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

Integrated transcriptome and metabolome analysis revealed differential drought stress response mechanisms of wheat seedlings with varying drought tolerance

BACKGROUND

Wheat (Triticum aestivum L.) is a staple crop frequently enduring drought stress, significantly impacting its quantity and quality. Therefore, elucidating the underlying mechanisms of wheat's drought stress response is crucial for developing drought-tolerant varieties through molecular breeding techniques.

RESULTS

This study analyzed the transcriptome and metabolome of wheat seedlings with varying drought tolerance (drought-tolerant T13, control CK, and drought-susceptible T2) under drought stress. Results suggested that T13 and T2 had partially similar drought stress response mechanisms. But the mainly drought response mechanisms in T13 (accumulated flavonoids and phenolic acids) was different from T2 (accumulated alkaloids). Integrated metabolome and transcriptome analyses demonstrated significant up-regulation of most flavonoids and phenolic acids biosynthesis-related metabolites and genes (HCT, FLS, CHS and F3'5'H) in T13 under drought stress.

CONCLUSIONS

These results indicated that flavonoids and phenolic acids metabolisms were associated with wheat seedling's drought resistance, with their biosynthesis-related differentially expressed metabolites and genes possibly being key factors underlining the difference in drought tolerance. Thus this study enhances our understanding of wheat seedling's drought response mechanism, providing valuable insights for breeding drought-tolerant wheat cultivars.

Competitive ion uptake and transcriptional regulation as a coordinated dual mechanism of NaCl-mediated cadmium detoxification in Suaeda salsa

Cadmium (Cd), a highly toxic heavy metal, severely inhibits plant growth. Salt alleviates Cd stress in halophytes, however, the molecular mechanisms governing salt-mediated regulation of Cd toxicity remain poorly understood. This study elucidates the protective mechanism of NaCl in Cd-stressed Suaeda salsa seedlings. Cd exposure suppressed seedling growth and induced membrane lipid peroxidation. Conversely, NaCl application not only maintained normal growth but also effectively ameliorated Cd-induced phytotoxicity, potentially through osmotic adjustment mechanisms. Notably, using ion flux analysis, we found that NaCl attenuated Cd2+ influx into root epidermal cells, thereby enhancing Cd resistance. Pharmacological inhibition studies confirmed that Na + competitively inhibits Cd2+ uptake through shared channels/transporters. Furthermore, RT-qPCR gene expression profiling revealed that NaCl coordinately activated both ionic compartmentalization and efflux systems through upregulating plasma membrane-localized SsSOS1 and tonoplast-associated SsNHX1 for Na + extrusion and vacuolar sequestration, enhancing Cd2+ compartmentalization via SsCAX and SsVHA-B mediated transport and maintaining cellular homeostasis through SsHKT1 and SsPIP-mediated regulation of water and K+ balance, or indirectly inhibit Cd2+ influx. It reveals that salt weakens Cd2+ influx and enhances Cd tolerance by activating a coordinated gene regulatory network in Suaeda salsa. This finding offers valuable insights into phytoremediation strategies for enhancing crop resilience in Cd-contaminated saline soils.

Integration of Phenotypic, Accumulative, Physiological-Biochemical, and Transcriptomic Analyses Reveals New Insights in Lettuce Response to Iodine: Enhancement or Toxic Effects

Iodine interferes with plant gene expression and affects plant growth, but the molecular mechanisms behind plant responses to iodine are not yet fully understood. In this study, lettuce (Lactuca sativa L.) was exposed to varying levels (0, 1, 5, 10, 50, and 100 μM) of iodine (NaI and NaIO3). The results indicate that NaI was more biologically effective than NaIO3. Low concentrations of iodine increased plant biomass, photosynthetic pigment content, and protein content while maintaining reactive oxygen species homeostasis by regulating antioxidant enzyme activities and antioxidant content. However, high concentrations of iodine caused toxic phenotypic symptoms and increased oxidative stress. Transcriptomic analysis showed that high concentration (50 μM) of NaI led to the downregulation of most genes related to photosynthetic metabolism, disrupting the electron transfer process and Calvin cycle of photosynthesis. Furthermore, iodine exposure activated plant hormone signaling. In conclusion, this study revealed the morpho-physiological, biochemical, and transcriptional response mechanisms of lettuce to iodine exposure.

Metabolomic Analysis of the Responses of Bryophyte Tortella tortuosa (Hedw.) Limpr. to Cadmium (Cd) Stress

In recent years, there have been many studies on the response of plants to heavy metal stress, but the metabolic changes in bryophytes, pioneer plants quickly responding to environmental changes, under exogenous cadmium (Cd) stress have yet to be explored. In this indoor experiment, the responses in the metabolome of bryophyte Tortella tortuosa (Hedw.) Limpr. to different Cd exposure levels (0 (CK), 5 (T1), and 10 (T2) mg·L-1) were analyzed. The results showed that the number of differentially accumulated metabolites (DAMs) secreted by T. tortuosa increased with the increase in the Cd concentration, and the biosynthesis of cofactors, D-Amino acid metabolism, Arginine biosynthesis, ATP-binding cassette transporters (ABC transporters), and biosynthesis of alkaloids derived from shikimate pathway were the main pathways enriched by DAMs. The relative abundances of malic acid, N-Formylkynurenine, L-Glutamine, L-Histidine, LL-2,6-Diaminopimelic acid, and fusaric acid in the T2 treatment increased by 16.06%, 62.51%, 14.51%, 11.92%, 21.37%, and 35.79%, respectively (p < 0.05), compared with those of the CK, and the correlation analysis results showed that the above DAMs were closely related to the changes in plant antioxidant enzyme activity and Cd concentration. These results indicate that the secretion of amino acid (N-Formylkynurenine, L-Histidine) and organic acids (isocitric acid, LL-2,6-Diaminopimelic acid, malic acid) through the metabolic pathways, including biosynthesis of amino acids, biosynthesis of cofactors, glyoxylate and dicarboxylate metabolism, and ABC transporters, is the metabolic mechanism of T. tortuosa to resist exogenous Cd stress. This study will provide a reference for the monitoring and remediation of heavy metal pollution.

Evaluation of the buffer-blocking capacity of acrocarpous moss Campylopus schmidii as candidate for copper and cadmium migration

This study evaluates the ability of Campylopus schmidii to inhibit the horizontal migration of copper and cadmium under simulated acid rain conditions. Experiments at varying pH levels (3.6, 4.7, and 5.6) revealed significant reductions in copper and cadmium migration rates, especially at pH 3.6, where concentrations dropped to 3.68% and 30.98% of those in exposed soil after 90 days. No leachate residue was collected from moss-covered groups, indicating effective soil and water loss control. Transcriptome analysis identified numerous differentially expressed genes under cadmium stress, highlighting enriched pathways related to cell structure, signaling, and metabolism, demonstrating Campylopus schmidii 's complex molecular mechanisms for heavy metal stress adaptation. These findings underscore the potential of Campylopus schmidii for environmental restoration and pollution control in mining areas.

AaMYC3 bridges the regulation of glandular trichome density and artemisinin biosynthesis in Artemisia annua

Artemisinin, the well-known natural product for treating malaria, is biosynthesised and stored in the glandular-secreting trichomes (GSTs) of Artemisia annua. While numerous efforts have clarified artemisinin metabolism and regulation, the molecular association between artemisinin biosynthesis and GST development remains elusive. Here, we identified AaMYC3, a bHLH transcription factor of A. annua, induced by jasmonic acid (JA), which simultaneously regulates GST density and artemisinin biosynthesis. Overexpressing AaMYC3 led to a substantial increase in GST density and artemisinin accumulation. Conversely, in the RNAi-AaMYC3 lines, both GST density and artemisinin content were markedly reduced. Through RNA-seq and analyses conducted both in vivo and in vitro, AaMYC3 not only directly activates AaHD1 transcription, initiating GST development, but also up-regulates the expression of artemisinin biosynthetic genes, including CYP71AV1 and ALDH1, thereby promoting artemisinin production. Furthermore, AaMYC3 acts as a co-activator, interacting with AabHLH1 and AabHLH113, to trigger the transcription of two crucial enzymes in the artemisinin biosynthesis pathway, ADS and DBR2, ultimately boosting yield. Our findings highlight a critical connection between GST initiation and artemisinin biosynthesis in A. annua, providing a new target for molecular design breeding of traditional Chinese medicine.

Rootstock Selection for Resisting Cucumber Fusarium Wilt in Hainan and Corresponding Transcriptome and Metabolome Analysis

Soilborne diseases are important problems in modern agricultural production. Fusarium oxysporum f. sp. cucumerinum (FOC) is one of the predominant soilborne pathogens threatening cucumber cultivation, especially in Hainan, China. This study assessed FOC-resistant rootstocks using incidence rate, disease severity index (DSI), and area under the disease severity index curve (AUDRC), revealing "JinJiaZhen (Mc-4)" as resistant and "JinGangZhuan 1901 (Mc-18)" as susceptible. Comprehensive transcriptome and metabolome analyses were conducted to investigate the defense mechanisms of these rootstocks, revealing key pathways, such as the mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis, which are crucial for plant disease resistance. Additionally, the study compared the resistance mechanisms of two other rootstocks, Mc-4 and Mc-18, against FOC infection through transcriptomic and metabolomic analyses. Mc-4 exhibited a higher number of differentially expressed genes (DEGs) related to phenylpropanoid biosynthesis compared to Mc-18. Untargeted metabolomics identified 4093 metabolites, with phenylpropanoid biosynthesis, isoquinoline alkaloid biosynthesis, and porphyrin metabolism as primary annotated pathways. On the sixth day post-inoculation, when the number of DEGs and differentially accumulated metabolites (DAMs) was highest, phenylpropanoid biosynthesis emerged as a key pathway in Mc-4, with 37 DEGs and 8 DAMs identified. Notably, Mc-4 showed upregulated expression of genes encoding enzymes involved in phenylpropanoid biosynthesis and increased accumulation of related metabolites, such as coniferyl-aldehyde, coniferyl alcohol, and coniferyl acetate. These findings highlight the differential defense mechanisms between resistant and sensitive rootstocks and provide insights into plant-pathogen interactions. This study's results will contribute to the development of better and disease-free cucumber varieties, promoting sustainable agriculture.

Applying cross-scale regulations to Sedum plumbizincicola for strengthening the bioremediation of the agricultural soil that contaminated by electronic waste dismantling and revealing the underlying mechanisms by multi-omics

Electronic waste dismantling has induced the surrounding agricultural soils suffered from combined contamination of heavy metals and organic pollutants. Lower efficiency and complex mechanisms of bioremediation remain to be resolved. Here, we adopted regulations to Sedum plumbizincicola cross aboveground and belowground scales to strengthen the bioremediation efficiency. Results showed that the S. plumbizincicola intercropping with the Astragalus sinicusL. that inoculated with Rhizobium had the highest performance in reductions of Cd, PBDEs and PCBs from soils by 0.11 mg/kg, 67.93 μg/kg and 38.91 μg/kg, respectively. Rhizosphere soil metabolomics analysis demonstrated that reductions in Cd and PBDEs significantly associated with 2-Methylhippuric acid and L-Saccharopine, which were involved in phenylalanine metabolism, biosynthesis of amino acids and lysine. Metagenomics analysis revealed that these functional pathways were mediated by Frankia, Mycobacterium, Blastococcus, etc. microbial taxa, which were also significantly altered by regulations. Moreover, regulation regimes significantly affected transcription genes of S. plumbizincicola. Functional annotation revealed that cross-scale regulations significantly improved bioremediation efficiency through microorganisms and metabolites in the rhizosphere and transcription genes of S. plumbizincicola, which were illustrated to promote plant growth and tolerance to environmental stress. Our integration of multi-omics provides comprehensive and deep insights into molecular mechanisms in the cross-scale regulations of S. plumbizincicola, which would favor remediation techniques advances for the soil contaminated by electronic waste dismantling.

Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of Alisma orientale to cadmium stress

Cadmium (Cd) pollution poses a serious challenge to the quality and safe utilization of traditional Chinese medicine plants as well as human health. In this study, seedlings of the medicinal plant species Alisma orientale were subjected to different levels of Cd stress for 7 days to investigate the effects of Cd stress on its growth, physiological response, and transcriptome profiling. The results showed that under different Cd stress levels, the growth of A. orientale displayed an inverted U-shaped dose response curve as low-dose stimulation and high-dose inhibition. Cd was mainly enriched in roots in the high concentration treatment, and Cd content reached maximum under 200-μM Cd stress. Cd stress-induced indicators including H2O2 (14.1-228.8 % in leaves; 29.7-131.7 % in roots) and MDA (22.0-161.1 % in leaves; 30.0-201.1 % in roots) showed different degree of increase, except under 200-μM Cd stress, which had a slight decrease. Antioxidant enzyme system (SOD, POD and CAT) and nonenzymatic substances (SS, SP, total flavonoid and total polyphenols) played a key role to mitigate Cd toxic effects. Transcriptome analysis revealed 26,442 significantly differentially expressed genes, and plant-pathogen interactions and phenylpropanoid biosynthesis were identified as two key pathways. Through WGCNA joint analysis, the transcription factor genes R2R3-MYB (AoMYB12) and WRKY (AoWRKY5 and AoWRKY6) were identified as hub regulators of A. orientale in response to Cd stress. Our study provides experimental data on the effects of Cd stress on A. orientale growth and Cd accumulation in different plant parts, and investigated the transcriptomic and physio-biochemical features, advancing our understanding of the response and detoxification mechanisms of plants under Cd stress.

Exogenous MgH2-derived hydrogen alleviates cadmium toxicity through m6A RNA methylation in rice

Cadmium (Cd) contamination poses a substantial threat to crop yields and human health. While magnesium hydride (MgH2) has been reported as a hydrogen (H2) donor that promotes plant growth under heavy metal contamination, its role in rice remains elusive. Herein, seedlings of Oryza sativa L. Japonica variety Zhonghua 11 (ZH11) were selected and exposed to 20 µL of 1-mol/L cadmium chloride (CdCl2) solution via hydroponics to simulate Cd stress. Meanwhile, 0.1 mg of MgH2 was used to slow-release H2 to the experimental group to explore its potential effects on rice over a 2-week period. The results indicated that Cd exposure severely inhibited the growth and development of ZH11 rice seedlings. However, the exogenous slow-release of H2 from MgH2 effectively mitigated this inhibitory effect by restoring the balance of reactive oxygen species (ROS), maintaining endogenous H2 homeostasis, and supporting the photosynthetic system. High-performance liquid chromatography analysis revealed that exogenous H2 reduces m6A RNA methylation levels in mRNA under Cd stress. Consequently, MeRIP-seq was conducted to investigate the effect of Cd exposure in rice in the presence and absence of H2. The m6A modifications were enriched at the start codon, stop codon, and 3' UTR. By integrating RNA-seq data, 118 transcripts were identified as differentially methylated and expressed genes under Cd stress. These gene annotations were associated with ROS, biological stress, and hormonal responses. Notably, 297 differentially methylated and expressed genes were identified under Cd stress in the presence of H2, linked to heavy metals, protein kinases, and calcium signaling regulation. Cd strongly activates the MAPK pathway in response to stress. Exogenous H2 reduces Cd accumulation as well as enhances plant tolerance and homeostasis by lowering m6A levels, thereby decreasing the mRNA stability of these genes. Our findings indicate that MgH2, by supplying H2, regulates gene expression through m6A RNA methylation and confers Cd tolerance in rice. This study provides potential candidate genes for studying the remediation of heavy metal pollution in plants.

Exploring genetics and genomics trends to understand the link between secondary metabolic genes and agronomic traits in cereals under stress

The plant metabolome is considered an important interface between the genome and its phenome, where it plays a significant role in regulating plant growth in response to various environmental cues. A wide array of specialized metabolites is produced by plants, which are essential for mediating environmental interactions and their adaptation. Notably, enhanced accumulation of these specialized metabolites, particularly plant secondary metabolites (PSMs), is a part of the chemical defense response that is directly linked to improved stress tolerance. Therefore, exploring the genetic diversity underlying the immense variation of the secondary metabolite pool could unravel the adaptation mechanisms in plants against different environmental stresses. The post-genomic profiling platforms have enabled the exploration of the link between metabolic diversity and important agronomic traits. The current review focuses on the major achievements and future challenges associated with plant secondary metabolite (PSM) research in graminaceous crops using advanced omics approaches. Given this, we briefly summarize different strategies adopted to explore the genetic diversity and evolution of PSMs in cereal crops. Further, we have discussed the recent technological advancements to integrate multi-omics approaches linking the metabolome diversity with the genome, transcriptome, and proteome of these crops under stress. Combining these data with phenomics (the omics of phenotypes) provides a holistic view of how plants respond to stress. Next, we outlined the genetic manipulation studies performed so far in cereals to engineer secondary metabolic pathways for enhanced stress tolerance. In summary, our review provides new insight into developing genetic and genomic trends in exploring the secondary metabolite diversity in graminaceous crops and discusses how this information can be utilized in designing strategies to generate future stress-resilient crops.

Effect of Ag+ and Cd2+ Elicitation on Polyphenol Production in Shoot Culture of Dracocephalum ruyschiana L

Abiotic elicitation with heavy metals has demonstrated considerable potential to stimulate the production of industrially important secondary metabolites in plant in vitro cultures. The present study investigates the effect of exogenous silver nitrate and cadmium chloride supplementation on flavonoid and phenolic acid production, as well as other indicators of oxidative stress, in shoot cultures of Dracocephalum ruyschiana L. Owing to the presence of bioactive polyphenolic compounds, this Mongolian medicinal plant is traditionally used as an anti-inflammatory, antibacterial and antipyretic agent. The shoots were cultured for three weeks, and then, cadmium (Cd2+) and silver (Ag+) ions (50 or 100 µM) were added to the medium. The maximum proliferation rate was observed in the presence of 100 µM Ag+ (almost 5), the highest chlorophyll content in the presence of 100 µM Cd2+ (0.6 mg/g FW) and the highest biomass was observed with both these treatments (73.4-75.7 g FW and 7.53-7.72 g DW). UPLC-PDA-ESI-MS analysis revealed four phenolic acids and five flavonoid derivatives in the hydromethanolic extract of D. ruyschiana shoots. All treatments stimulated the production of rosmarinic acid (RA), which was the dominant compound in the analyzed culture; the highest level of RA, i.e., about three times higher than the control, was noted in shoots exposed to 50 µM Cd2+ (14.72 mg/g DW), whereas the level of most flavonoids in the culture increased most significantly when exposed to Cd2+ at a concentration of 100 µM. Moreover, the shoots grown in the presence of 100 µM Cd2+ exhibited significantly higher antioxidant potential in comparison to the control. Our findings indicate that heavy metals are able to stimulate phenolic compound biosynthesis in Dracocephalum shoots without any negative impact on their growth. These results could be of significant importance for the medical, nutraceutical and agronomic industries.

Citric acid-driven cadmium uptake and growth promotion mechanisms in Brassica napus

Citric acid (CA) is well-known for mitigating cadmium (Cd) toxicity in plants. Yet, the underlying mechanisms driving growth promotion, Cd detoxification/tolerance, and enhanced phytoremediation processes remain incompletely understood. This study investigated the effects of CA application (2.5 mM) on Brassica napus grown in Cd-contaminated (30 mg kg-1) growth medium through a controlled pot experiment. Cd exposure alone significantly impaired various plant physiological parameters in B. napus. Whereas CA application significantly (p < 0.05) enhanced physiological attributes, Cd detoxification and tolerance by modulating key genes involved in photosynthesis and Cd transport, including the metal-transporting P1B-type ATPases (Cd/zinc heavy metal-transporting ATPase 1; HMA1) and light-harvesting chlorophyll a/b-binding 3 (LHCB3). Notably, CA application increased Cd accumulation in stems and leaves by 4% and 35%, respectively, enhancing bioconcentration factors (BCF) by 12% in stems and 40% in leaves while reducing root BCF by 10%. This translocation was facilitated by the upregulation of HMA4, HMA2, and plant Cd resistance (PCR2) genes in plant leaves, improving Cd mobility within the plant. Furthermore, CA induced a 34% increase in phytochelatins and a 32% upregulation in metallothioneins, accompanied by a significant reduction in oxidative stress markers, including a 40% decrease in hydrogen peroxide and a 44% decline in malondialdehyde levels in leaves. Enhanced antioxidant enzyme activity and osmolyte accumulation further contributed to improved Cd detoxification/sequestration in leaves, reduced oxidative stress, and improved photosynthetic efficiency, resulting in enhanced plant biomass production and Cd tolerance. Transcriptomic analysis showed that CA treatment substantially influenced the expression of 12,291 differentially expressed genes (DEGs), with 750 common genes consistently downregulated in CK vs Cd treatment group but upregulated in Cd vs Cd-CA treatment group. Additionally, CA modulated 11 DEGs associated with 32 gene ontologies in the citrate pathway under Cd stress, highlighting its targeted regulatory effect on metabolic pathways involved in Cd stress response. This study offers novel insights into the synergistic role of CA in promoting plant growth and regulating Cd uptake in B. napus, highlighting its potential to enhance phytoremediation strategies.

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.

Exposure to toxic cadmium concentration induce physiological and molecular mechanisms alleviating herbivory infestation in Wedelia

Cadmium (Cd) toxicity induces significant disruptions in growth and development, plants have developed strategies to alleviate metal toxicity promoting establishment even during herbivores infestation. The study demonstrates that W. trilobata maintains growth and development under the combined stress of Cd exposure and herbivore invasion by Spodoptera litura, in contrast to W. chinensis. Cd toxicity markedly reduce shoot elongation and total fresh biomass, and a significant decrease in the dry weight of the shoot biomass and leaf count by 19%, 18%, 16%, and 19% in W. trilobata compared to controls. An even more pronounced decrease of 35%, 43%, 45% and 43% was found in W. chinensis. Compared to W. chinensis, W. trilobata showed a higher increase in phytohormone production including abscisic acid (ABA), gibberellic acid (GA3), indole-3-acetic acid (IAA) and methyl jasmonic acid (JA-me) under both Cd and herbivory stress as compared with respective controls. In addition, leaf ultra-structure also showed the highest damage to cell membranous structures by Cd-toxicity in W. chinensis. Furthermore, RNA-seq analysis revealed numerous genes viz., EMSY, MCCA, TIRI, BED-type, ABA, JAZ, CAB-6, CPSI, LHCII, CAX, HNM, ABC-Cd-trans and GBLP being differentially expressed between Cd-stress and herbivory groups in both W. trilobata and W. chinensis, with a particular emphasis on genes associated with metal transport and carbohydrate metabolism. Analyses employing the Gene Ontology (GO) system, the Clusters of Orthologous Groups (COG) categorization, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, highlight the functional and evolutionary relationships among the genes of the Phenylpropanoid and Flavonoid biosynthesis pathways and brassinosterod metabolism, associated with plant growth and development under Cd-toxicity and herbivory. W. trilobata opposite of W. chinensis, significantly improve plant growth and mitigates Cd toxicity through modulation of metabolic processes, and regulation of responsible genes, to sustain its growth under Cd and herbivory stress, which can be used in stress improvement in plants for sustainable ecosystem biodiversity and food security.

Seed priming with graphene oxide improves salinity tolerance and increases productivity of peanut through modulating multiple physiological processes

Graphene oxide (GO), beyond its specialized industrial applications, is rapidly gaining prominence as a nanomaterial for modern agriculture. However, its specific effects on seed priming for salinity tolerance and yield formation in crops remain elusive. Under both pot-grown and field-grown conditions, this study combined physiological indices with transcriptomics and metabolomics to investigate how GO affects seed germination, seedling salinity tolerance, and peanut pod yield. Peanut seeds were firstly treated with 400 mg L⁻¹ GO (termed GO priming). At seed germination stage, GO-primed seeds exhibited higher germination rate and percentage of seeds with radicals breaking through the testa. Meanwhile, omics analyses revealed significant enrichment in pathways associated with carbon and nitrogen metabolisms in GO-primed seeds. At seedling stage, GO priming contributed to strengthening plant growth, enhancing photosynthesis, maintaining the integrity of plasma membrane, and promoting the nutrient accumulation in peanut seedlings under 200 mM NaCl stress. Moreover, GO priming increased the activities of antioxidant enzymes, along with reduced the accumulation of reactive oxygen species (ROS) in response to salinity stress. Furthermore, the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) of peanut seedlings under GO priming were mainly related to photosynthesis, phytohormones, antioxidant system, and carbon and nitrogen metabolisms in response to soil salinity. At maturity, GO priming showed an average increase in peanut pod yield by 12.91% compared with non-primed control. Collectively, our findings demonstrated that GO plays distinguish roles in enhancing seed germination, mitigating salinity stress, and boosting pod yield in peanut plants via modulating multiple physiological processes.

Physiological and molecular responses of strawberry plants to Cd stress

Cadmium (Cd), a toxic metal element, can be absorbed by plants via divalent metal ion transporters, thereby retarding plant growth and posing a threat to human health. Strawberries are popular and economically valuable berry species that are sensitive to soil pollutants, especially Cd. However, the mechanisms underlying Cd stress responses in strawberry plants remain largely unclear. Here, we investigated the physiological and molecular basis of Cd stress responses in strawberry plants using the diploid strawberry 'Yellow Wonder' as a material. The results indicated that Cd stress induced oxidative damage, repressed photosynthetic efficiency, and interfered with the accumulation and redistribution of trace elements. Furthermore, Cd stress reduced the concentrations of indoleacetic acid, trans-zeatin riboside and gibberellic acid while increasing the concentration of abscisic acid, thus altering the phytohormone signaling pathway in strawberry plants. Cd stress also inhibited the expression of genes involved in nitrogen uptake and assimilation while promoting the energy supply for plant survival under Cd toxicity. Moreover, the flavonoid biosynthesis pathway was induced, and the anthocyanin concentration increased, thereby improving the free radical scavenging capacity of strawberry plants under Cd toxicity. Additionally, we identified several transcription factors and functional genes as hub genes based on a weighted gene coexpression network analysis. These results collectively provide a theoretical foundation for strawberry breeding and ensuring agriculture and food safety.

Physiology and transcriptome analysis of Artemisia argyi adaptation and accumulation to soil cadmium

The soil pollution caused by cadmium (Cd) poses a significant threat to the environment. Therefore, identifying plants that can effectively remediate Cd-contaminated soils is urgently needed. In this study, physiological, cytological, and transcriptome analyses were performed to comprehensively understand the changes in Artemisia argyi under Cd stress. Physiological and cytological analyses indicated that A. argyi maintained normal growth with intact cell structure under Cd stress levels up to 10 mg/kg. Cytological analysis showed that Cd precipitation in leaf cells occurred in the cytoplasm and intercellular spaces. As the levels of Cd stress increased, proline accumulation in leaves increased, whereas soluble protein and soluble sugar initially increased, followed by a subsequent decline. The translocation factor was above 1 under 0.6 mg/kg Cd stress but decreased when it exceeded this concentration. Transcriptome analyses revealed several crucial Cd-influenced pathways, including amino acid, terpenoid, flavonoid, and sugar metabolisms. This study not only proved that A. argyi could enrich Cd in soil but also revealed the response of A. argyi to Cd and its resistance mechanisms, which provided insight into the cleaner production of A. argyi and the remediation of Cd-contaminated soil.

Overexpression of SQUAMOSA promoter binding protein-like 4a (NtSPL4a) alleviates Cd toxicity in Nicotiana tabacum

Squamosa Promoter Binding Protein-Like (SPL) plays a crucial role in regulating plant development and combating stress, yet its mechanism in regulating resistance to Cd toxicity remains unclear. In this study, we cloned a nuclear-localized transcription factor, NtSPL4a, from the tobacco cultivar TN90. Transient co-expression results showed that miR156 significantly reduced the expression of NtSPL4a by binding to the 3'-UTR of its transcript. We obtained transgenic tobacco overexpressing NtSPL4a (including the 3'-UTR) and NtSPL4aΔ (lacking the 3'-UTR) through Agrobacterium-mediated genetic transformation. Compared to the wild type (WT), overexpression of NtSPL4a/NtSPL4aΔ shortened the flowering time and exhibited a more developed root system. The transgenic tobacco showed significantly reduced Cd content, being 85.1% (OE-NtSPL4a) and 46.7% (OE-NtSPL4aΔ) of WT, respectively. Moreover, the upregulation of NtSPL4a affected the mineral nutrient homeostasis in transgenic tobacco. Additionally, overexpression of NtSPL4a/NtSPL4aΔ effectively alleviated leaf chlorosis and oxidative stress induced by Cd toxicity. One possible reason is that the overexpression of NtSPL4a/NtSPL4aΔ can effectively promote the accumulation of non-enzymatic antioxidants. A comparative transcriptomic analysis was performed between transgenic tobacco and WT to further unravel the global impacts brought by NtSPL4a. The tobacco overexpressing NtSPL4a had 183 differentially expressed genes (77 upregulated, 106 downregulated), while the tobacco overexpressing NtSPL4aΔ had 594 differentially expressed genes (244 upregulated, 350 downregulated) compared to WT. These differentially expressed genes mainly included transcription factors, metal transport proteins, flavonoid biosynthesis pathway genes, and plant stress-related genes. Our study provides new insights into the role of the transcript factor SPL in regulating Cd tolerance.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

Genome-Wide Identification and Analysis of the EPF Gene Family in Sorghum bicolor (L.) Moench

The EPIDERMAL PATTERNING FACTOR (EPF) plays a crucial role in plant response to abiotic stress. While the EPF has been extensively studied in model plants such as Arabidopsis thaliana, there is a lack of research on identifying EPF genes in the whole sorghum genome and its response to drought stress. In this study, we employed bioinformatics tools to identify 12 EPF members in sorghum. Phylogenetic tree analysis revealed that SbEPFs can be categorized into four branches. Further examination of the gene structure and protein conservation motifs of EPF family members demonstrated the high conservation of the SbEPF sequence. The promoter region of SbEPFs was found to encompass cis-elements responsive to stress and plant hormones. Moreover, real-time fluorescence quantitative results indicated that the SbEPFs have a tissue-specific expression. Under drought stress treatment, most SbEPF members were significantly up-regulated, indicating their potential role in drought response. Our research findings establish a foundation for investigating the function of SbEPFs and offer candidate genes for stress-resistant breeding and enhanced production in sorghum.

Transcriptomics and metabolomics association analysis revealed the responses of Gynostemma pentaphyllum to cadmium

Gynostemma pentaphyllum an important medicinal herb, can absorb high amounts of cadmium (Cd) which can lead to excessive Cd contamination during the production of medicines and tea. Hence, it is crucial to investigate the response mechanism of G. pentaphyllum under Cd stress to develop varieties with low Cd accumulation and high tolerance. Physiological response analysis, transcriptomics and metabolomics were performed on G. pentaphyllum seedlings exposed to Cd stress. Herein, G. pentaphyllum seedlings could significantly enhance antioxidant enzyme activities (POD, CAT and APX), proline and polysaccharide content subject to Cd stress. Transcriptomics analysis identified the secondary metabolites, carbohydrate metabolism, amino acid metabolism, lipid metabolism, and signal transduction pathways associated with Cd stress, which mainly involved the XTH, EXP and GST genes. Metabolomics analysis identified 126 differentially expressed metabolites, including citric acid, flavonoid and amino acids metabolites, which were accumulated under Cd stress. Multi-omics integrative analysis unraveled that the phenylpropanoid biosynthesis, starch, and sucrose metabolism, alpha-linolenic acid metabolism, and ABC transporter were significantly enriched at the gene and metabolic levels in response to Cd stress in G. pentaphyllum. In conclusion, the genetic regulatory network sheds light on Cd response mechanisms in G. pentaphyllum.