Transcriptome characterization of candidate genes related to chromium uptake, transport and accumulation in Miscanthus sinensis

Epigenetic changes induced by chronic and acute chromium stress treatments in Arabidopsis thaliana identified by the MSAP-Seq

Chromium (Cr) is an highly toxic metal to plants and causes severe damage to their growth, development, and reproduction. Plant exposure to chronic and acute Cr stress treatments results in significant changes at short time in the gene expression profile and at long time in the genomic DNA methylation profile at a transgenerational level and, consequently, in gene expression. These epigenetic modifications and their implications imposed by the Cr stress are not yet completely known in plants. Herein, were identified the epigenetic changes induced by chronic and acute Cr stress treatments in Arabidopsis thaliana plants using Methylation Sensitive Amplification Polymorphism coupled with next-generation sequencing (MSAP-Seq). First-generation Arabidopsis plants (termed F0 plants) kept under hoagland solution were subjected to Cr stress treatments. For chronic Cr stress, plants were treated through hoagland solution with 2.5 μM Cr during the entire cultivation period until seed harvest. Meanwhile, for acute Cr stress, plants were treated with 5 μM Cr during the first three weeks and returned to unstressful control condition until seed harvest. Seeds from F0 plants were sown and F1 plants were re-submitted to the same Cr stress treatments. The seed germination rate was evaluated from F-2 seeds harvested of F1 plants kept under different Cr stress treatments (0, 10, 20, and 40 μM) compared to the unstressful control condition. These data showed significant changes in the germination rate of F-2 seeds originating from stressed F1 plants compared to F-2 seeds harvested from unstressful control plants. Given this data, F1 plants kept under these chronic and acute Cr stress treatments and unstressful control condition were evaluated for the transgenerational epigenetic modifications using MSAP-Seq. The MSAP-Seq data showed that several genes were modified in their methylation status as a consequence of chronic and acute Cr stress treatment to maintain plant defenses activated. In particular, RNA processing, protein translation, photorespiration, energy production, transmembrane transport, DNA transcription, plant development, and plant resilience were the major biological processes modulated by epigenetic mechanisms identified in F1 plants kept under chronic and acute Cr stress. Therefore, collective data suggested that Arabidopsis plants kept under Cr stress regulate their epigenetic status over generations based on DNA methylation to modulate defense and resilience mechanisms.

Efficient reduction of Cr(VI) by guava (Psidium guajava) leaf extract and its mitigation effect on Cr toxicity in rice seedlings

Hexavalent chromium (Cr(VI)) is a toxic element that has negative impacts on crop growth and yield. Using plant extracts to convert toxic Cr(VI) into less toxic Cr(III) may be a more favorable option compared to chemical reducing agents. In this study, the potential effects and mechanisms of using an aqueous extract of Psidium guajava L. leaves (AEP) in reducing Cr(VI) toxicity in rice were comprehensively studied. Firstly, the reducing power of AEP for Cr(VI) was confirmed by the cyclic voltammetry combined with X-ray photoelectron spectroscopy (XPS) assays. The highest Cr(VI) reduction efficiency reached approximately 78% under 1.5 mg gallic acid equivalent (GAE)/mL of AEP and 10 mg/L Cr(VI) condition. Additionally, Cr(VI) stress had a significant inhibitory effect on rice growth. However, the exogenous application of AEP alleviated the growth inhibition and oxidative damage of rice under Cr(VI) stress by increasing the activity and level of enzymatic and non-enzymatic antioxidants. Furthermore, the addition of AEP restored the ultrastructure of root cells, promoted Cr adsorption onto root cell walls, and limited the translocation Cr to shoots. In shoots, AEP application also triggered the expression of specific genes involved in Cr defense and detoxification response, including photosynthesis pathways, antioxidant systems, flavonoids biosynthesis, and plant hormone signal transduction. These results suggest that AEP is an efficient reduction agent for Cr(VI), and exogenous application of AEP may be a promising strategy to mitigate the harm of Cr(VI) on rice, ultimately contributing to improved crop yield in Cr-contaminated environments.

Comprehensive physiology and proteomics analysis revealed the resistance mechanism of rice (Oryza sativa L) to cadmium stress

Cadmium contamination can lead to a decrease in crop yield and quality. However, Cd-tolerant rice can improve rice resistance genes, improve crop tolerance to heavy metals, and protect plants from oxidative damage. In this study, Japonica rice: Chunyou 987 and Indica rice: Chuanzhong you 3607 were used to reveal the molecular response mechanism of Cd-tolerant rice under cadmium concentration of 3 mg/kg through comparative experiments combined with physiology and proteomics. The results showed that compared with indica rice, japonica rice showed more robust resistance to Cd stress and effectively retained many Cd ions in roots. Moreover, it enhanced its enzymatic and non-enzymatic anti-oxidative stress mechanism, which increased the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) by 47.37%, 21.75%, and 55.42%, respectively. The contents of non-enzymatic antioxidant substances ascorbic acid (AsA), glutathione (GSH), cysteine (Cys), proline (PRO), anthocyanins (OPC), and flavonoids were increased by 25.32%, 42.67%, 21.43%, 50.81%, 33.23%, and 72.16%, respectively. Through proteomics analysis, it was found that in response to the damage caused by cadmium stress, Japonica rice makes Photosynthesis functional proteins (psbO and PetH), Photosynthesis antenna proteins (LHCA and ASCAB9), Carbon fixation functional proteins (PEPC and OsAld), Porphyrin metabolism functional proteins (OsRCCR1 and SE5), Glyoxylate and dicarboxylate The expression of metabolism functional proteins (CATC and GLO4.) and Glutathione metabolism functional proteins (APX8 and OsGSTU13) were significantly up-regulated, which stimulated the antioxidant stress mechanism and photosynthetic system, and constructed a robust energy supply system to ensure the normal metabolic activities of life. Strengthening the mechanisms of plant homeostasis. In summary, this study revealed the molecular mechanism of tolerance to Cd stress in japonica rice, and the results of this study will provide a possible way to improve Cd-resistant rice seedlings.

Amelioration of chromium toxicity in wheat plants through exogenous application of nano silicon

Chromium (Cr) contamination in agricultural soils poses a risk to crop productivity and quality. Emerging nano-enabled strategies show great promise in remediating soils contaminated with heavy metals and enhancing crop production. The present study was aimed to investigate the efficacy of nano silicon (nSi) in promoting wheat growth and mitigating adverse effects of Cr-induced toxicity. Wheat seedlings exposed to Cr (K2Cr2O7) at a concentration of 100 mg kg-1 showed significant reductions in plant height (29.56%), fresh weight (35.60%), and dry weight (38.92%) along with enhanced Cr accumulation in roots and shoots as compared to the control plants. However, the application of nSi at a concentration of 150 mg kg-1 showcased substantial mitigation of Cr toxicity, leading to a decrease in Cr accumulation by 27.30% in roots and 35.46% in shoots of wheat seedlings. Moreover, nSi exhibited the capability to scavenge oxidative stressors, such as hydrogen peroxide (H2O2), and malondialdehyde (MDA) and electrolyte leakage, while significantly enhancing gas exchange parameters, total chlorophyll content, and antioxidant activities (enzymatic and nonenzymatic) in plants grown in Cr-contaminated soil. This study further found that the reduced Cr uptake by nSi application was due to downregulating the expression of HMs transporter genes (TaHMA2 and TaHMA3), alongwith upregulating the expression of antioxidant-responsive genes (TaSOD and TaSOD). The findings of this investigation highlight the remarkable potential of nSi in ameliorating Cr toxicity. This enhanced efficacy could be ascribed to the distinctive size and structure of nSi, which augment its ability to counteract Cr stress. Thus, the application of nSi could serve as a viable solution for production of crops in metal contaminated soils, offering an effective alternative to time-consuming and costly remediation techniques.

Review: Nitrogen acquisition, assimilation, and seasonal cycling in perennial grasses

Perennial grasses seasonal nitrogen (N) cycle extends the residence and reuse time of N within the plant system, thereby enhancing N use efficiency. Currently, the mechanism of N metabolism has been extensively examined in model plants and annual grasses, and although perennial grasses exhibit similarities, they also possess distinct characteristics. Apart from assimilating and utilizing N throughout the growing season, perennial grasses also translocate N from aerial parts to perennial tissues, such as rhizomes, after autumn senescence. Subsequently, they remobilize the N from these perennial tissues to support new growth in the subsequent year, thereby ensuring their persistence. Previous studies indicate that the seasonal storage and remobilization of N in perennial grasses are not significantly associated with winter survival despite some amino acids and proteins associated with low temperature tolerance accumulating, but primarily with regrowth during the subsequent spring green-up stage. Further investigation can be conducted in perennial grasses to explore the correlation between stored N and dormant bud outgrowth in perennial tissues, such as rhizomes, during the spring green-up stage, building upon previous research on the relationship between N and axillary bud outgrowth in annual grasses. This exploration on seasonal N cycling in perennial grasses can offer valuable theoretical insights for new perennial grasses varieties with high N use efficiency through the application of gene editing and other advanced technologies.

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.

Silicon dioxide nanoparticles enhance plant growth, photosynthetic performance, and antioxidants defence machinery through suppressing chromium uptake in Brassica napus L

Chromium (Cr) is a highly toxic heavy metal that is extensively released into the soil and drastically reduces plant yield. Silicon nanoparticles (Si NPs) were chosen to mitigate Cr toxicity due to their ability to interact with heavy metals and reduce their uptake. This manuscript explores the mechanisms of Cr-induced toxicity and the potential of Si NPs to mitigate Cr toxicity by regulating photosynthesis, oxidative stress, and antioxidant defence, along with the role of transcription factors and heavy metal transporter genes in rapeseed (Brassica napus L.). Rapeseed plants were grown hydroponically and subjected to hexavalent Cr stress (50 and 100 μM) in the form of K2Cr2O7 solution. Si NPs were foliar sprayed at concentrations of 50, 100 and 150 μM. The findings showed that 100 μM Si NPs under 100 μM Cr stress significantly increased the leaf Si content by 169% while reducing Cr uptake by 92% and 76% in roots and leaves, respectively. The presence of Si NPs inside the plant leaf cells was confirmed by using energy-dispersive spectroscopy, inductively coupled plasma‒mass spectrometry, and confocal laser scanning microscopy. The study's findings showed that Cr had adverse effects on plant growth, photosynthetic gas exchange attributes, leaf mesophyll ultrastructure, PSII performance and the activity of enzymatic and nonenzymatic antioxidants. However, Si NPs minimized Cr-induced toxicity by reducing total Cr accumulation and decreasing oxidative damage, as evidenced by reduced ROS production (such as H2O2 and MDA) and increased enzymatic and nonenzymatic antioxidant activities in plants. Interestingly, Si NPs under Cr stress effectively increased the NPQ, ETR and QY of PSII, indicating a robust protective response of PSII against stress. Furthermore, the enhancement of Cr tolerance facilitated by Si NPs was linked to the upregulation of genes associated with antioxidant enzymes and transcription factors, alongside the concurrent reduction in metal transporter activity.

Systems biology of chromium-plant interaction: insights from omics approaches

Plants are frequently subjected to heavy metal (HM) stress that impedes their growth and productivity. One of the most common harmful trace metals and HM discovered is chromium (Cr). Its contamination continues to increase in the environment due to industrial or anthropogenic activities. Chromium is severely toxic to plant growth and development and acts as a human carcinogen that enters the body by inhaling or taking Cr-contaminated food items. Plants uptake Cr via various transporters, such as sulfate and phosphate transporters. In nature, Cr is found in various valence states, commonly Cr (III) and Cr (VI). Cr (VI) is soil's most hazardous and pervasive form. Cr elevates reactive oxygen species (ROS) activity, impeding various physiological and metabolic pathways. Plants have evolved various complex defense mechanisms to prevent or tolerate the toxic effects of Cr. These defense mechanisms include absorbing and accumulating Cr in cell organelles such as vacuoles, immobilizing them by forming complexes with organic chelates, and extracting them by using a variety of transporters and ion channels regulated by various signaling cascades and transcription factors. Several defense-related proteins including, metallothioneins, phytochelatins, and glutathione-S-transferases aid in the sequestration of Cr. Moreover, several genes and transcriptional factors, such as WRKY and AP2/ERF TF genes, play a crucial role in defense against Cr stress. To counter HM-mediated stress stimuli, OMICS approaches, including genomics, proteomics, transcriptomics, and metallomics, have facilitated our understanding to improve Cr stress tolerance in plants. This review discusses the Cr uptake, translocation, and accumulation in plants. Furthermore, it provides a model to unravel the complexities of the Cr-plant interaction utilizing system biology and integrated OMICS approach.

Physio-anatomical modifications and element allocation pattern in Alternanthera tenella Colla. associated with phytoextraction of chromium

Intensive industrial activities have elevated chromium (Cr) concentrations in the environment, particularly in soil and water, posing a significant threat due to its cytotoxic and carcinogenic properties. Phytoremediation has emerged as a sustainable and economical alternative for detoxifying pollutants. In this context, an attempt has been made to assess the efficacy of Cr remediation by the invasive plant Alternanthera tenella Colla. The study investigated morphological, anatomical, and physiological adaptations in plant tissues in response to 240 µM of K2Cr2O7, considering elemental distribution patterns and bioaccumulation potential. Growth parameter assessments revealed a notable 50% reduction in root elongation and biomass content; however, the plant exhibited a comparatively higher tolerance index (47%) under Cr stress. Chromium significantly influenced macro and micro-elemental distribution in plant tissues, particularly in roots and leaves. Structural modifications, including changes in the thickness and diameter of xylem walls in the root, stem, and leaf tissues of Cr-treated A. tenella, were observed. Distinct cell structural distortions and Cr deposit inclusions in the xylem wall and inner parenchyma cells were distinct. Under Cr stress, there was a reduction in pigment content and metabolites such as proteins and soluble sugars, while proline, phenol, and malondialdehyde showed a twofold increase. The concentration of Cr was higher in the shoots of A. tenella (185.7 mg/kg DW) than in the roots (179.625 mg/kg DW). With a high BCFroot value (16.23) and TF > 1, coupled with effective mechanisms to cope with metal stress, A. tenella emerges as an ideal candidate for chromium phytoextraction.

Effects of Chromium Exposure on the Gene Expression of the Midgut in Silkworms, Bombyx mori

Chromium is a severe heavy metal pollutant with significant environmental risks. The effects of Chromium on the digestion of Bombyx mori (silkworms) are of particular importance due to their ecological and economic significance. Herein, RNA sequencing was conducted on nine midgut samples from silkworms exposed to control, 12 g/kg and 24 g/kg Chromium chemical diets. Comparative transcriptomics revealed that under moderate Chromium exposure, there was a significant increase in up-regulated genes (1268 up-regulated to 857 down-regulated), indicating a stimulation response. At higher stress levels, a weakened survival response was observed, with a decrease in up-regulated genes and an increase in down-regulated genes (374 up-regulated to 399 down-regulated). A notable shift in cellular responses under medium chromium exposure was exposed, signifying the activation of crucial metabolic and transport systems and an elevation in cellular stress and toxicity mechanisms. The observation of up-regulated gene expression within xenobiotic metabolism pathways suggests a heightened defense against Chromium-induced oxidative stress, which was primarily through the involvement of antioxidant enzymes. Conversely, high-dose Chromium exposure down-regulates the folate biosynthesis pathway, indicating biological toxicity. Two novel genes responsive to pressure were identified, which could facilitate future stress adaptation understanding. The findings provide insights into the molecular mechanisms underlying silkworms' digestion response to Chromium exposure and could inform its biological toxicity.

The alleviating effects and underlying mechanisms of exogenous selenium on both Sb(III) and Sb(V) toxicity in rice seedlings (Oryza sativa L.)

Selenium (Se) has been used to detoxify various heavy metals in plants. However, the effects and underlying mechanisms of exogenous Se application on the toxicity of antimonite [Sb(III)] and antimonate [Sb(V)] in crops are still poorly understood. Therefore, the potential alleviating roles of Se on the plant growth, antioxidant system, uptake and subcellular distribution of Sb, and expression of Sb-related genes were comprehensively investigated in rice seedlings (Oryza sativa L.) under both Sb(III) and Sb(V) stress conditions. The results showed that high concentrations of Sb(III) (100 µM) and Sb(V) (300 µM) caused a significant decrease in plant growth parameters, photosynthetic pigments and relative water content in rice seedlings. In contrast, the addition of Se (20 or 2 µM) improved rice growth, decreased Sb accumulation, and reduced oxidative stress in rice seedlings when exposed to 100 µM Sb(III) and 300 µM Sb(V), respectively. Furthermore, Se application could effectively improve the physiological adaptability of rice seedlings under Sb(III) and Sb(V) stress by regulating enzymatic and non-enzymatic antioxidant systems, Sb subcellular distribution and transcription levels of Sb-related genes, including in antioxidant response (OsCuZnSOD2, OsCATA and OsGSH1), detoxification (OsPCS1, OsPCS2 and OsABCC1) and Sb transport and sequestration (OsLsi1 and OsWAK11). Moreover, we also discovered that the mitigation effect of Se was dose-dependent and depended on Sb valence states. Thus, these findings contribute to our understanding of the mechanisms underlying Se-Sb antagonism in rice, offering a potentially useful method for producing both safe and Se-rich crops.

Transcriptomic analysis reveals key genes and pathways corresponding to Cd and Pb in the hyperaccumulator Arabis paniculata

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata, and aid in future efforts to utilize this plant in phytoremediation.

Differences in Physiological Metabolism and Antioxidant System of Different Ecotypes of Miscanthus floridulus under Cu Stress

To reveal the similarities and differences in the resistance mechanisms of different ecotypes to Cu stress, a pot experiment was used to systematically compare the physiological responses of non-mining ecotype Miscanthus floridulus (collected from Boluo County, Huizhou City) and mining ecotype Miscanthus floridulus (collected from Dabaoshan mining area) under different Cu concentrations. The results showed that chlorophyll a, chlorophyll b and total chlorophyll in the leaves of the two ecotypes of M. floridulus were negatively correlated with Cu stress concentration (p < 0.01), but the extent of decrease for the ecotypes in the mining area was lower than that for the ecotypes in the non-mining area. The values of chlorophyll a/b for both ecotypes increased with increasing Cu treatment concentration, indicating that Cu is more harmful to chlorophyll b than to chlorophyll a for M. floridulus. Cu stress can lead to the accumulation of malondialdehyde (MDA) in the leaves of M. floridulus with the amount of MDA accumulation observed being greater in the non-mining ecotype than in the mining ecotype (p < 0.05). The content of antioxidant substances (ascorbic acid and reduced glutathione) in the mining ecotype M. floridulus was significantly higher than that in the non-mining ecotype. The activity of SOD in the leaves of non-mining ecotypes was inhibited by Cu stress and the activity of POD was increased by Cu stress. However, the increase in POD in the mining ecotypes was greater than that in the non-mining ecotypes and the activities of the two enzymes in the mining ecotypes were significantly higher than those in the non-mining ecotypes at the highest concentration of Cu. Cu had different effects on PPO activity in the leaves of the two ecotypes of M. floridulus. The plant leaves of the non-mining ecotype at 400 and 800 mg·kg−1 were significantly fewer than those of the control group (p < 0.05), which were 87.1% and 65.2% of the control group, respectively. The PPO activity in the plant leaves of the mining ecotype was higher than that in the leaves of the non-mining ecotype and was significantly higher at 400 and 800 mg·kg−1 than that of the control group (p < 0.05), at 226.5% and 268.1% of the control group, respectively. These results indicate that the mining ecotype M. floridulus is more resistant to copper stress, that resistant ecotypes have been formed, and that small-molecule antioxidant substances play an important role in increasing resistance levels.

The Difference of Lead Accumulation and Transport in Different Ecotypes of Miscanthus floridulus

Miscanthus floridulus is a plant with a high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. Pot experiments were conducted to compare the growth response, Pb enrichment ability, and the effect on Pb speciation of two ecotypes of M. floridulus from the Dabaoshan Mining Area and the non-mining area of Boluo County, Huizhou, in soils with different Pb contents. The results showed that two ecotypes of M. floridulus had different growth responses to Pb concentrations in soil. Under a low concentration of Pb (100 mg·kg−1) treatment, the aboveground biomass of the non-mining area plant ecotype was significantly affected, while the plants with the mining area ecotype were not significantly affected. When the concentration of Pb increased, the aboveground biomass of the non-mining ecotype was 30.2–41.1% of the control, while that of the mining ecotype was 57.8–65.0% of the control. The root biomass of the non-mining ecotype decreased with the increase of treatment concentration, accounting for 57.8–64.2% of the control, while that of the mining ecotype increased significantly, accounting for 119.5–138.6% of the control. The Pb content in the shoots and roots of the mining ecotype M. floridulus increased rapidly with the increase of the Pb treatment concentration in the soil, and the increase in speed was obviously faster than that of the non-mining ecotype. The total amount of Pb accumulated in the roots of the ecotype from the mining area was much greater than that of the ecotype from the non-mining area, and increased significantly with the increase of Pb concentration in the soil (p < 0.05). With the aggravation of Pb stress, the transfer coefficient and tolerance index of the two ecotypes decreased by different degrees. The transfer coefficient and tolerance index of the mining ecotype were significantly higher than those of the non-mining ecotype. Pearson correlation analysis showed that root biomass was positively correlated with shoot biomass, and shoot biomass was negatively correlated with Pb content in both root and shoot, indicating that Pb accumulation in root and shoot was toxic to plants and inhibited the growth of M. floridulus. The mining ecotypes showed stronger tolerance to and enrichment of Pb.

Proline-mediated modulation on DNA repair pathway in rice seedlings under chromium stress by integrating gene chip and co-expression network analysis

Chromium (Cr) stress can cause oxidative burst to plants. Application of exogenous proline (Pro) is one of the most effective approaches to improve the tolerance of plants to Cr stress. In this study, we integrated the data of gene chip with co-expression network analysis to identify the key pathways involved in the DNA repair processes in rice seedlings under Cr(VI) stress. Based on KEGG pathway analysis, 158 genes identified are activated in five different types of DNA repair pathways, namely base excision repair (BER, 20 genes), mismatch repair (MMR, 30 genes), nonhomologous end joining (NHEJ, 8 genes), nucleotide excision repair (NER, 56 genes) and homologous recombination (HR, 44 genes). Co-expression network analysis showed that genes activated in DNA repair pathways were categorized into six different modules, wherein Module 1 (45.36%), Module 2 (27.84%) and Module 3 (19.59%) carried more weight than others. Integrating the data of gene chip and co-expression network analysis indicated that coordinated actions of HR and NER pathways are mainly associated with DNA repair processes in Cr(VI)-treated rice seedlings supplied with exogenous Pro. OsCSB, OsXPG, OsBRIP1, OsRAD51C, OsRAD51A2, OsRPA, OsTOPBP1C, OsTOP3, and OsXRCC3 activated in the HR pathway had a stronger impact on repairing DNA damage induced by Cr(VI) stress in rice seedlings supplied with exogenous Pro, while OsXPB1, OsTTDA2, OsTFIIH1, OsXPC, OsRAD23, OsDSS1, and OsRPA located at the NER pathway showed more contribution to repairing DNA damage than others.