Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars

Cadmium accumulation potential and detoxication mechanism of Koenigia tortuosa: A novel extremely hardy plant from high altitude lead-zinc mine in Qinghai-Tibet Plateau

Hardy plants play a crucial role in restoring high-altitude tailings ponds, but the accumulation of potentially toxic elements (PTEs) and detoxification mechanisms in alpine plants are understudied. This study first investigated the cadmium (Cd) accumulation capacity and detoxification mechanisms by comparative transcriptomics with different Cd stress (0, 5, 10, 20 and 40 mg L-1 Cd2+) of Koenigia tortuosa from a lead-zinc mine (4950 m above sea level) in Qinghai-Tibet Plateau. The findings revealed that, despite elevated Cd concentrations suppressed the growth of Koenigia tortuosa, the plant retained a notable ability to accumulate Cd. The content of soluble protein and antioxidant enzyme activities increased with the concentration of Cd from 5 mg L-1 to 20 mg L-1, and then decreased when the concentration of Cd increased to 40 mg L-1. The maximum Cd accumulation in roots was 269.44 mg kg-1 at the 20 mg L-1 Cd concentration, with 61.83% of Cd extracted by NaCl. In addition, transcriptome analysis showed that differentially expressed genes (DEGs) were mainly distributed in the nucleotide metabolism, oxidative phosphorylation pathway, glutathione metabolism and plant signaling, which were significantly up-regulated in ribosomal protein genes, translational factor genes and glutathione-related genes. These results will contribute to revealing the physiological response and molecular mechanism of Cd tolerance in Koenigia tortuosa, supporting the ecological remediation of Cd contaminated sites in high-altitude mining areas.

Comparative transcriptomics reveals the key pathways and genes of cadmium accumulation in the high cadmium-accumulating rice (Oryza Sativa L.) line

The high cadmium (Cd)-accumulating rice line Lu527-8 (H8) has already been proven to exhibit elevated Cd concentration and translocation over the normal rice line Lu527-4 (N4). H8 and N4 are sister lines that diverged from the same parents, while the molecular mechanisms underlying the genotypic differences in Cd enrichment between the two rice lines remains unclear. Here an in-depth exploration was performed via transcriptome analysis with 2919 and 2563 differentially expressed genes (DEGs) in H8 and N4 identified, respectively. Gene ontology(GO) enrichment revealed that Cd-stressed rice both exhibited enhanced defense and antioxidant responses, while N4 displayed unique categories related to cell wall biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 5 mutual pathways between H8 and N4. Many genes associated with cell wall biosynthesis were identified as the Cd-responsive DEGs. Enhanced phenylpropanoid biosynthesis and unique diterpenoid biosynthesis resulted in intensified lignin biosynthesis, which likely led to apoplastic barrier formation, subsequently blocked Cd inflow and reduced radial Cd transport in the root, thereby limited Cd translocation into aerial parts in N4. The key genes OsPAL6 and OsPAL8 that encode phenylalanine ammonia lyase (PAL), and gibberellin (GA) biosynthesis-related key genes including OsCPS2, OsCPS4, OsKSL4, OsKSL7 and some CYP superfamily members played vital roles in the process. Meanwhile, the greater upregulation of Cd transporters, such as OsIRT1/2, some OsABCs, OsYSLs, and OsZIPs in H8, accounted for the higher root absorption of Cd compared to N4. These findings unveil the molecular basis of the differential Cd concentration and translocation between the two rice lines, contributing valuable insights to the theory of Cd accumulation in rice.

Temporal variations in absorption and translocation of heavy metal(loid)s in pak choi (Brassica rapa L.) under open-field and greenhouse cultivation

Elucidating the absorption and translocation of heavy metal(loid)s by common vegetables across different growth environments and stages is crucial for conducting accurate environmental risk assessments and for associated control. This study investigated temporal variations in the absorption and translocation capacities of pak choi (Brassica rapa L.) for As, Cd, Cr, Cu, Pb, and Zn in polluted soils during the plant growth cycle under greenhouse and open-field cultivation modes. Results showed high root metal(loid) bioconcentration factors and root-to-shoot translocation factors for Cd (0.25 and 1.44, respectively) and Zn (0.26 and 1.01), but low values for As (0.06 and 0.88) and Pb (0.06 and 0.87). The Cd concentration in the aerial edible parts peaked during the early slow growth period, whereas other heavy metal(loid)s peaked during the later stable maturity period. Root bioconcentration and root-to-shoot translocation factors did not significantly differ between cultivation modes. However, greenhouse cultivation exhibited lower average Cd and Zn concentrations in the edible parts and cumulative uptake amounts of most metal(loid)s than open-field cultivation during the typical harvest period spanning days 60 and 90. Short-term transitioning from open-field to greenhouse cultivation may reduce health risks associated with heavy metal(loid) intake via pak choi consumption. These findings facilitate sustainable agricultural practices and food safety management.

Cadmium Stress Signaling Pathways in Plants: Molecular Responses and Mechanisms

Heavy metal (HM) pollution, specifically cadmium (Cd) contamination, is a worldwide concern for its consequences for plant health and ecosystem stability. This review sheds light on the intricate mechanisms underlying Cd toxicity in plants and the various strategies employed by these organisms to mitigate its adverse effects. From molecular responses to physiological adaptations, plants have evolved sophisticated defense mechanisms to counteract Cd stress. We highlighted the role of phytochelatins (PCn) in plant detoxification, which chelate and sequester Cd ions to prevent their accumulation and minimize toxicity. Additionally, we explored the involvement of glutathione (GSH) in mitigating oxidative damage caused by Cd exposure and discussed the regulatory mechanisms governing GSH biosynthesis. We highlighted the role of transporter proteins, such as ATP-binding cassette transporters (ABCs) and heavy metal ATPases (HMAs), in mediating the uptake, sequestration, and detoxification of Cd in plants. Overall, this work offered valuable insights into the physiological, molecular, and biochemical mechanisms underlying plant responses to Cd stress, providing a basis for strategies to alleviate the unfavorable effects of HM pollution on plant health and ecosystem resilience.

Mechanisms of low cadmium accumulation in crops: A comprehensive overview from rhizosphere soil to edible parts

Cadmium (Cd) is a toxic heavy metal often found in soil and agricultural products. Due to its high mobility, Cd poses a significant health risk when absorbed by crops, a crucial component of the human diet. This absorption primarily occurs through roots and leaves, leading to Cd accumulation in edible parts of the plant. Our research aimed to understand the mechanisms behind the reduced Cd accumulation in certain crop cultivars through an extensive review of the literature. Crops employ various strategies to limit Cd influx from the soil, including rhizosphere microbial fixation and altering root cell metabolism. Additional mechanisms include membrane efflux, specific transport, chelation, and detoxification, facilitated by metalloproteins such as the natural resistance-associated macrophage protein (Nramp) family, heavy metal P-type ATPases (HMA), zinc-iron permease (ZIP), and ATP-binding cassette (ABC) transporters. This paper synthesizes differences in Cd accumulation among plant varieties, presents methods for identifying cultivars with low Cd accumulation, and explores the unique molecular biology of Cd accumulation. Overall, this review provides a comprehensive resource for managing agricultural lands with lower contamination levels and supports the development of crops engineered to accumulate minimal amounts of Cd.

OsPDR20 is an ABCG metal transporter regulating cadmium accumulation in rice

Cadmium (Cd) is a non-essential toxic heavy metal, seriously posing high environmental risks to human health. Digging genetic resources relevant to functional genes is important for understanding the metal absorption and accumulation in crops and bioremediation of Cd-polluted environments. This study investigated a functionally uncharacterized ATP binding cassette transporter G family (ABCG) gene encoding a Pleiotropic Drug Resistance 20 (PDR20) type metal transporter which is localized to the plasma membrane of rice. OsPDR20 was transcriptionally expressed in almost all tissues and organs in lifespan and was strongly induced in roots and shoots of young rice under Cd stress. Ectopic expression of OsPDR20 in a yeast mutant ycf1 sensitive to Cd conferred cellular tolerance with less Cd accumulation. Knockdown of OsPDR20 by RNA interference (RNAi) moderately attenuated root/shoot elongation and biomass, with reduced chlorophylls in rice grown under hydroponic medium with 2 and 10 µmol/L Cd, but led to more Cd accumulation. A field trial of rice grown in a realistic Cd-contaminated soil (0.40 mg/kg) showed that RNAi plants growth and development were also compromised compared to wild-type (WT), with smaller panicles and lower spikelet fertility but little effect on yield of grains. However, OsPDR20 suppression resulted in unexpectedly higher levels of Cd accumulation in rice straw including lower leaves and culm and grain. These results suggest that OsPDR20 is actively involved in Cd accumulation and homeostasis in rice crops. The increased Cd accumulation in the RNAi plants has the potential application in phytoremediation of Cd-polluted wetland soils.

Transcriptome analysis reveals different mechanisms of selenite and selenate regulation of cadmium translocation in Brassica rapa

Selenium (Se) inhibits cadmium (Cd) root-to-shoot translocation and accumulation in the shoots of pak choi; however, the mechanism by which Se regulates Cd retention in roots is still poorly understood. A time-dependent hydroponic experiment was conducted to compare the effects of selenite and selenate on Cd translocation and retention in the roots. The underlying mechanisms were investigated regarding Se biotransformation and metal transportation in roots using HPLC and transcriptome analyses. Selenite showed reducing effects on Cd translocation and accumulation in shoots earlier than selenate. Selenite is mainly biotransformed into selenomethionine (80% of total Se in roots) at 72 h, while SeO42- was the dominant species in the selenate treatments (68% in shoots). Selenite up-regulated genes involved in the biosynthesis of lignin, suberin, and phytochelatins and those involved in stress signaling, thereby helping to retain Cd in the roots, whereas essentially, selenate had opposite effects and impaired the symplastic and apoplastic retention of Cd. These results suggest that cell-wall reinforcement and Cd retention in roots may be the key processes by which Se regulates Cd accumulation, and faster biotransformation into organic seleno-compounds could lead to earlier effects.

Effect of potassium intake on cadmium transporters and root cell wall biosynthesis in sweet potato

Large areas of farmland soil in southern China are deficient in potassium (K) and are contaminated with cadmium (Cd). Previously, we suggested that the K supplementation could reduce Cd accumulation in sweet potatoes (Ipomoea batatas (L.) Lam). In the present study, we investigated the underlying physiological and molecular mechanisms. A hydroponic experiment with different K and Cd treatments was performed to compare the transcriptome profile and the cell wall structure in the roots of sweet potato using RNA sequencing, Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). The results showed that K supply inhibits the expressions of IRT1 and YSL3, which are responsible for root Cd uptake under Cd exposure. Furthermore, the expressions of COPT5 and Nramp3 were downregulated by K, which increased Cd retention in the root vacuoles. The upregulation of POD, CAD, INT1 and SUS by K contributed to lignin and cellulose biosynthesis and thickening of root xylem cell wall, which further reduced Cd translocation to the shoot. In addition, K affected the expressions of LHT, ACS, TPS and TPP associated with the production of ethylene and trehalose, which involved in plant resistance to Cd toxicity. In general, K application could decrease the uptake and translocation of Cd in sweet potatoes by regulating the expression of genes associated with Cd transporters and root cell wall components.

Knowledge Mapping of the Phytoremediation of Cadmium-Contaminated Soil: A Bibliometric Analysis from 1994 to 2021

Cadmium pollution of soil threatens the environmental quality and human health. Phytoremediation of cadmium-contaminated soil has attracted global attention in recent decades. This study aimed to conduct a comprehensive and systematic review of the literature on phytoremediation of cadmium-contaminated soil based on bibliometric analysis. A total of 5494 articles published between 1994 and 2021 were retrieved from the Web of Science Core Collection. Our knowledge mapping presented the authors, journals, countries, institutions, and other basic information to understand the development status of phytoremediation of cadmium-contaminated soil. Based on a keyword cluster analysis, the identified major research domains were "biochar", "Thlaspi caerulescens", "endophytic bacteria", "oxidative stress", "EDTA", and "bioconcentration factor". Overall, this study provided a detailed summary of research trends and hotspots. Based on the keyword co-occurrence and burst analysis, the core concepts and basic theories of this field were completed in 2011. However, the pace of theoretical development has been relatively slow. Finally, future research trends/frontiers were proposed, such as biochar addition, rhizosphere bacterial community manipulation, cadmium subcellular distribution, and health risk assessment.

Transcriptomic analyses of sweet potato in response to Cd exposure and protective effects of K on Cd-induced physiological alterations

We aimed to understand the molecular mechanism of differential cadmium (Cd) accumulation in two cultivars of sweet potato and to clarify the effects of potassium (K) supply on Cd accumulation. Comparative transcriptomes were employed to identify key genes and pathways using a low-Cd (N88) and a high-Cd cultivar (X16) in a pot experiment. The antioxidant capacity and cell wall components of root tips were analyzed to account for the effect of K regulating Cd accumulation in N88 via a hydroponic experiment. Transcriptome analysis revealed that 29 and 20 genes were differentially expressed in N88 and X16, respectively, when comparing the control with the two Cd treatments. X16 had more differentially expressed genes (DEGs), including 2649 common up-regulated and 3173 common down-regulated than N88 in any treatment. GO and KEGG analyses showed that the DEGs were assigned and enriched in different pathways. Some critical DEGs such as PDR, HMA3, COPT5, CAX3, GAUT, CCR, AUX1, CAT, SOD, GSR, and GST were identified. The DEGs were involved in pathways including heavy metal transport or detoxification, cell wall biosynthesis, plant hormone signal transduction, and glutathione metabolism. Additionally, K supply substantially decreased Cd accumulation and reactive oxygen species production and promoted the production of cellulose, pectin and lignin in the root tips when exposed to Cd. Several critical DEGs associated with heavy metal transport and cell wall biosynthesis were responsible for the difference of Cd accumulation between the two cultivars. Application of K could help decrease Cd accumulation in sweet potato.

Unraveling Cadmium Toxicity in Trifolium repens L. Seedling: Insight into Regulatory Mechanisms Using Comparative Transcriptomics Combined with Physiological Analyses

Trifolium repens (T. repens) can accumulate significant amounts of heavy metal ions, and has strong adaptability to wide environmental conditions, and relatively large biomass, which is considered a potential plant for phytoremediation. However, the molecular mechanisms of T. repens involved in Cd tolerance have not yet been studied in detail. This study was conducted to examine the integrative responses of T. repens exposed to a high-level CdCl₂ by investigating the physiological and transcriptomic analyses. The results suggested that T. repens seedlings had a high degree of tolerance to Cd treatment. The roots accumulated higher Cd concentration than leaves and were mainly distributed in the cell wall. The content of MDA, soluble protein, the relative electrolyte leakage, and three antioxidant enzymes (POD, SOD, and APX) was increased with the Cd treatment time increasing, but the CAT enzymes contents were decreased in roots. Furthermore, the transcriptome analysis demonstrated that the differentially expressed genes (DEGs) mainly enriched in the glutathione (GSH) metabolism pathway and the phenylpropanoid biosynthesis in the roots. Overexpressed genes in the lignin biosynthesis in the roots might improve Cd accumulation in cell walls. Moreover, the DEGs were also enriched in photosynthesis in the leaves, transferase activity, oxidoreductase activity, and ABA signal transduction, which might also play roles in reducing Cd toxicity in the plants. All the above, clearly suggest that T. repens employ several different mechanisms to protect itself against Cd stress, while the cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of T. repens.

Incorporating in vitro bioaccessibility into human health risk assessment of heavy metals and metalloid (As) in soil and pak choi (Brassica chinensis L.) from greenhouse vegetable production fields in a megacity in Northwest China

The rapid development of greenhouse vegetable production (GVP) in densely populated areas may cause the heavy metal/metalloid accumulation in soil and pose a threat to human health. In this study, 180 pairs of topsoil and pak choi (Brassica chinensis L.) samples were collected from GVP fields in Xi'an city in Northwest China to analyze health risks of Cd, Cr, Pb, and As in soil and pak choi combining in vitro bioaccessibility investigation. The results showed that Cd and Cr were common pollutants in both soil and pak choi. In the soil-pak choi system, the indexes of non-carcinogenic and carcinogenic risk for adults and children were 1.53, 2.68, and 1.37 × 10^-4, 8.14 × 10^-5, respectively, thereby indicating the presence of heavy metal/metalloid health risks for both groups. Based on the results, procedures to mitigate heavy metal/metalloid contamination risks should be discussed more during the development of GVP in the largest city in Northwest China.

Cadmium Phytotoxicity, Tolerance, and Advanced Remediation Approaches in Agricultural Soils; A Comprehensive Review

Cadmium (Cd) is a major environmental contaminant due to its widespread industrial use. Cd contamination of soil and water is rather classical but has emerged as a recent problem. Cd toxicity causes a range of damages to plants ranging from germination to yield suppression. Plant physiological functions, i.e., water interactions, essential mineral uptake, and photosynthesis, are also harmed by Cd. Plants have also shown metabolic changes because of Cd exposure either as direct impact on enzymes or other metabolites, or because of its propensity to produce reactive oxygen species, which can induce oxidative stress. In recent years, there has been increased interest in the potential of plants with ability to accumulate or stabilize Cd compounds for bioremediation of Cd pollution. Here, we critically review the chemistry of Cd and its dynamics in soil and the rhizosphere, toxic effects on plant growth, and yield formation. To conserve the environment and resources, chemical/biological remediation processes for Cd and their efficacy have been summarized in this review. Modulation of plant growth regulators such as cytokinins, ethylene, gibberellins, auxins, abscisic acid, polyamines, jasmonic acid, brassinosteroids, and nitric oxide has been highlighted. Development of plant genotypes with restricted Cd uptake and reduced accumulation in edible portions by conventional and marker-assisted breeding are also presented. In this regard, use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics to enhance the adverse impacts of Cd in plants may be quite helpful. The review's results should aid in the development of novel and suitable solutions for limiting Cd bioavailability and toxicity, as well as the long-term management of Cd-polluted soils, therefore reducing environmental and human health hazards.

Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress

It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation.

IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.

Comparative transcriptome analysis provides insights into steviol glycoside synthesis in stevia (Stevia rebaudiana Bertoni) leaves under nitrogen deficiency

Transcriptome analysis revealed the potential mechanism of nitrogen regulating steviol glycosides synthesis via shifting of leaf carbon metabolic flux or inducing certain transcription factors. Nitrogen (N) plays key regulatory roles in both stevia (Stevia rebaudiana) growth and the synthesis of its functional metabolite steviol glycosides (SGs), but the mechanism by which this nutrient regulates SGs synthesis remains to be elucidated. To address this question, a pot experiment was performed in a greenhouse where stevia plants fertilized with N (the control as CK plants) and compared with plants without the supply of N. Physiological and biochemical analyses were conducted to test the growth and metabolic responses of plants to N regimes. Our results showed that N deficiency significantly inhibited plant growth and leaf photosynthesis, while increased leaf SGs contents in stevia (49.97, 46.64 and 84.80% respectively for rebaudioside A, stevioside, and rebaudioside C), which may be partly due to "concentration effect". Then, transcriptome analysis was conducted to understand the underlying mechanisms. A total of 535 differentially expressed genes were identified, and carbon metabolism-related events were highlighted by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Many of these genes were significantly upregulated by N-deficiency, including those involved in "phenylpropanoid biosynthesis", "flavonoid biosynthesis" and "starch and sucrose metabolism". Our study also analyzed the expression patterns of SGs synthesis-related genes under two N regimes and the potential transcription factors linking N nutrition and SG metabolism. N-deficiency may promote SGs synthesis by changing the carbon metabolism flux or inducing certain transcription factors. Our results provide deeper insight into the relationship between N nutrition and SGs synthesis in stevia plants.

Comparative transcriptomics analysis reveals differential Cd response processes in roots of two turnip landraces with different Cd accumulation capacities

Understanding the molecular mechanisms of cadmium (Cd) tolerance and accumulation in plants is important to address Cd pollution. In the present study, we performed comparative transcriptome analysis to identify the Cd response processes in the roots of two turnip landraces, KTRG-B14 (high-Cd accumulation) and KTRG-B36 (low-Cd accumulation). Two common enhanced processes, glutathione metabolism and antioxidant system, were identified in both landraces. However, some differential antioxidant processes are likely employed by two landraces, namely, several genes encoding peptide methionine sulfoxide reductases and thioredoxins were up-regulated in B14, whereas flavonoid synthesis was potentially induced to fight against oxidative stress in B36. In addition to the commonly upregulated ZINC INDUCED FACILITATOR 1-like gene in two landraces, different metal transporter-encoding genes identified in B14 (DETOXIFICATION 1) and B36 (PLANT CADMIUM RESISTANCE 2-like, probable zinc transporter 10, and ABC transporter C family member 3) were responsible for Cd accumulation and distribution in cells. Several genes that encode extensins were specifically upregulated in B14, which may improve Cd accumulation in cell walls or regulate root development to absorb more Cd. Meanwhile, the induced high-affinity nitrate transporter 2.1-like gene was also likely to contribute to the higher Cd accumulation in B14. However, Cd also caused some toxic symptoms in both landraces. Cd stress might inhibit iron uptake in both landraces whereas many apoenzyme-encoding genes were influenced in B36, which may be attributed to the interaction between Cd and other metal ions. This study provides novel insights into the molecular mechanism of plant root response to Cd at an early stage. The transporters and key enzymes identified in this study are helpful for the molecular-assisted breeding of low- or high-Cd-accumulating plant resources.

Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.)

BACKGROUND

The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium.

RESULTS

A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress.

CONCLUSIONS

Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.

Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (Stevia rebaudiana) Bertoni

Nitrogen forms (nitrate (NO₃⁻) or ammonium (NH₄⁺)) are vital to plant growth and metabolism. In stevia (Stevia rebaudiana), it is important to assess whether nitrogen forms can influence the synthesis of the high-value terpene metabolites-steviol glycosides (SGs), together with the underlying mechanisms. Field and pot experiments were performed where stevia plants were fertilized with either NO₃⁻ or NH₄⁺ nutrition to the same level of nitrogen. Physiological measurements suggested that nitrogen forms had no significant impact on biomass and the total nitrogen content of stevia leaves, but NO₃⁻-enhanced leaf SGs contents. Transcriptomic analysis identified 397 genes that were differentially expressed (DEGs) between NO₃⁻ and NH₄⁺ treatments. Assessment of the DEGs highlighted the responses in secondary metabolism, particularly in terpenoid metabolism, to nitrogen forms. Further examinations of the expression patterns of SGs synthesis-related genes and potential transcription factors suggested that GGPPS and CPS genes, as well as the WRKY and MYB transcription factors, could be driving N form-regulated SG synthesis. We concluded that NO₃⁻, rather than NH₄⁺, can promote leaf SG synthesis via the NO₃⁻-MYB/WRKY-GGPPS/CPS module. Our study suggests that insights into the molecular mechanism of how SG synthesis can be affected by nitrogen forms.

Research on the Mechanisms of Plant Enrichment and Detoxification of Cadmium

The heavy metal cadmium (Cd), as one of the major environmentally toxic pollutants, has serious impacts on the growth, development, and physiological functions of plants and animals, leading to deterioration of environmental quality and threats to human health. Research on how plants absorb and transport Cd, as well as its enrichment and detoxification mechanisms, is of great significance to the development of phytoremediation technologies for ecological and environmental management. This article summarises the research progress on the enrichment of heavy metal cadmium in plants in recent years, including the uptake, transport, and accumulation of Cd in plants. The role of plant roots, compartmentalisation, chelation, antioxidation, stress, and osmotic adjustment in the process of plant Cd enrichment are discussed. Finally, problems are proposed to provide a more comprehensive theoretical basis for the further application of phytoremediation technology in the field of heavy metal pollution.

Combined transcriptomic, proteomic and biochemical approaches to identify the cadmium hyper-tolerance mechanism of turnip seedling leaves

Cadmium (Cd) pollution is a prominent environment problem, and great interests have been developed towards the molecular mechanism of Cd accumulation in plants. In this study, we conducted combined transcriptomic, proteomic and biochemical approaches to explore the detoxification of a Cd-hyperaccumulating turnip landrace exposed to 5 μM (T5) and 25 μM (T25) Cd treatments. A total of 1090 and 2111 differentially expressed genes (DEGs) and 161 and 303 differentially expressed proteins (DEPs) were identified in turnips under T5 and T25, respectively. However, poor correlations were observed in expression changes between mRNA and protein levels. The enriched KEGG pathways of DEGs with a high proportion (> 80%) of upregulated genes were focused on the flavonoid biosynthesis, sulphur metabolism and glucosinolate biosynthesis pathways, whereas those of DEPs were enriched on the glutathione metabolism pathway. This result suggests that these pathways contribute to Cd detoxification in turnips. Furthermore, induced antioxidant enzymes, heat stock proteins and stimulated protein acetylation modification seemed to play important roles in Cd tolerance in turnips. In addition, several metal transporters were found responsible for the Cd accumulation capacity of turnips. This study may serve as a basis for breeding low-Cd-accumulating vegetables for foodstuff or high-Cd-abstracting plants for phytoremediation.

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.

Use of Comparative Transcriptomics Combined With Physiological Analyses to Identify Key Factors Underlying Cadmium Accumulation in Brassica juncea L

The contamination of soils with cadmium (Cd) has become a serious environmental issue that needs to be addressed. Elucidating the mechanisms underlying Cd accumulation may facilitate the development of plants that accumulate both high and low amounts of Cd. In this study, a combination of phenotypic, physiological, and comparative transcriptomic analyses was performed to investigate the effects of different Cd concentrations (0, 5, 10, 30, 50 mg/kg) on Brassica juncea L. Our results suggest that B. juncea L. seedlings had a degree of tolerance to the 5 mg/kg Cd treatment, whereas higher Cd stress (10-50 mg/kg) could suppress the growth of B. juncea L. seedlings. The contents of soluble protein, as well as MDA (malondialdehyde), were increased, but the activities of CAT (catalase) enzymes and the contents of soluble sugar and chlorophyll were decreased, when B. juncea L. was under 30 and 50 mg/kg Cd treatment. Comparative transcriptomic analysis indicated that XTH18 (xyloglucan endotransglucosylase/hydrolase enzymes), XTH22, and XTH23 were down-regulated, but PME17 (pectin methylesterases) and PME14 were up-regulated, which might contribute to cell wall integrity maintenance. Moreover, the down-regulation of HMA3 (heavy metal ATPase 3) and up-regulation of Nramp3 (natural resistance associated macrophage proteins 3), HMA2 (heavy metal ATPase 2), and Nramp1 (natural resistance associated macrophage proteins 1) might also play roles in reducing Cd toxicity in roots. Taken together, the results of our study may help to elucidate the mechanisms underlying the response of B. juncea L. to various concentrations of Cd.

Potential of cotton for remediation of Cd-contaminated soils

The present research was conducted to study the potential of cotton for the remediation of soils contaminated with Cd, to understand the biochemical basis of its tolerance to, and to investigate the plant-microbe interaction in the rhizosphere for enhancement of phytoextraction of Cd. Cotton (Bt RCH-2) was exposed to four Cd levels (0, 50, 100, and 200 mg/kg soil) in a completely randomised design and found that the plant could tolerate up to 200 mg/kg soil. Cd stress increased the total phenol, proline, and free amino acid contents in the plant leaf tissue compared with control but inhibited basal soil respiration, fluorescein diacetate hydrolysis, and activities of several enzymes viz. dehydrogenase, phosphatases, and β-glucosidase in the soil over control. The concentration of Cd in the shoot was less than the critical concentration of 100 µg/g dry weight, and bioconcentration and translocation factors were < 1 to classify the plant as a hyperaccumulator of Cd. This was further confirmed by another experiment in which the cotton plant was exposed various higher levels of Cd (200, 400, 600, 800, and 1000 mg/kg soil). Though the concentration of Cd in the shoot was > 100 µg g ^-1dw beyond 600 mg Cd/kg soil, the bioconcentration and translocation factors were < 1. The study on plant-microbe (Aspergillus awamori) interaction revealed that the fungus did not affect the absorption of Cd by cotton. It was concluded that the cotton was classified as an excluder of Cd and therefore could be suitable for the phytostabilization of Cd-contaminated soils.

Pseudomonas fluorescens accelerates a reverse and long-distance transport of cadmium and sucrose in the hyperaccumulator plant Sedum alfredii

Plant growth-promoting bacteria (PGPB) can promote root uptake and shoot accumulation of cadmium (Cd) in hyperaccumulator plants, but the mechanisms by which PGPB accelerate root-to-shoot transport of Cd is still unknown. A better understanding of these mechanisms is necessary to develop the strategies that can promote the practical phytoextraction of Cd-polluted soils. In this study, we found that Pseudomonas fluorescens accelerates a reversed and a long-distance transport of Cd and sucrose in Sedum alfredii, by examining the xylem and phloem sap and by quantifying the concentrations of Cd and sucrose in shoot and root. The transcriptome sequencing has revealed the up-regulated expressions of starch metabolism and sucrose biosynthesis related genes in the shoots of Cd hyperaccumulator plant S. alfredii that was inoculated with PGPB P. fluorescens. In addition, the genes of sugar, cation and anion transporters were also up-regulated by bacterial treatment, showing a complicated co-expression network with sucrose biosynthesis related genes. The expression levels of Cd transporter genes, such as ZIP1, ZIP2, HMA2, HMA3 and CAX2, were elevated after PGPB inoculation. As a result, the PGPB successfully colonized the root, and promoted the sucrose shoot-to-root transport and Cd root-to-shoot transport in S. alfredii. Since non-photosynthetic root-associated bacteria usually obtain sugars from photosynthetic plants, our results highlight the importance of PGPB-induced changes in hyperaccumlator plants for both the host and the PGPB.

Selenium Uptake and Biotransformation in Brassica rapa Supplied with Selenite and Selenate: A Hydroponic Work with HPLC Speciation and RNA-Sequencing

Vegetables are an ideal source of human Se intake; it is important to understand selenium (Se) speciation in plants due to the distinct biological functions of selenocompounds. In this hydroponic study, the accumulation and assimilation of selenite and selenate in pak choi (Brassica rapa), a vastly consumed vegetable, were investigated at 1-168 h with HPLC speciation and RNA-sequencing. The results showed that the Se content in shoots and Se translocation factors with selenate addition were at least 10.81 and 11.62 times, respectively, higher than those with selenite addition. Selenite and selenate up-regulated the expression of SULT1;1 and PHT1;2 in roots by over 240% and 400%, respectively. Selenite addition always led to higher proportions of seleno-amino acids, while SeO₄^2- was dominant under selenate addition (>49% of all Se species in shoots). However, in roots, SeO₄^2- proportions declined substantially by 51% with a significant increase of selenomethionine proportions (63%) from 1 to 168 h. Moreover, with enhanced transcript of methionine gamma-lyase (60% of up-regulation compared to the control) plus high levels of methylselenium in shoots (approximately 70% of all Se species), almost 40% of Se was lost during the exposure under the selenite treatment. This work provides evidence that pak choi can rapidly transform selenite to methylselenium, and it is promising to use the plant for Se biofortification.

Comparative proteomics analysis of peanut roots reveals differential mechanisms of cadmium detoxification and translocation between two cultivars differing in cadmium accumulation

BACKGROUND

Peanut is one of the most important oil and protein crops, and it exhibits wide cultivar variations in shoot Cd accumulation ability. However, the mechanism of Cd accumulation in peanut shoots has not been well understood. In this study, the root proteomics of two cultivars differing in seed Cd accumulation, Fenghua 1 (F, low Cd cultivar) and Silihong (S, high Cd cultivar), were investigated under 0 (CK) and 2 μM Cd conditions.

RESULTS

A total of 4676 proteins were identified by proteomics screening. Of them, 375, 1762, 1276 and 771 proteins were identified to be differentially expressed proteins (DEPs) for comparison of F_Cd/F_CK, S_Cd/S_CK, F_CK/S_CK and F_Cd/S_Cd, respectively. Silihong is more sensitive to Cd exposure than Fenghua 1 in terms of root proteomics. A total of 30 and 86 DEPs were identified to be related with heavy metal transport and cell wall modification, respectively. The up-regulation of ABCB25, ABCC14, ABCC2, PDR1 and V-ATPases by Cd exposure in Silihong might enhance vacuolar sequestration of Cd and its efflux from symplast to apoplast. The higher Cd accumulation in the root CWs of Silihong might be resulted from its higher capability of CW modification, in which many proteins such as IRX10L, BGLU12-like, BGLU42, EXLB1, XTH30, XTH6, XYL7, PAL3, COMT, CAD1, and CCR1 were involved.

CONCLUSIONS

The vacuolar sequestration and efflux of Cd as well as its adsorption in CW might be the principal mechanism of cadmium detoxification in Silihong. The higher capacity of Cd accumulation and translocation of Silihong is an inherent characteristics in which ACA8 and ZIP1 might be involved.

Variations in cadmium accumulation and distribution among different oilseed rape cultivars in Chengdu Plain in China

Cadmium (Cd) is a widespread toxic heavy metal trace pollutant worldwide. The ability of Cd absorption and accumulation highly varies among different species and varieties. In order to screen oilseed rape cultivars which are appropriate for cultivation and application in Cd-contaminated soils, we conducted the field trial of 32 oilseed rape varieties in Shifang County of Chengdu Plain. The various biomass, Cd accumulation, and distribution patterns were investigated via determining the Cd concentration in different plant tissues. Moreover, the food safety risks of rapeseeds were finally assessed. The results indicated diverse responses to Cd stress appeared in various tested varieties, including plant biomass, seed yield, Cd concentration, and proportion in different tissues. And most Cd were concentrated in non-edible parts. Through cluster analysis, we found that Nanchongjie, Pengzhoubai, and J-25 belong to high-biomass and high-Cd-accumulated groups in experimental cultivars, which indicated that they could possess more biomass and gather higher Cd content in overground part, so they could be great materials for phytoremediation in Cd-polluted area. Besides, combined with the risk assessment of food safety in rapeseeds, cultivars 72A and 47 with the traits of high yield, low-Cd concentration, and low food safety risk can be considered as suitable materials to widely plant as cash crop. These results provide valuable reference for practical planting and application of oilseed rape in Cd-polluted areas.

Non-invasive microelectrode cadmium flux measurements reveal the decrease of cadmium uptake by zinc supply in pakchoi root (Brassica chinensis L.)

Zinc (Zn) possesses similar properties to cadmium (Cd) and inhibits Cd uptake in plants. To get more detailed mechanisms of Zn-inhibited Cd uptake in pakchoi, a hydroponic experiment was conducted to investigate the effects of various Zn levels on Cd concentrations, real time flux of Cd, expressions of genes related to Cd uptake under Cd exposure. The results showed that the Cd concentrations and Cd accumulations in pakchoi root decreased with increasing Zn levels, which were coincident with that real time Cd influx and net Cd influx of pakchoi root decreased with increasing Zn levels by non-invasive micro-test technology (NMT). Additionally, the expressions of Cd-related transporters including BcNRAMP5, BcIRT1 and BcMGT1 decreased with the increase of Zn levels under Cd exposure, especially BcIRT1 with the highest decreased rates. Furthermore, the expressions of these genes decreased gradually with the prolongation of Zn treated time under Cd toxicity. The results indicate that Zn inhibits Cd uptake by inhibition of the expressions of Cd-related transporters, especially BcIRT1 in pakchoi root.

Comparative transcriptome analysis reveals gene network regulating cadmium uptake and translocation in peanut roots under iron deficiency

BACKGROUND

Iron (Fe) is an essential element for plant growth and development, whereas cadmium (Cd) is non-essential and highly toxic. Previous studies showed that Fe deficiency enhanced Cd uptake and accumulation in peanuts. However, the molecular mechanism underlying the increased Cd accumulation in Fe-deficient peanut plants is poorly understood.

RESULTS

We employed a comparative transcriptome analysis approach to identify differentially expressed genes (DEGs) in peanut roots exposed to Fe-sufficient without Cd, Fe-deficient without Cd, Fe-sufficient with Cd and Fe-deficient with Cd. Compared with the control, Fe deficiency induced 465 up-regulated and 211 down-regulated DEGs, whereas the up- and down-regulated DEGs in Cd exposed plants were 329 and 189, respectively. Under Fe-deficient conditions, Cd exposure resulted in 907 up-regulated DEGs and 953 down-regulated DEGs. In the presence of Cd, Fe deficiency induced 1042 up-regulated and 847 down-regulated genes, respectively. Based on our array data, we found that metal transporter genes such as CAX4, COPT1, IRT1, NRAMP5, OPT3, YSL3, VIT3 and VIT4 might be involved in iron homeostasis. Moreover, combined with quantitative real-time PCR, IRT1, NRAMP3, NRAMP5, OPT3, YSL3, ABCC3, ZIP1, and ZIP5 were verified to be responsible for Cd uptake and translocation in peanut plants under iron deficiency. Additionally, a larger amount of ABC transporter genes was induced or suppressed by iron deficiency under Cd exposure, indicating that this family may play important roles in Fe/Cd uptake and transport.

CONCLUSIONS

The up-regulated expression of NRAMP5 and IRT1 genes induced by iron deficiency may enhance Cd uptake in peanut roots. The decrease of Cd translocation from roots to shoots may be resulted from the down-regulation of ZIP1, ZIP5 and YSL3 under iron deficiency.

Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

BACKGROUND

Peanut is the world's fourth largest oilseed crop that exhibits wide cultivar variations in cadmium (Cd) accumulation. To establish the mechanisms of Cd distribution and accumulation in peanut plants, eight cDNA libraries from the roots of two contrasting cultivars, Fenghua 1 (low-Cd cultivar) and Silihong (high-Cd cultivar), were constructed and sequenced by RNA-sequencing. The expression patterns of 16 candidate DEGs were validated by RT-qPCR analysis.

RESULTS

A total of 75,634 genes including 71,349 known genes and 4484 novel genes were identified in eight cDNA libraries, among which 6798 genes were found to be Cd-responsive DEGs and/or DEGs between these two cultivars. Interestingly, 183 DEGs encoding ion transport related proteins and 260 DEGs encoding cell wall related proteins were identified. Among these DEGs, nine metal transporter genes (PDR1, ABCC4 and ABCC15, IRT1, ZIP1, ZIP11, YSL7, DTX43 and MTP4) and nine cell wall related genes (PEs, PGIPs, GTs, XYT12 CYP450s, LACs, 4CL2, C4H and CASP5) showed higher expression in Fenghua 1 than in Silihong.

CONCLUSIONS

Both the metal transporters and cell wall modification might be responsible for the difference in Cd accumulation and translocation between Fenghua 1 and Silihong. These findings would be useful for further functional analysis, and reveal the molecular mechanism responsible for genotype difference in Cd accumulation.

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

Background

Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress.

Results

To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress.

Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize.

Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves.

Conclusions

These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5109-8) contains supplementary material, which is available to authorized users.

Genome-wide analysis reveals four key transcription factors associated with cadmium stress in creeping bentgrass (Agrostis stolonifera L.)

Cadmium (Cd) toxicity seriously affects the growth and development of plants, so studies on uptake, translocation, and accumulation of Cd in plants are crucial for phytoremediation. However, the molecular mechanism of the plant response to Cd stress remains poorly understood. The main objective of this study was to reveal differentially expressed genes (DEGs) under lower (BT2_5) and higher (BT43) Cd concentration treatments in creeping bentgrass. A total of 463,184 unigenes were obtained from creeping bentgrass leaves using RNA sequencing technology. Observation of leaf tissue morphology showed that the higher Cd concentration damages leaf tissues. Four key transcription factor (TF) families, WRKY, bZIP, ERF, and MYB, are associated with Cd stress in creeping bentgrass. Our findings revealed that these four TFs play crucial roles during the creeping bentgrass response to Cd stress. This study is mainly focused on the molecular characteristics of DEGs under Cd stress using transcriptomic analysis in creeping bentgrass. These results provide novel insight into the regulatory mechanisms of respond to Cd stress and enrich information for phytoremediation.