Ethylene positively regulates Cd tolerance via reactive oxygen species scavenging and apoplastic transport barrier formation in rice

ACS2 and ACS6, especially ACS2 is involved in MPK6 evoked production of ethylene under Cd stress, which exacerbated Cd toxicity in Arabidopsis thaliana

As one of the heavy metal pollutants with strong biological toxicity, cadmium (Cd) is easily absorbed by plant roots, which seriously restricts the growth of plants, causes the quality of agricultural products to decline and threatens human health. Many complex signal transduction pathways are involved in the process of plant response to Cd stress. Among them, plant hormone ethylene is an important signal molecule for plant response to various environmental stresses, and its regulatory mechanism and signal transduction pathway in Cd stress response need to be further clarified. Here, we discovered that Cd stress induced a significant increment in ethylene production in Arabidopsis roots, and the amount of ethylene produced was positively correlated with the inhibition of Arabidopsis root growth and Cd accumulation. Simultaneously, Cd stress stimulated the detoxification mechanism within cells and promoted the expression of METAL TOLERANCE PROTEIN 3 (MTP3), IRON-REGULATED TRANSPORTER2 (IRT2), IRON REGULATED GENE 2 (IREG2) genes implicated in Cd vacuolar compartmentation. However, whether this is associated with ethylene signal transduction remains to be further explored. Further studies have revealed that the Cd induced ethylene burst is attributed to the up-regulation of the expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes that mediated by MITONGEN-ACTIVATED PROTEIN KINASE 6 (MAPK6) in Arabidopsis roots, and among them, ACS2 and ACS6, especially ACS2, are involved in MAPK6-induced ethylene production under Cd stress. The results of this study provide new ideas for understanding the signal transduction pathway of plant response to Cd stress.

Calcium regulates the physiological and molecular responses of Morus alba roots to cadmium stress

Heavy metal cadmium (Cd) is toxic to organisms. Mulberry (Morus alba L.) is a fast-growing perennial that is also an economical Cd phytoremediation material with large biomass. However, the molecular mechanisms underlying its Cd tolerance remain unclear. Here, we reveal the physiological and molecular mechanisms underlying Cd toxicity under varying calcium (Ca) treatments. First, under low-Ca treatment (0.1 mM Ca), mulberry growth was severely inhibited and the root surface structure was damaged by Cd stress. Second, electrophysiological data demonstrated that 0.1 mM Ca induced an increased Cd2+ influx, leading to its accumulation in the entire root and root cell walls. Third, high-Ca treatment (10 mM Ca) largely alleviated growth inhibition, activated antioxidant enzymes, increased Ca content, decreased Cd2+ flux, and inhibited Cd uptake by roots. Finally, 0.1 mM Ca resulted in the activation of metal transporters and the disruption of Ca signaling-related gene expression, which facilitated Cd accumulation in the roots, aggravating oxidative stress. These adverse effects were reversed by treatment with 10 mM Ca. This study preliminarily revealed the mechanism by which varying Ca levels regulate Cd uptake and accumulation in mulberry roots, provided an insight into the interrelationships between Ca and Cd in the ecological and economic tree mulberry and offered a theoretical basis for Ca application in managing Cd pollution.

A plant growth-promoting bacterium supports cadmium detoxification of rice by inducing phenylpropanoid and flavonoid biosynthesis

Cadmium (Cd) is easily absorbed by rice and enters the food chain, posing a health risk to humans. Plant growth promoting bacteria (PGPB) can help the plant respond to Cd stress, but the mechanism of PGPB for Cd reduction is unclear. Therefore, this study was conducted and found inoculation with a newly isolated Pseudomonas koreensis promoted the growth of rice and reduced its Cd content. Fluorescent staining using PI and H2O2 probe indicated that PGPB attenuated oxidative damage in rice. Metabolomics revealed that 59 metabolites were upregulated after inoculation, with phenylpropanoids and flavonoids being significantly activated. Spectrophotometry analysis comfirmed the content of flavonoid, lignin, phenol, glutathione, proline and the activities of antioxidant enzymes were higher in the inoculated rice than in the control. Quantitative PCR showed the expression of genes related to phenylpropanoids (OsPAL, OsC4H, Os4CL) and flavonoids (OsCHS, OsCHI) was significantly increased by PGPB, while the genes of heavy metal transporters (OsNRAMP5, OsHMA2, OsIRT1) were significantly decreased. Overall, this study provides an insight into the PGPB-mediated detoxification mechanism in rice under Cd stress and emphasizes the role of phenylpropanoids and flavonoids in the production of low-Cd rice to ensure human health.

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.

Ethylene-mediated root endodermal barrier development in impeding Cd radial transport and accumulation in rice (Oryza sativa L.)

Ethylene plays crucial roles in the adaptation to cadmium (Cd) stress. Nevertheless, the impact of endogenous ethylene on radial transport of Cd in different rice cultivars are insufficiently understood. Herein, we investigated how ethylene involved in the formation of endodermal barriers in roots of Nipponbare with low-Cd accumulation and IR32307 with high-Cd accumulation ability and further assessed its influence on Cd radial transport. Our analysis indicated that both Cd stress and external ACC (1-aminocyclopropane-1-carboxylic acid, ethylene biosynthesis precursor) promoted the ethylene production. Intriguingly, the positive response of ethylene signal to Cd was more intensive in roots of Nipponbare than that of IR32307. The increased endogenous ethylene in rice roots promoted development of casparian strips (CSs) and suberin lamellae (SL). Specifically, external addition of ACC decreased the percentage of the DTIP-CS/DTIP-SL to root length by 44.4-79.6%/49.3-11.4% in Nipponbare and 18.7-19.9%/10.7-35.3% in IR32307, individually. The intrinsic molecular mechanism was mainly due to changes in the genes expression levels related to CSs/SL biosynthesis. Simultaneously, the analyses of apoplastic tracer (Propidium Iodide, PI) and cell-to-cell tracer (Fluorescein Diacetate, FDA) confirmed that the ethylene-mediated endodermal barriers were functional, which were in accordance with the increased/reduced Cd transport in roots. Eventually, the results of transcriptome analysis further shed a comprehensive insight that ethylene constructed the endodermal barrier through phenylpropanoid and cutin, suberine and wax biosynthesis to reduce Cd radial transport in rice, which are beneficial for the breeding of rice with low-Cd accumulating capacity in the future.

A Nucleotide-Binding Domain Leucine-Rich Repeat Gene Regulates Plant Growth and Defense Against Chewing Herbivores

Plant nucleotide-binding leucine-rich repeat immune receptor genes (NLRs) play an important role in plant defenses against pathogens, pathogenic nematodes, and piercing-sucking herbivores. However, little is known about their functions in plant defenses against chewing herbivores. Here, we identified a plasma membrane-localized coiled-coil-type NLR protein, OsPik-2-like, whose transcript levels were induced by the infestation of rice leaf folder (LF, Cnaphalocrocis medinalis) larvae, and by treatment with mechanical wounding. Knocking out OsPik-2-like in rice increased the LF-induced levels of jasmonic acid (JA) and jasmonoyl-isoleucine (JA-Ile), the activity of trypsin protease inhibitors (TrypPIs), and the basal levels of some flavonoids, which in turn decreased the performance of LF larvae. Moreover, knocking out OsPik-2-like reduced plant growth. These findings demonstrate that OsPik-2-like regulates the symbiosis between rice and LF by balancing plant growth and defense.

Responses of Brassica napus to soil cadmium under elevated CO2 concentration based on rhizosphere microbiome, root transcriptome and metabolome

Rising atmospheric carbon dioxide (CO2) and soil heavy metal pollution affect crop safety and production. Exposure to elevated CO2 (ECO2) increases cadmium (Cd) uptake in some crops like wheat and rice, however, it remains unclear how ECO2 affects Cd uptake by Brassica napus. Here, we investigated the responses of B. napus seedlings exposed to ECO2 and Cd through analyses of physiology, transcriptome, metabolome, and rhizosphere microbes. Compared with Cd-stress alone (Cd50_ACO2), ECO2 boosted the uptake of Cd by B. napus roots by 38.78% under coupled stresses (Cd50_ECO2). The biomass and leaf chlorophyll a content increased by 38.49% and 79.66% respectively in Cd50_ECO2 relative to Cd50_ACO2. Activities of superoxide dismutase (SOD) and peroxidase (POD) enhanced by 8.42% and 185.01%, respectively, while glutathione (GSH) and ascorbic acid (AsA) contents increased by 16.44% and 52.48%, and abundances of rhizosphere microbes changed significantly under coupled stresses (Cd50_ECO2) relative to Cd-stress alone (Cd50_ACO2). Also, the upregulation of glutathione, glutathione transferase genes, and heavy metal ATPase expression promoted the detoxification effect of rapeseed on Cd. Changes in the expression of transcription factors like MAPK, WRKY, BAK1 and PR1, as well as changes in metabolic pathways like β-alanine, may be involved in the regulatory mechanism of stress response. These findings provide new insights for studying the regulatory mechanism of rapeseed under ECO2 on soil Cd stress, and also provide a basis for further research on Cd tolerant rapeseed varieties in the future climate context.

Mechanisms of Cadmium stress response in watermelon: Insights from physiological, transcriptomic, and metabolic analyses

Cadmium (Cd) contamination of soil may lead to Cd stress for plants, which significantly hinders plant growth and development, posing a risk to human health through the consumption of Cd-contaminated foods. Watermelon (Citrullus lanatus), a widely consumed fruit, is particularly affected by Cd stress globally, yet the mechanisms underlying its response are not well understood. Here, we subjected watermelon seedlings to simulated Cd stress treatment and explored the physiological, transcriptomic, and metabolic response. Our findings revealed that Cd stress treatment led to increased accumulation of reactive oxygen species (ROS) in watermelon leaves. Transcriptome sequencing unveiled a multitude of osmotic and oxidative stress-responsive genes, including peroxidase (POD), MYB, voltage-dependent anion channel (SLAC1), and ABC transporter. KEGG enrichment analysis highlighted the predominant enrichment of Cd stress-responsive genes in pathways such as glutathione (GSH) metabolism, MAPK signaling, and biosynthesis of secondary metabolites. Within the GSH metabolism pathway, several glutathione S-transferase (GST) genes were up-regulated, alongside phytochelatin synthetase (PCS) genes involved in phytochelatin synthesis. In the MAPK signaling pathway, genes associated with ABA and ethylene signal transduction showed up-regulation following Cd stress. Metabolomic analysis demonstrated that Cd stress enhanced the production of amino acids, phenolamines, and esters. Overall, our study elucidates that watermelon responds to Cd stress by activating its antioxidant system, GSH metabolism pathway, MAPK signal pathway, and biosynthesis of key metabolites. These findings offer valuable insights for the remediation of heavy metal pollution in soil affecting plant life.

Phytohormones-mediated strategies for mitigation of heavy metals toxicity in plants focused on sustainable production

KEY MESSAGE

In this manuscript, authors reviewed and explore the information on beneficial role of phytohormones to mitigate adverse effects of heavy metals toxicity in plants. Global farming systems are seriously threatened by heavy metals (HMs) toxicity, which can result in decreased crop yields, impaired food safety, and negative environmental effects. A rise in curiosity has been shown recently in creating sustainable methods to reduce HMs toxicity in plants and improve agricultural productivity. To accomplish this, phytohormones, which play a crucial role in controlling plant development and adaptations to stress, have emerged as intriguing possibilities. With a particular focus on environmentally friendly farming methods, the current review provides an overview of phytohormone-mediated strategies for reducing HMs toxicity in plants. Several physiological and biochemical activities, including metal uptake, translocation, detoxification, and stress tolerance, are mediated by phytohormones, such as melatonin, auxin, gibberellin, cytokinin, ethylene, abscisic acid, salicylic acid, and jasmonates. The current review offers thorough explanations of the ways in which phytohormones respond to HMs to help plants detoxify and strengthen their resilience to metal stress. It is crucial to explore the potential uses of phytohormones as long-term solutions for reducing the harmful effects of HMs in plants. These include accelerating phytoextraction, decreasing metal redistribution to edible plant portions, increasing plant tolerance to HMs by hormonal manipulation, and boosting metal sequestration in roots. These methods seek to increase plant resistance to HMs stress while supporting environmentally friendly agricultural output. In conclusion, phytohormones present potential ways to reduce the toxicity of HMs in plants, thus promoting sustainable agriculture.

OsEIL1 and OsEIL2, two master regulators of rice ethylene signaling, promote the expression of ROS scavenging genes to facilitate coleoptile elongation and seedling emergence from soil

Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural environment. In rice, coleoptile elongation facilitates seedling emergence and establishment, and ethylene plays an important role in this process. However, the underlying regulatory mechanism remains largely unclear. Here, we report that ethylene promotes cell elongation and inhibits cell expansion in rice coleoptiles, resulting in longer and thinner coleoptiles that facilitate seedlings emergence from the soil. Transcriptome analysis showed that genes related to reactive oxygen species (ROS) generation are upregulated and genes involved in ROS scavenging are downregulated in the coleoptiles of ethylene-signaling mutants. Further investigations showed that soil coverage promotes accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) and OsEIL2 in the upper region of the coleoptile, and both OsEIL1 and OsEIL2 can bind directly to the promoters of the GDP-mannose pyrophosphorylase (VTC1) gene OsVTC1-3 and the peroxidase (PRX) genes OsPRX37, OsPRX81, OsPRX82, and OsPRX88 to activate their expression. This leads to increased ascorbic acid content, greater peroxidase activity, and decreased ROS accumulation in the upper region of the coleoptile. Disruption of ROS accumulation promotes coleoptile growth and seedling emergence from soil. These findings deepen our understanding of the roles of ethylene and ROS in controlling coleoptile growth, and this information can be used by breeders to produce rice varieties suitable for direct seeding.

Ethylene Modulates Rice Root Plasticity under Abiotic Stresses

Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.

Integrated comparative transcriptome and physiological analysis reveals the metabolic responses underlying genotype variations in NH4+ tolerance

Several mechanisms have been proposed to explain NH4 + toxicity. However, the core information about the biochemical regulation of plants in response to NH4 + toxicity is still lacking. In this study, the tissue NH4 + concentration is an important factor contributing to variations in plant growth even under nitrate nutrition and NH4 + tolerance under ammonium nutrition. Furthermore, NH4 + led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4 +- tolerant ecotype Or-1. These results suggested that the NH4 +-tolerant ecotype showed a more intense response to NH4 + by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4 + uptake and nitrogen utilization efficiency, but lower NH4 +, indicating the tolerant ecotype maintained a low NH4 + level, mainly by promoting NH4 + assimilation rather than inhibiting NH4 + uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton production capacity with higher levels of hexokinase, pyruvate kinase, and glutamate dehydrogenase activity to assimilate free NH4 +, Taken together, the results revealed the core mechanisms utilized by plants in response to NH4 +, which are consequently of ecological and agricultural importance.

Hydrogel-potassium humate composite alleviates cadmium toxicity of tobacco by regulating Cd bioavailability

Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects plant growth and development. Hydrogels can easily combine with Cd, thereby altering its bioavailability in soil. However, few studies have evaluated the effects of hydrogel on the complex phytotoxicity caused by Cd uptake in plants and the microbial community structure. Herein, a new poly (acrylic acid)-grafted starch and potassium humate composite (S/K/AA) hydrogel was added to soil to evaluate its impact on tobacco growth and the soil microenvironment. The results indicate that the addition of S/K/AA hydrogel can significantly improve the biomass, chlorophyll (Chl) content, and photosynthetic capacity of tobacco plants during Cd stress conditions, and decrease Cd concentration, probably by affecting Cd absorption through the expression of Cd absorption transporters (e.g., NRAMP5, NRAMP3, and IRT1). Moreover, the application of S/K/AA hydrogel not only reduced the accumulation of reactive oxygen species (ROS), but also reduced the antioxidant activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), suggesting that S/K/AA hydrogel alleviates Cd toxicity via a non-antioxidant pathway. Notably, we further analyzed the effectiveness of the hydrogel on microbial communities in Cd-contaminated soil and found that it increased the Cd-tolerant microbial community (Arthrobacter, Massilia, Streptomyces), enhancing the remediation ability of Cd-contaminated soil and helping tobacco plants to alleviate Cd toxicity. Overall, our study provides primary insights into how S/K/AA hydrogel affects Cd bioavailability and alleviates Cd toxicity in plants.

Effect of chromium stress on metal accumulation and cell wall fractions in Cosmos bipinnatus

As one of the major pollutants in the environment, chromium (Cr), a heavy metal, poses a serious threat to urban green spaces and human life and health. Cosmos bipinnatus is considered a potential accumulator of Cr, and the differences in cellular Cr distribution and compartmentalization may uncover the mechanisms involved in its tolerance to Cr. To elucidate the effects of Cr stress on C. bipinnatus and determine the mechanism of Cr tolerance in C. bipinnatus, we investigated the physiological indicators, subcellular distribution and chemical forms, cell wall fractions and their Cr contents, uronic acid content in the cell wall fractions, and Fourier transform infrared spectroscopy (FTIR) of the cell wall. The results showed that the antioxidant enzyme activities in C. bipinnatus under Cr stress and most of the Cr were fixed in the cell wall. Notably, changes in the content of pectin fractions in the cell wall affected the accumulation of Cr in the cell wall of C. bipinnatus and the stability of negatively charged groups. In addition, the carboxyl and hydroxyl groups played a role in fixing metal in various parts of the C. bipinnatus cell wall.

Rhizospheric microbiomics integrated with plant transcriptomics provides insight into the Cd response mechanisms of the newly identified Cd accumulator Dahlia pinnata

Phytoremediation that depends on excellent plant resources and effective enhancing measures is important for remediating heavy metal-contaminated soils. This study investigated the cadmium (Cd) tolerance and accumulation characteristics of Dahlia pinnata Cav. to evaluate its Cd phytoremediation potential. Testing in soils spiked with 5-45 mg kg-1 Cd showed that D. pinnata has a strong Cd tolerance capacity and appreciable shoot Cd bioconcentration factors (0.80-1.32) and translocation factors (0.81-1.59), indicating that D. pinnata can be defined as a Cd accumulator. In the rhizosphere, Cd stress (45 mg kg-1 Cd) did not change the soil physicochemical properties but influenced the bacterial community composition compared to control conditions. Notably, the increased abundance of the bacterial phylum Patescibacteria and the dominance of several Cd-tolerant plant growth-promoting rhizobacteria (e.g., Sphingomonas, Gemmatimonas, Bryobacter, Flavisolibacter, Nocardioides, and Bradyrhizobium) likely facilitated Cd tolerance and accumulation in D. pinnata. Comparative transcriptomic analysis showed that Cd significantly induced (P < 0.001) the expression of genes involved in lignin synthesis in D. pinnata roots and leaves, which are likely to fix Cd2+ to the cell wall and inhibit Cd entry into the cytoplasm. Moreover, Cd induced a sophisticated signal transduction network that initiated detoxification processes in roots as well as ethylene synthesis from methionine metabolism to regulate Cd responses in leaves. This study suggests that D. pinnata can be potentially used for phytoextraction and improves our understanding of Cd-response mechanisms in plants from rhizospheric and molecular perspectives.

Diverse Physiological Roles of Flavonoids in Plant Environmental Stress Responses and Tolerance

Flavonoids are characterized as the low molecular weight polyphenolic compounds universally distributed in planta. They are a chemically varied group of secondary metabolites with a broad range of biological activity. The increasing amount of evidence has demonstrated the various physiological functions of flavonoids in stress response. In this paper, we provide a brief introduction to flavonoids' biochemistry and biosynthesis. Then, we review the recent findings on the alternation of flavonoid content under different stress conditions to come up with an overall picture of the mechanism of involvement of flavonoids in plants' response to various abiotic stresses. The participation of flavonoids in antioxidant systems, flavonoid-mediated response to different abiotic stresses, the involvement of flavonoids in stress signaling networks, and the physiological response of plants under stress conditions are discussed in this review. Moreover, molecular and genetic approaches to tailoring flavonoid biosynthesis and regulation under abiotic stress are addressed in this review.

Effects of Organic Acid Root Exudates of Malus hupehensis Rehd. Derived from Soil and Root Leaching Liquor from Orchards with Apple Replant Disease

Organic acids secreted by plants, such as p-hydroxybenzoic acid, ferulic acid, cinnamic acid, and benzoic acid, can inhibit seed germination and root growth. The effects of root and soil leaching liquor from orchards on the growth of M. hupehensis Rehd. seedlings under sand culture are studied; the seedlings are sampled at 15, 30, 45, and 60 d. Changes in the amount of root exudates are determined using HPLC. Low concentrations of root leaching liquor (A1) and soil leaching liquor (B1) significantly promoted plant growth and chlorophyll synthesis; high concentrations of root leaching liquor (A6) and soil leaching liquor (B4-6) inhibited growth. Low concentrations of soil leaching liquor had no significant effect on the POD, SOD, and CAT activities. A5-6 and B5-6 significantly decreased Fv/Fm and qP values, respectively, and increased NPQ values. All root and soil leaching liquor treatments inhibited the secretion of gallic acid, hydroxybenzoic acid, benzoic acid, and phloridzin, and promoted the secretion of caffeic acid. The root leaching liquor treatments inhibited the secretion of catechin and promoted the secretion of phloretin. The soil leaching liquor treatments promoted the secretion of cinnamic acid. The secretion of other phenolic acids is likely associated with the different concentrations of leaching liquor.

Mining Candidate Genes Related to Heavy Metals in Mature Melon (Cucumis melo L.) Peel and Pulp Using WGCNA

The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H⁺-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT–PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.