data on the transcriptional regulatory mechanisms of foliar PM_2.5-Pb uptake by Chinese cabbage. The present study investigated the retention of PM_2.5-Pb in foliar apoplast and symplasm and the underlying molecular mechanisms of reduced Pb in LPA leaves. It appeared more Pb in apoplast and less Pb in symplasm of LPA leaves, whereas the pattern was opposite in HPA. There were 2646 and 3095 differentially expressed genes (DEGs) in LPA and HPA leaves under PM_2.5-Pb stress with clearly genotype-specific function, respectively. Furthermore, mRNA levels of XTH16 regulating cell wall thickening, PME2 and PME6 involved in cell wall remodification were significantly expressed in LPA, but not in HPA. Meanwhile, foliar PM_2.5-Pb stress downregulated expression of ZIP1, YSL1, and CNGC3 responsible for Pb influx to cell, and upregulated expression of ABCG36 regulated Pb efflux from symplasm in LPA leaves. These results improve our understanding to the mechanisms underlying foliar Pb uptake from PM_2.5-Pb at transcriptomic level.

Transcriptomic Analysis Provides Novel Insights into the Heat Stress-Induced Response in Codonopsis tangshen

Codonopsis tangshen Oliv (C. tangshen) is a valuable traditional Chinese medicinal herb with tremendous health benefits. However, the growth and development of C. tangshen are seriously affected by high temperatures. Therefore, understanding the molecular responses of C. tangshen to high-temperature stress is imperative to improve its thermotolerance. Here, RNA-Seq analysis was performed to investigate the genome-wide transcriptional changes in C. tangshen in response to short-term heat stress. Heat stress significantly damages membrane stability and chlorophyll biosynthesis in C. tangshen, as evidenced by pronounced malonaldehyde (MDA), electrolyte leakage (EL), and reduced chlorophyll content. Transcriptome analysis showed that 2691 differentially expressed genes (DEGs) were identified, including 1809 upregulated and 882 downregulated. Functional annotations revealed that the DEGs were mainly related to heat shock proteins (HSPs), ROS-scavenging enzymes, calcium-dependent protein kinases (CDPK), HSP-HSP network, hormone signaling transduction pathway, and transcription factors such as bHLHs, bZIPs, MYBs, WRKYs, and NACs. These heat-responsive candidate genes and TFs could significantly regulate heat stress tolerance in C. tangshen. Overall, this study could provide new insights for understanding the underlying molecular mechanisms of thermotolerance in C. tangshen.

Transcriptome analysis of perennial ryegrass reveals the regulatory role of Aspergillus aculeatus under salt stress

Perennial ryegrass (Lolium perenne) is an important turf grass and forage grass with moderately tolerant to salinity stress. Aspergillus aculeatus has been documented to involved in salt stress response of perennial ryegrass, while the A. aculeatus-mediated molecular mechanisms are unclear. Therefore, to investigate the molecular mechanisms underlying A. aculeatus-mediated salt tolerance, the comprehensive transcriptome analysis of the perennial ryegrass roots was performed. Twelve cDNA libraries from roots were constructed after 12 h of plant-fungus cocultivation under 300 mM salt stress concentrations. A total of 21,915 differentially expressed genes (DEGs) were identified through pairwise comparisons. Enrichment analysis revealed that potentially important A. aculeatus-induced salt responsive genes belonging to specific categories, such as hormonal metabolism (auxin and salicylic acid metabolism related genes), secondary metabolism (flavonoid's metabolism related genes) and transcription factors (MYB, HSF and AP2/EREBP family). In addition, weighted gene co-expression network analysis (WGCNA) showed that blue and black modules were significantly positively correlated with the peroxidase activity and proline content, then the hub genes within these two modules were further identified. Taken together, we found the categories of A. aculeatus-induced salt responsive genes, revealing underlying fungus-induced molecular mechanisms of salt stress response in perennial ryegrass roots. Besides, fungus-induced salt-tolerant hub genes represent a foundation for further exploring the molecular mechanisms.

Transcriptomic profiling revealed the role of 24-epibrassinolide in alleviating salt stress damage in tall fescue (Festuca arundinacea)

Soil salinization is a major problem all over the world. The accumulation of salt in soil reduces the root water uptake and directly affects plant growth and metabolic activities. Brassinosteroid is a plant hormone that plays an important role in regulation of plant growth and physiological process, including promotion of cell expansion and elongation, signal transduction and stress response. Exogenous 24-epibrassinolide (EBL) has been proved to alleviate various environmental stress in plants. However, the role that EBL plays in salt stress response is still unknown in tall fescue (Festuca arundinacea). In this study, the physiology and molecular mechanisms regulated by exogenous EBL of salt stress response in tall fescue was investigated. Tall fescue plants were divided into four groups, including control (CK), NaCl solution (SALT), 24-epibrassinolide (EBL), NaCl solution + 24-epibrassinolide (SE). During the growth period of tall fescue, we found that electrolyte leakage (EL) and malondialdehyde (MDA) were decreased, chlorophyll (Chl) content and antioxidant enzyme activity were increased in leaves of tall fescue in SE group compared with SALT group, indicating that EBL improved the salt tolerance in grasses. Transcriptomic profiling analysis showed that after 12 h of treatments, 10,265, 13,830 and 10,537 differential genes were expressed in EBL, SALT, and SE groups compared with control, respectively. These differentially expressed genes (DEGs) mainly focused on binding, catalytic activity, cellular process, metabolic process, cellular anatomical entity. Moreover, most of the differential genes were expressed in the plant hormone signal transduction pathway. These results helped us to better understand the mechanism of exogenous 24-epibrassinolide to improve the salt tolerance of tall fescue.

Transcriptome analysis provides novel insights into the soil amendments induced response in continuously cropped Codonopsis tangshen

Codonopsis tangshen Oliv (C. tangshen) is an important Chinese traditional medicinal plant with various health benefits. However, the growth of C. tangshen are seriously affected by continuous cropping, which led to the decrease of the yield and quality. A field experiment was conducted to learn the effects of soil amendments on the growth of C. tangshen under continuous cropping condition, and the biological events which occurred at molecular level were investigated. The results indicated that the content of chlorophyll a (Chl a), chlorophyll b (Chl b), and carotenoid (Car) was significantly higher in SCPM (silicon-calcium-potassium-magnesium fertilizer), SCPMA (SCPM combined with azoxystrobin) and SCPMAOM (SCPM combined with azoxystrobin and organic manure) treatments. Moreover, the yield and the levels of alkaloid, polysaccharide, flavone and total protein in the treatments of SCPM, SCPMA and SCPMAOM were significantly higher than those in the control, and these indexes were all highest in the SCPMAOM treatment. RNA-sequencing (RNA-Seq) is an economical and efficient method to obtain genetic information for species with or without available genome data. In this study, RNA-Seq was performed to understand how continuously cropped C. tangshen responded to the soil amendments at the transcriptome level. The number of differentially expressed genes (DEGs) were as follows: CK vs. SCPM (719 up- and 1456 down-), CK vs. SCPMA (1302 up- and 1748 down-), CK vs. SCPMAOM (1274 up- and 1678 down-). The soil amendments affected the growth of C. tangshen mainly by regulating the genes involved in pathways of 'photosynthesis,' 'plant hormone signal transduction,' 'biosynthesis of unsaturated fatty acids,' 'phenylpropanoid biosynthesis,' and 'starch and sucrose metabolism,' etc. qRT-PCR was performed to validate the expressions of 10 target genes such as CP26, PsaF, and POX, etc., which verified the reliability of RNA-Seq results. Overall, this study revealed the roles and underlying mechanisms of the soil amendments in regulating the growth of continuously cropped C. tangshen at transcriptome level. These findings are beneficial for improving the continuous cropping tolerance and may be valuable for future genetic improvement of C. tangshen.

Transcriptome analysis of the toxicity response of green macroalga Caulerpa lentillifera J. Agardh to high dissolved arsenite

Arsenic (As) is a hazardous pollutant that negatively impacts the physiological functions of alga. So far, a detailed understanding of algal response to As stress is still lacking. In this study, a transcriptome analysis was performed to illustrate the toxicity response of Caulerpa lentillifera J. Agardh, an edible algae with rich nutrition, to arsenite [As(III)], a toxic form of As. Totally, 1913 differentially expressed genes (DEGs) were screened, of which 642 were up- and 1271 were downregulated in C. lentillifera under As(III) stress (30 mg·L^-1) compared with control. As(III) stress promoted the growth of C. lentillifera at low concentration (0.1 mg·L^-1) and inhibited the growth at high concentration (≥ 0.5 mg·L^-1). Multiple DEGs involved in oxidoreductase activities were significantly affected by As(III), and several DEGs related to antioxidant enzyme activity were downregulated, resulting in suffering from oxidative stress in C. lentillifera. Results also showed that As(III) stress inhibited chlorophyll and carotenoid synthesis, destroyed the integrity of chloroplasts, and interfered with the absorption of light energy, thereby inhibiting photosynthesis in C. lentillifera. The highly enriched ABC transporter-related genes involved in the detoxification process were upregulated under As(III) stress, indicating their critical role in the resistance to As stress in C. lentillifera. The gene expressions for 10 selected DEGs were confirmed by qRT-PCR, showing the reliability of the data revealed by RNA sequencing. Our novel work illustrated the toxicity of C. lentillifera under As(III) stress at the molecular level, serving as a basis for future investigations on the prevention and treatment of such pollutants.

Changes in phenotype and gene expression under lead stress revealed key genetic responses to lead tolerance in Medicago sativa L

Lead (Pb) is a serious heavy metal soil pollutant. It can be absorbed and accumulated by plant roots and impact plant growth. Medicago sativa L. (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Little is known about the mechanism by which alfalfa responds to Pb stress at the molecular level. In this study, three alfalfa genotypes (a lead-resistant type (LR), a lead-sensitive type (LS) and an intermediate type (IN)) with contrasting abilities to resist lead were exposed to different durations of Pb treatment. Next-generation sequencing (NGS)-based RNA-seq technology was employed to characterize the root transcriptomes of three genotypes of alfalfa and identify differentially expressed genes (DEGs) during Pb stress. Genotypes LR and LS displayed different mechanisms of tolerance. In LR, the accumulation of more resistant substances was induced by the upregulation of sucrose synthase, glucan endo-1,3-beta-glucosidase, beta-amylase 3, probable trehalose-phosphate phosphatase J, 6-phosphofructo-2-kinase delta-1-pyrroline-5-carboxylate synthase (P5CS) and δ-ornithine aminotransferase (δ-OAT). In addition, flavin monooxygenase (YUCCA), 4-coumarate:CoA ligase-like protein (4CL), cinnamoyl-CoA reductase-like protein (CCR), ferulate 5-hydroxylase (F5H) and caffeic acid O-methyltransferase (COMT) were upregulated, leading to root development in a short time under Pb stress. Further study of the expression levels of metal transport-related genes, such as NRAMP (metal transporter), MATE (multidrug and toxin extrusion), HIPPs (heavy metal-associated isoprenylated plant proteins), MTP (metal tolerance protein), and ABC transporter, suggested that these genes were differentially expressed after lead treatment in the three alfalfa genotypes. Our research provides useful information for further studies on the molecular mechanism of Pb resistance in Medicago sativa L.

A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses

Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.

Comparative transcriptomic analysis reveals the coordinated mechanisms of Populus × canadensis 'Neva' leaves in response to cadmium stress

Cadmium (Cd), a heavy metal element has strong toxicity to living organisms. Excessive Cd accumulation directly affects the absorption of mineral elements, inhibits plant tissue development, and even induces mortality. Populus × canadensis 'Neva', the main afforestation variety planted widely in northern China, was a candidate variety for phytoremediation. However, the genes relieving Cd toxicity and increasing Cd tolerance of this species were still unclear. In this study, we employed transcriptome sequencing on two Cd-treated cuttings to identify the key genes involved in Cd stress responses of P. × canadensis 'Neva' induced by 0 (CK), 10 (C10), and 20 (C20) mg/L Cd(NO3)2 4H2O. We discovered a total of 2,656 (1,488 up-regulated and 1,168 down-regulated) and 2,816 DEGs (1,470 up-regulated and 1,346 down-regulated) differentially expressed genes (DEGs) between the CK vs C10 and CK vs C20, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses in response to the Cd stress indicated that many DEGs identified were involved in the catalytic activity, the oxidoreductase activity, the transferase activity, and the biosynthesis of secondary metabolites. Based on the enrichment results, potential candidate genes were identified related to the calcium ion signal transduction, transcription factors, the antioxidant defense system, and transporters and showed divergent expression patterns under the Cd stress. We also validated the reliability of transcriptome data with the real-time PCR. Our findings deeper the understanding of the molecular responsive mechanisms of P. × canadensis 'Neva' on Cd tolerance and further provide critical resources for phytoremediation applications.

Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects

Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.

Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

BACKGROUND

It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches.

RESULTS

The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with Carboxy-PTIO (c-PTIO) together with Nitro-L-arginine methyl ester (L-NAME) (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd (only Cd treatment) and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism.

CONCLUSIONS

In general, the results revealed that there are three major mechanisms involved in NO-mediated Cd detoxification in tall fescue, including (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.

Selenium supplementation alleviates cadmium-induced damages in tall fescue through modulating antioxidant system, photosynthesis efficiency, and gene expression

Selenium (Se) is beneficial for plant growth under different stressful conditions. In this study, we investigated the protective effects of Se supply from Cd-induced damages in tall fescue under Cd stress. Tall fescue seedlings (40 days old) were treated with Cd (30 mg/L, as CdSO₄·8/3 H₂O) and Se (0.1 mg/L, as Na₂SeO₃) individually and in combination using 1/2 Hoagland's solution system for 7 days. Various physiological parameters, photosynthetic behaviors, and gene expressions were measured. The results showed that Cd-stressed plants displayed obvious toxicity symptoms such as leaf yellowing, decreasing plant height, and root length. Cd stress significantly increased the malondialdehyde (MDA) content and electrolyte leakage (EL), and remarkably reduced the chlorophyll and soluble protein content, antioxidant enzyme activities, and photosynthetic efficiency. Cd stress significantly inhibited the expression of two photosynthesis-related genes (psbB and psbC), but not psbA. In addition, it significantly inhibited the expression of antioxidant system-related genes such as ChlCu/ZnSOD, CytCu/ZnSOD, GPX, and pAPX, but significantly increased the expression of GR. However, Se improved the overall physiological and photosynthetic behaviors of Cd-stressed plants. Se significantly enhanced the chlorophyll and soluble protein content and CAT and SOD activities, but decreased MDA contents, EL, and Cd content and translocation in tall fescue under Cd stress. Furthermore, under Cd stress, Se increased the expression of psbA, psbB psbC, ChlCu/ZnSOD, CytCu/ZnSOD, GPx, and PAPx. The result suggests that Se alleviated the deleterious effects of Cd and improved Cd resistance in tall fescue through upregulating the antioxidant system, photosynthesis activities, and gene expressions.

Transcriptome -wide modulation combined with morpho-physiological analyses of Typha orientalis roots in response to lead challenge

Lead (Pb) is a common pollutant in many environments, including in the soil, water, and/or air. Typha orientalis Presl, a large emergent aquatic plant, has been reported to function as a Pb-tolerant and Pb-accumulating plant; however, very little molecular information regarding the tolerance of T. orientalis towards Pb is known. In this study, Pb accumulation and key factors involved in the Pb stress response at different Pb concentrations were investigated. Pb was primarily accumulated in the roots and was mainly located in the cell wall and membrane systems. Differentially expressed genes (DEGs) were identified in T. orientalis roots after Pb exposure via RNA-seq analyses. In the 0.10 mM and 0.25 mM Pb²⁺-treated groups, a total of 3275 DEGs were detected relative to the control. Many of these genes were associated with oxidation-reduction processes, metal transport, protein kinase/phosphorylation, and DNA binding transcription factors, which were shown to be Pb-responsive DEGs. Mapping Kyoto Encyclopedia of Genes and Genomes (KEGG) database, "phenylpropanoid biosynthesis" was analyzed as the major pathway of the important modules of overlapping DEGs of 0.10 mM and 0.25 mM Pb²⁺ treatments. Furthermore, a lead response gene named ToLR1 with unknown function was of particular interest. The full-length of ToLR1 sequence was cloned using rapid amplification of cDNA ends (RACE) and overexpressed in Arabidopsis thaliana, which resulted in enhanced resistance to Pb stress. This is the first report providing genomic information detailing Pb responsive genes in T. orientalis. Moreover, this study provides novel insights into the molecular mechanisms underlying the response of T. orientalis and other accumulators towards Pb stress. The key genes identified in this study may serve as potential targets for genetic engineering targeting phytoremediation.

Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress

BACKGROUND

Lead (Pb) pollution is a widespread environmental problem that is harmful to living organisms. Tartary buckwheat (Fagopyrum tataricum), a member of the family Polygonaceae, exhibits short growth cycles and abundant biomass production, could be an ideal plant for phytoremediation due to its high Pb tolerance. Here, we aimed to explore the molecular basis underlying the responses of this plant to Pb stress.

RESULTS

In our study, ultrastructural localization assays revealed that Pb ions primarily accumulate in leaf vacuoles. RNA deep sequencing (RNA-Seq) of tartary buckwheat leaves was performed on two Pb-treated samples, named Pb1 (2000 mg/kg Pb (NO₃)₂) and Pb2 (10,000 mg/kg Pb (NO₃)₂), and a control (CK). A total of 88,977 assembled unigenes with 125,203,555 bases were obtained. In total, 2400 up-regulated and 3413 down-regulated differentially expressed genes (DEGs) were identified between CK and Pb1, and 2948 up-regulated DEGs and 3834 down-regulated DEGs were generated between CK and Pb2, respectively. Gene Ontology (GO) and pathway enrichment analyses showed that these DEGs were primarily associated with 'cell wall', 'binding', 'transport', and 'lipid and energy' metabolism. The results of quantitative real-time PCR (qRT-PCR) analyses of 15 randomly selected candidate DEGs and 6 regulated genes were consistent with the results of the transcriptome analysis. Heterologous expression assays in the yeast strain Δycf1 indicated that overexpressing CCCH-type zinc finger protein 14 (ZFP14) enhanced sensitivity to Pb²⁺, while 5 other genes, namely, metal transporter protein C2 (MTPC2), phytochelatin synthetase-like family protein (PCSL), vacuolar cation/proton exchanger 1a (VCE1a), natural resistance-associated macrophage protein 3 (Nramp3), and phytochelatin synthetase (PCS), enhanced the Pb tolerance of the mutant strain.

CONCLUSION

Combining our findings with those of previous studies, we generated a schematic model that shows the metabolic processes of tartary buckwheat under Pb stress. This study provides important data for further genomic analyses of the biological and molecular mechanisms of Pb tolerance and accumulation in tartary buckwheat.

Transcriptome analysis reveals novel insights into the continuous cropping induced response in Codonopsis tangshen, a medicinal herb

Codonopsis tangshen Oliv. (C. tangshen Oliv.), a famous medicinal herb in China, is seriously affected by continuous cropping (C-cro). The physiological and biochemical results indicated that C-cro significantly affected the malonaldehyde (MDA) and chlorophyll content, as well as activities of catalase (CAT) and superoxide dismutase (SOD) when compared with the non-continuous cropping (NC-cro) group. Transcriptome profiling found 762 differentially expressed genes, including 430 up-regulated and 332 down-regulated genes by C-cro. In addition, pathway enrichment analysis revealed that genes related to 'Tyrosine degradation I', 'Glycogen synthesis' and 'Phenylalanine and tyrosine catabolism' were up-regulated, and genes associated with 'Signal transduction', 'Immune system', etc. were down-regulated by C-cro. The expression of target genes was further validated by Q-PCR. In this study, we demonstrated the effects of C-cro on C. tangshen at the transcriptome level, and found possible C-cro responsive candidate genes. These findings could be further beneficial for improving the continuous cropping tolerance.

Morphological and Transcriptome Analysis of Wheat Seedlings Response to Low Nitrogen Stress

Nitrogen (N) is one of the essential macronutrients that plays an important role in plant growth and development. Unfortunately, low utilization rate of nitrogen has become one of the main abiotic factors affecting crop growth. Nevertheless, little research has been done on the molecular mechanism of wheat seedlings resisting or adapting to low nitrogen environment. In this paper, the response of wheat seedlings against low nitrogen stress at phenotypic changes and gene expression level were studied. The results showed that plant height, leaf area, shoot and root dry weight, total root length, and number under low nitrogen stress decreased by 26.0, 28.1, 24.3, 38.0, 41.4, and 21.2 percent, respectively compared with plants under normal conditions. 2265 differentially expressed genes (DEGs) were detected in roots and 2083 DEGs were detected in leaves under low nitrogen stress (N-) compared with the control (CK). 1688 genes were up-regulated and 577 genes were down-regulated in roots, whilst 505 genes were up-regulated and 1578 were down-regulated in leaves. Among the most addressed Gene Ontology (GO) categories, oxidation reduction process, oxidoreductase activity, and cell component were mostly represented. In addition, genes involved in the signal transduction, carbon and nitrogen metabolism, antioxidant activity, and environmental adaptation were highlighted. Our study provides new information for further understanding the response of wheat to low nitrogen stress.

Arabinogalactan Proteins Are the Possible Extracellular Molecules for Binding Exogenous Cerium(III) in the Acidic Environment Outside Plant Cells

Rare earth elements [REE(III)] increasingly accumulate in the atmosphere and can be absorbed by plant leaves. Our previous study showed that after treatment of REE(III) on plant, REE(III) is first bound by some extracellular molecules of plant cells, and then the endocytosis of leaf cells will be initiated, which terminates the endocytic inertia of leaf cells. Identifying the extracellular molecules for binding REE(III) is the crucial first step to elucidate the mechanism of REE(III) initiating the endocytosis in leaf cells. Unfortunately, the molecules are unknown. Here, cerium(III) [Ce(III)] and Arabidopsis served as a representative of REE(III) and plants, respectively. By using interdisciplinary methods such as confocal laser scanning microscopy, immune-Au and fluorescent labeling, transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible spectroscopy, circular dichroism spectroscopy, fluorescent spectrometry and molecular dynamics simulation, we obtained two important discoveries: first, the arabinogalactan proteins (AGP) inside leaf cells were sensitively increased in protein expression and recruited onto the plasma membrane; second, to verify whether AGP can bind to Ce(III) in the acidic environment outside leaf cells, by choosing fasciclin-like AGP11 (AtFLA11) as a representative of AGP, we found that Ce(III) can form stable [Ce(H2O)7](III)-AtFLA11 complexes with an apparent binding constant of 1.44 × 10-6 in simulated acidic environment outside leaf cells, in which the secondary and tertiary structure of AtFLA11 was changed. The structural change in AtFLA11 and the interaction between AtFLA11 and Ce(III) were enhanced with increasing the concentration of Ce(III). Therefore, AtFLA11 can serve as Lewis bases to coordinately bind to Ce(III), which broke traditional chemical principle. The results confirmed that AGP can be the possible extracellular molecules for binding to exogenous Ce(III) outside leaf cells, and provided references for elucidating the mechanism of REE(III) initiating the endocytosis in leaf cells.

Plant-lead interactions: Transport, toxicity, tolerance, and detoxification mechanisms

Natural and human activities introduced an excess level of toxic lead (Pb) to the environment. Pb has no known biological significance and its interactions with plants lead to the production of reactive oxygen species (ROS). Pb and/or ROS have the potential to cause phytotoxicity by damaging the tissue ultrastructure, cellular components, and biomolecules. These damaging effects may possibly result in the inhibition of normal cellular functioning, physiological reactions, and overall plant performances. ROS play a dual role and act as a signaling molecule in plant defense system. This system encircles enzymatic and non-enzymatic antioxidative mechanisms. Catalase, superoxide dismutase, peroxidase, and enzymes from the ascorbate-glutathione cycle are the major enzymatic antioxidants, while non-enzymatic antioxidants include phenols, flavonoids, ascorbic acid, and glutathione. Pb removal from contaminated sites using plants depend on the plant's Pb accumulation capacity, Pb-induced phytotoxicity, and tolerance and detoxification mechanisms plants adopted to combat against this phytotoxicity. However, the consolidated information discussing Pb-plant interaction including Pb uptake and its translocation within tissues, Pb-mediated phytotoxic symptoms, antioxidative mechanisms, cellular, and protein metabolisms are rather limited. Thus, we aimed to present a consolidated information and critical discussions focusing on the recent studies related to the Pb-induced toxicity and oxidative stress situations in different plants. The important functions of different antioxidants in plants during Pb stress have been reviewed. Additionally, tolerance responses and detoxification mechanisms in the plant through the regulation of gene expression, and glutathione and protein metabolisms to compete against Pb-induced phytotoxicity are also briefly discussed herein.

Transcriptome analysis providing novel insights for Cd-resistant tall fescue responses to Cd stress

Cadmium (Cd) is a severely toxic heavy metal and environmental pollutant. Tall fescue is a cold season turf grass which has high resistance to Cd as well as the ability to enrich it. To investigate the molecular mechanism underlying the adaptability of tall fescue to Cd stress, RNA-Seq was used to examine Cd stress responses of tall fescue at a transcriptional level. A total of 12 cDNA libraries were constructed from the total RNA of roots or leaves of tall fescue with or without Cd treatments. A total of 2594 (1768 up- and 826 down-regulated) differentially expressed genes (DEGs) were detected in the roots of Cd-stressed tall fescue compared with control roots (R_cd vs R_ck), while only 52 (29 up- and 23 down-regulated) DEGs were found in the leaves of Cd-stressed plants versus the controls (L_cd vs L_ck). The genes encoding glutathione S-transferase (GST), transporter proteins including the ABC transporter, ZRT/IRT-like protein, potassium transporter/channel, nitrate transporter, putative iron-phytosiderophore transporter, copper-transporting ATPase or transporter and multidrug and toxic compound extrusion (MATE) proteins, and numerous transcription factors were found to be significantly induced in Cd-treated roots. In addition, pathogenesis/disease-related gene mRNAs were accumulated in Cd-treated roots of tall fescue. Furthermore, the significantly enriched KEGG pathways in roots were related to 'Glutathione metabolism', 'Ribosome', 'alpha-Linolenic acid metabolism', 'Diterpenoid biosynthesis', 'Sulfur metabolism', 'Phenylpropanoid biosynthesis', 'Protein processing in endoplasmic reticulum', 'Protein export' and 'Nitrogen metabolism'. The study provides novel insights for further understanding the molecular mechanisms of tall fescue responses to Cd stress.

Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

Direct imaging of how lanthanides break the normal evolution of plants

After rare earth elements [REE(III)] are anchored outside of the plasma membrane, REE(III) break plant evolution to initiate leaf cell endocytosis, which finally affects plant growth. However, the molecule for anchoring REE(III) in the acidic environment outside of the plasma membrane is not clear, which is crucial for exploring the mechanism of REE(III) breaking plant evolution. Here, lanthanum(III) [La(III)] and terbium(III) [Tb(III)] were respectively served as a representative of REE(III) without and with f electrons, and Arabidopsis was served as a representative of plants, cellular and molecular basis for arabinogalactan proteins (AGP) anchoring REE(III) outside of the plasma membrane was investigated. By using interdisciplinary methods, when REE(III) initiated leaf cell phagocytosis, we observed the increase in the expression of AGP and their migration to the outside of the plasma membrane. In the acidic environment outside of the plasma membrane, Tb(III) formed more stable Lewis acid-base [REE(III)-AGP] complexes with a higher apparent binding constant (1.51 × 10^-6) than La(III) (1.24 × 10^-6). In REE(III)-AGP complexes, the bond lengths of REE(III)-O were in normal range and H-bonds were strong H-bonds. The formation of REE(III)-AGP complexes sequentially disturbed the secondary and tertiary structure of AGP, which were enhanced with increasing the concentration of REE(III), and Tb(III) caused stronger structural changes than La(III). Hence, AGP could be molecules for anchoring REE(III) outside of the plasma membrane. The results of this study are direct imaging of how lanthanides break the normal evolution of plants, and can serve as an important guidance for investigating mechanism of lanthanides in organisms.

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.