Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine

Integrative physiological, critical plant endogenous hormones, and transcriptomic analyses reveal the difenoconazole stress response mechanism in wheat (Triticum aestivum L.)

Difenoconazole (DFN) is widely utilized as a fungicide in wheat production. However, its accumulation in plant tissues has a profound impact on the physiological functions of wheat plants, thus severely threatening wheat growth and even jeopardizing human health. This study aims to comprehensively analyze the dynamic dissipation patterns of DFN, along with an investigation into the physiological, hormonal, and transcriptomic responses of wheat seedlings exposed to DFN. The results demonstrated that exposure of wheat roots to DFN (10 mg/kg in soil) led to a significant accumulation of DFN in wheat plants, with the DFN content in roots being notably higher than that in leaves. Accumulating DFN triggered an increase in reactive oxygen species content, malonaldehyde content, and antioxidant enzyme activities, while concurrently inhibiting photosynthesis. Transcriptome analysis further revealed that the number of differentially expressed genes was greater in roots compared with leaves under DFN stress. Key genes in roots and leaves that exhibited a positive response to DFN-induced stress were identified through weighted gene co-expression network analysis. Metabolic pathway analysis indicated that these key genes mainly encode proteins involved in glutathione metabolism, plant hormone signaling, amino acid metabolism, and detoxification/defense pathways. Further results indicated that abscisic acid and salicylic acid play vital roles in the detoxification of leaf and root DFN, respectively. In brief, the abovementioned findings contribute to a deeper understanding of the detrimental effects of DFN on wheat seedlings, while shedding light on the molecular mechanisms underlying the responses of wheat root and leaves to DFN exposure.

Symbiotic compatibility between rice cultivars and arbuscular mycorrhizal fungi genotypes affects rice growth and mycorrhiza-induced resistance

Introduction

Arbuscular mycorrhizal fungi (AMF) belong to the Glomeromycota clade and can form root symbioses with 80% of Angiosperms, including crops species such as wheat, maize and rice. By increasing nutrient availability, uptake and soil anchoring of plants, AMF can improve plant's growth and tolerance to abiotic stresses. AMF can also reduce symptoms and pathogen load on infected plants, both locally and systemically, through a phenomenon called mycorrhiza induced resistance (MIR). There is scarce information on rice mycorrhization, despite the high potential of this symbiosis in a context of sustainable water management in rice production systems.

Methods

We studied the symbiotic compatibility (global mycorrhization & arbuscules intensity) and MIR phenotypes between six rice cultivars from two subspecies (indica: IR64 & Phka Rumduol; japonica: Nipponbare, Kitaake, Azucena & Zhonghua 11) and three AMF genotypes (Funneliformis mosseae FR140 (FM), Rhizophagus irregularis DAOM197198 (RIR) & R. intraradices FR121 (RIN)). The impact of mycorrhization on rice growth and defence response to Xanthomonas oryzae pv oryzae (Xoo) infection was recorded via both phenotypic indexes and rice marker gene expression studies.

Results

All three AMF genotypes colonise the roots of all rice varieties, with clear differences in efficiency depending on the combination under study (from 27% to 84% for Phka Rumduol-RIN and Nipponbare-RIR combinations, respectively). Mycorrhization significantly (α=0.05) induced negative to beneficial effects on rice growth (impact on dry weight ranging from -21% to 227% on Azucena-FM and Kitaake-RIN combinations, respectively), and neutral to beneficial effects on the extent of Xoo symptoms on leaves (except for Azucena-RIN combination which showed a 68% increase of chlorosis). R. irregularis DAOM197198 was the most compatible AMF partner of rice, with high root colonisation intensity (84% of Nipponbare's roots hyphal colonisation), beneficial effects on rice growth (dry weight +28% (IR64) to +178% (Kitaake)) and decrease of Xoo-induced symptoms (-6% (Nipponbare) to -27% (IR64)). Transcriptomic analyses by RT-qPCR on leaves of two rice cultivars contrasting in their association with AMF show two different patterns of response on several physiological marker genes.

Discussion

Overall, the symbiotic compatibility between rice cultivars and AMF demonstrates adequate colonization, effectively restricting the nutrient starvation response and mitigating symptoms of phytopathogenic infection.

Multiple Metabolism Pathways of Bentazone Potentially Regulated by Metabolic Enzymes in Rice

Bentazone (BNTZ) is a selective and efficient herbicide used in crop production worldwide. However, the persistence of BNTZ residues in the environment has led to their increasing accumulation in farmland and crops, posing a high risk to human health. To evaluate its impact on crop growth and environmental safety, a comprehensive study was conducted on BNTZ toxicity, metabolic mechanism, and resultant pathways in rice. The rice growth was compromised to the treatment with BNTZ at 0.2-0.8 mg/L (529.95-1060.05 g a.i./ha), while the activities of enzymes including SOD, POD, CAT, GST, GT, and CYP450 were elevated under BNTZ stress. A genome-wide RNA-sequencing (RNA-Seq) was performed to dissect the variation of transcriptomes and metabolic mechanisms in rice exposed to BNTZ. The degradative pathways of BNTZ in rice are involved in glycosylation, hydrolysis, acetylation, and conjugation processes catalyzed by the enzymes. Our data provided evidence that helps understand the BNTZ metabolic and detoxic mechanisms.

Molecular Responses and Degradation Mechanisms of the Herbicide Diuron in Rice Crops

Diuron [DU; 3-(3,4-dichlorophenyl)-1,1-dimethylurea], a widely used herbicide for weed control, arouses ecological and health risks due to its environment persistence. Our findings revealed that DU at 0.125-2.0 mg L^-1 caused oxidative damage to rice. RNA-sequencing profiles disclosed a globally genetic expression landscape of rice under DU treatment. DU mediated downregulated gene encoding photosynthesis and biosynthesis of protein, fatty acid, and carbohydrate. Conversely, it induced the upregulation of numerous genes involved in xenobiotic metabolism, detoxification, and anti-oxidation. Furthermore, 15 DU metabolites produced by metabolic genes were identified, 7 of which include two Phase I-based and 5 Phase II-based derivatives, were reported for the first time. The changes of resistance-related phytohormones, like JA, ABA, and SA, in terms of their contents and molecular-regulated signaling pathways positively responded to DU stress. Our work provides a molecular-scale perspective on the response of rice to DU toxicity and clarifies the biotransformation and degradation fate of DU in rice crops.

Herbicide resistance in grass weeds: Epigenetic regulation matters too

Although herbicides have been successfully used for controlling weeds, their continuous use has developed in the evolution of resistance to all major herbicide modes of action worldwide. Reports suggest that the members of Poaceae family are more prone to developing herbicide resistance than other families. In plants, epigenetic mechanisms play critical roles by increasing their stress-adaptive potential in a rapidly changing environment. Epigenetic mechanisms involve alteration of the expression of genetic elements, but without any changes in the DNA sequence. Although the possible roles of epigenetic mechanisms in contributing to survival and fitness under various stresses are well documented in model plants and crops, their contribution to herbicide resistance in weeds is still in its infancy. A few studies with herbicides have shown differential expression of DNA methyltransferases, histone methyltransferases and DNA demethylases in response to the herbicides; however, no further studies were conducted. In the case of herbicide stress, exploring how these epigenetic processes affect the gene expression pattern in individual plants subjected to recurrent selection would be exciting. Hence, our mini-review will focus on the potential contributions of epigenetic mechanisms to the adaptive responses of grass-weedy species to herbicide stress. A better understanding of these epigenetic changes will add novel perceptions to our knowledge of herbicide resistance evolution in weeds enabling the development of herbicides with novel targets.

OsBR6ox, a member in the brassinosteroid synthetic pathway facilitates degradation of pesticides in rice through a specific DNA demethylation mechanism

This manuscript described a comprehensive study on a pesticide degradation factor OsBR6ox that promoted the degradation of pesticides atrazine (ATZ) and acetochlor (ACT) in rice tissues and grains through an epigenetic mechanism. OsBR6ox was transcriptionally induced under ATZ and ACT stress. Genetic disruption of OsBR6ox increased rice sensitivity and led to more accumulation of ATZ and ACT, whereas transgenic rice overexpressing OsBR6ox lines (OEs) showed opposite effects with improved growth and lower ATZ and ACT accumulation in various tissues, including grains. OsBR6ox-mediated detoxification of ATZ and ACT was associated with the increased abundance of brassinolide (one of the brassinosteroids, BRs), a plant growth regulator for stress responses. Some Phase I-II reaction protein genes for pesticide detoxification such as genes encoding laccase, O-methyltransferase and glycosyltransferases were transcriptionally upregulated in OE lines under ATZ and ACT stress. HPLC-Q-TOF-MS/MS analysis revealed an enhanced ATZ/ATC metabolism in OE plants, which removed 1.21-1.49 fold ATZ and 1.31-1.44 fold ACT from the growth medium but accumulated only 83.1-87.1 % (shoot) and 71.7-84.1 % (root) of ATZ and 69.4-83.4 % of ACT of the wild-type. Importantly, an ATZ-responsive demethylated region in the upstream of OsBR6ox was detected. Such an epigenetic modification marker was responsible for the increased OsBR6ox expression and consequent detoxification of ATZ/ACT in rice and environment. Overall, this work uncovered a new model showing that plants utilize two mechanisms to co-regulate the detoxification and metabolism of pesticides in rice and provided a new approach for building up cleaner crops and eliminating residual pesticides in environments.

Degradation of Residual Herbicide Atrazine in Agri-Food and Washing Water

Atrazine, an herbicide used to control grassy and broadleaf weed, has become an essential part of agricultural crop protection tools. It is widely sprayed on corn, sorghum and sugar cane, with the attendant problems of its residues in agri-food and washing water. If ingested into humans, this residual atrazine can cause reproductive harm, developmental toxicity and carcinogenicity. It is therefore important to find clean and economical degradation processes for atrazine. In recent years, many physical, chemical and biological methods have been proposed to remove atrazine from the aquatic environment. This review introduces the research works of atrazine degradation in aqueous solutions by method classification. These methods are then compared by their advantages, disadvantages, and different degradation pathways of atrazine. Moreover, the existing toxicological experimental data for atrazine and its metabolites are summarized. Finally, the review concludes with directions for future research and major challenges to be addressed.

Minimized Atrazine Risks to Crop Security and Its Residue in the Environment by a Rice Methyltransferase as a Regulation Factor

Atrazine (ATZ) is an agricultural pesticide for controlling field weeds. ATZ accumulates in many crops, posing high risks to crop production and food safety. Characterizing one of the novel rice MT genes named Oryza sativa atrazine-responsive methyltransferase (OsARM) showed that the expression of OsARM was associated with DNA demethylation (hypomethylation) in its promoter region. The enhancement of OsARM expression was manifested by the attenuated symptoms of ATZ toxicity including better growth and lower ATZ accumulation in plants. The promoted capacity of detoxification was confirmed by transgenic rice overexpression OsARM lines and also functionally proved by CRISPR-Cas9 knockout mutants. The transgenic lines accumulate more ATZ metabolites in rice and lower concentrations in the growth environment, pointing out that ATZ metabolism or degradation can be intensified. The ATZ-induced DNA demethylation is an important hallmark representing the epigenetic mechanism, which is required for the extra OsARM expression to facilitate ATZ disappearance in rice and the environment.

Pup1 QTL Regulates Gene Expression Through Epigenetic Modification of DNA Under Phosphate Starvation Stress in Rice

Cytosine methylation, epigenetic DNA modification, is well known to regulate gene expression. Among the epigenetic modifications, 5-methylcytosine (5-mC) has been one of the extensively studied epigenetic changes responsible for regulating gene expression in animals and plants. Though a dramatic change in 5-mC content is observed at the genome level, the variation in gene expression is generally less than that it is expected. Only less is understood about the significance of 5-mC in gene regulation under P-starvation stress in plants. Using whole-genome bisulfite sequencing of a pair of rice [Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL] genotypes, we could decipher the role of Pup1 on DNA (de)methylation-mediated regulation of gene expression under P-starvation stress. We observed 13-15% of total cytosines to be methylated in the rice genome, which increased significantly under the stress. The number of differentially methylated regions (DMRs) for hypomethylation (6,068) was higher than those (5,279) for hypermethylated DMRs under the stress, particularly in root of NIL-23. Hypomethylation in CHH context caused upregulated expression of 489 genes in shoot and 382 genes in root of NIL-23 under the stress, wherein 387 genes in shoot and 240 genes in root were upregulated exclusively in NIL-23. Many of the genes for DNA methylation, a few for DNA demethylation, and RNA-directed DNA methylation were upregulated in root of NIL-23 under the stress. Methylation or demethylation of DNA in genic regions differentially affected gene expression. Correlation analysis for the distribution of DMRs and gene expression indicated the regulation of gene mainly through (de)methylation of promoter. Many of the P-responsive genes were hypomethylated or upregulated in roots of NIL-23 under the stress. Hypermethylation of gene body in CG, CHG, and CHH contexts caused up- or downregulated expression of transcription factors (TFs), P transporters, phosphoesterases, retrotransposon proteins, and other proteins. Our integrated transcriptome and methylome analyses revealed an important role of the Pup1 QTL in epigenetic regulation of the genes for transporters, TFs, phosphatases, carbohydrate metabolism, hormone-signaling, and chromatin architecture or epigenetic modifications in P-starvation tolerance. This provides insights into the molecular function of Pup1 in modulating gene expression through DNA (de)methylation, which might be useful in improving P-use efficiency or productivity of rice in P-deficient soil.

Residues of Reduced Herbicides Terbuthylazine, Ametryn, and Atrazine and Toxicology to Maize and the Environment through Salicylic Acid

Terbuthylazine (TBA), ametryn (AME), and atrazine (ATZ) are triazine family herbicides. They are dominantly used in the field of cereal crops like wheat and maize for prevention of upland from annual gramineous and broad-leaved weeds, with attributes of weed efficiency broad spectrum and good market performance. Salicylic acid (SA) is a kind of natural plant growth regulator existing widely in the plant kingdom and participating in many physiological and defense processes. In this study, the effects of SA on the detoxification and degradation of herbicides TBA, AME, and ATZ in maize were investigated. When maize plants were exposed to 6 mg kg^-1 of the triazine herbicides, the growth and chlorophyll concentration were reduced, while the membrane permeability increased. After maize was sprayed with 5 mg kg^-1 SA, the herbicide-induced phytotoxicity was significantly assuaged, with the increased content of chlorophyll and decreased cellular damage in plants. Activities of several biomarker enzymes such as SOD, POD, and GST were repressed in the presence of SA. The concentration of the triazine herbicides in maize and the soil determined by high-performance liquid chromatography was drastically reduced by spraying SA. Using LC/Q-TOF-MS/MS, six metabolites and nine conjugates of AME in maize and soil were characterized. The relative contents of AME metabolites and conjugates in maize with SA were higher than those without SA. These results suggest that SA is able to promote the detoxification and decay of these triazine herbicides in maize and soil.

Metabolism and detoxification of pesticides in plants

Pesticides make indispensable contributions to agricultural productivity. However, the residues after their excessive use may be harmful to crop production, food safety and human health. Although the ability of plants (especially crops) to accumulate and metabolize pesticides has been intensively investigated, data describing the chemical and metabolic processes in plants are limited. Understanding how pesticides are metabolized is a key step toward developing cleaner crops with minimal pesticides in crops, creating new green pesticides (or safeners), and building up the engineered plants for environmental remediation. In this review, we describe the recently discovered mechanistic insights into pesticide metabolic pathways, and development of improved plant genotypes that break down pesticides more effectively. We highlight the identification of biological features and functions of major pesticide-metabolized enzymes such as laccases, glycosyltransferases, methyltransferases and ATP binding cassette (ABC) transporters, and discuss their chemical reactions involved in diverse pathways including the formation of pesticide S-conjugates. The recent findings for some signal molecules (phytohomormes) like salicylic acid, jasmonic acid and brassinosteroids involved in metabolism and detoxification of pesticides are summarized. In particular, the emerging research on the epigenetic mechanisms such DNA methylation and histone modification for pesticide metabolism is emphasized. The review would broaden our understanding of the regulatory networks of the pesticide metabolic pathways in higher plants.

The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles

In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil

Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.

Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

DNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

BACKGROUND

Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood.

RESULTS

Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH.

CONCLUSIONS

Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.

Identification of a novel function of a component in the jasmonate signaling pathway for intensive pesticide degradation in rice and environment through an epigenetic mechanism

Developing a biotechnical system with rapid degradation of pesticide is critical for reducing environmental, food security and health risks. Here, we investigated a novel epigenetic mechanism responsible for the degradation of the pesticide atrazine (ATZ) in rice crops mediated by the key component CORONATINE INSENSITIVE 1a (OsCOI1a) in the jasmonate-signaling pathway. OsCOI1a protein was localized to the nucleus and strongly induced by ATZ exposure. Overexpression of OsCOI1a (OE) significantly conferred resistance to ATZ toxicity, leading to the improved growth and reduced ATZ accumulation (particularly in grains) in rice crops. HPLC/Q-TOF-MS/MS analysis revealed increased ATZ-degraded products in the OE plants, suggesting the occurrence of vigorous ATZ catabolism. Bisulfite-sequencing and chromatin immunoprecipitation assays showed that ATZ exposure drastically reduced DNA methylation at CpG context and histone H3K9me2 marks in the upstream of OsCOI1a. The causal relationships between the DNA demethylation (hypomethylatioin), OsCOI1a expression and subsequent detoxification and degradation of ATZ in rice and environment were well established by several lines of biological, genetic and chemical evidence. Our work uncovered a novel regulatory mechanism implicated in the defense linked to the epigenetic modification and jasmonate signaling pathway. It also provided a modus operandi that can be used for metabolic engineering of rice to minimize amounts of ATZ in the crop and environment.

Proteogenomic insight into the basis of the insecticide tolerance/resistance of the pollen beetle Brassicogethes (Meligethes) aeneus

The pollen beetle is a major pest of oilseed rape. Although various resistance mechanisms have been identified, such as kdr (mutation in the sodium channel) and metabolic resistance (CYP overexpression), other "hidden" factors also exist. Some studies have stressed the importance of epistasis as a genetic background. The combination of kdr and metabolic resistance appears to be unfavorable under field conditions in the absence of pesticide selection. The regulation of detoxification enzymes can play an important role, but we highlight different detoxification markers compared to those emphasized in other studies. We also stress the importance of studying the role of markers identified as pathogenesis-related protein 5-like (PR5; upregulated by insecticides) and highlight the role of RNA (DEAD-box) helicases (downregulated by insecticides). Thus, we suggest the importance of epigenetic drivers of resistance/tolerance to pesticides. The key results are similar to those of our previous study, in which deltamethrin treatment of the pollen beetle was also investigated by a proteogenomic approach. Indeed, the mechanism leading to resistance of the pollen beetle may be an innate mechanism that the pollen beetle can also employ in natural habitats, but under field conditions (pesticide exposure), this mechanism is used to survive in response to insecticides. SIGNIFICANCE: Pesticide resistance is a serious problem that hampers the successful production of crops. Understanding the mechanisms of insecticide resistance is highly important for successful pest control, especially when considering integrated pest management. Here, using a proteogenomic approach, we identified novel markers for understanding pollen beetle resistance to pesticides. In addition, future studies will reveal the role of these markers in the multiresistance of pollen beetle populations. We highlight that the proteins identified as PR5, which are known to occur in beetles and are similar to those in plants, may be responsible for tolerance to multiple stresses. In addition, our results indicate that the RNA helicases that exhibited changes in expression may be the epigenetic drivers of multiresistance. The nature of these changes remains an open question, and their relevance in different situations (responses to different stresses) in natural habitats in the absence of pesticides can be proposed.

Suppression of the genes responsible for transporting hydrophobic pollutants leads to the production of safer crops

Hydrophobic pollutants have become widely distributed across the world. From an agricultural perspective, their accumulation in crops from contaminated soil threatens food security and quality, leading to many diseases in humans. The Cucurbitaceae family can accumulate high concentrations of hydrophobic pollutants in their aerial parts. The Cucurbitaceae family contains major latex-like proteins (MLPs) as transporting factors for hydrophobic pollutants. MLP genes are expressed in the roots in which the MLPs bind hydrophobic pollutants. MLPs transport these hydrophobic pollutants to the aerial parts of the plant through the xylem vessels. As a result, hydrophobic pollutant contamination occurs in the Cucurbitaceae family. In this study, we suppressed the expression of MLP genes in the roots and reduced the amounts of MLPs with pesticide treatments. First, the fungicides Benlate and Daconil that deceased the hydrophobic pollutant, perylene, concentration in the xylem sap of zucchini plants were selected. Daconil suppressed the transcription activity of MLP in the roots. In the Daconil treatment, the amount of MLPs in the roots and xylem sap of zucchini plants was decreased, and the concentrations of the hydrophobic pollutants, pyrene and dieldrin, were significantly decreased. Our research contributes to the production of safer crops.

PkGPPS.SSU interacts with two PkGGPPS to form heteromeric GPPS in Picrorhiza kurrooa: Molecular insights into the picroside biosynthetic pathway

Geranyl geranyl pyrophosphate synthase (GGPPS) is known to form an integral subunit of the heteromeric GPPS (geranyl pyrophosphate synthase) complex and catalyzes the biosynthesis of monoterpene in plants. Picrorhiza kurrooa Royle ex Benth., a medicinally important high altitude plant is known for picroside biomolecules, the monoterpenoids. However, the significance of heteromeric GPPS in P. kurrooa still remains obscure. Here, transient silencing of PkGGPPS was observed to reduce picroside-I (P-I) content by more than 60% as well as picroside-II (P-II) by more than 75%. Thus, PkGGPPS was found to be involved in the biosynthesis of P-I and P-II besides other terpenoids. To unravel the mechanism, small subunit of GPPS (PkGPPS.SSU) was identified from P. kurrooa. Protein-protein interaction studies in yeast as well as bimolecular fluorescence complementation (BiFC) in planta have indicated that large subunit of GPPS PkGPPS.LSUs (PkGGPPS1 and PkGGPPS2) and PkGPPS.SSU form a heteromeric GPPS. Presence of similar conserved domains such as light responsive motifs, low temperature responsive elements (LTRE), dehydration responsive elements (DREs), W Box and MeJA responsive elements in the promoters of PkGPPS.LSU and PkGPPS.SSU documented their involvement in picroside biosynthesis. Further, the tissue specific transcript expression analysis vis-à-vis epigenetic regulation (DNA methylation) of promoters as well as coding regions of PkGPPS.LSU and PkGPPS.SSU has strongly suggested their role in picroside biosynthesis. Taken together, the newly identified PkGPPS.SSU formed the heteromeric GPPS by interacting with PkGPPS.LSUs to synthesize P-I and P-II in P. kurrooa.

Low herbicide doses can change the responses of weeds to subsequent treatments in the next generation: metamitron exposed PSII-target-site resistant Chenopodium album as a case study

BACKGROUND

It is well known that exposure to mild stress can precondition organisms to better tolerate subsequent stress exposure in the same or future generations. Since herbicide hormesis also represents a moderate stress to exposed plants, a transgenerational priming is likely but not proven. Especially in herbicide-resistant weeds showing enhanced reproductive fitness after regular herbicide treatments, the ability to induce resilient offspring phenotypes via hormesis may hasten the evolution of herbicide resistance in weeds. This hypothesis was studied for the triazinone metamitron in an F1 offspring generation of PSII target-site resistant (TSR) plants of Chenopodium album propagated after parental conditioning with various metamitron doses.

RESULTS

In two independent dose-response greenhouse trials, there was a positive correlation between the strength of the stimulatory response during parental preconditioning and the magnitude of transgenerational changes in herbicide sensitivity and hormesis expression. Parental conditioning at subhormetic and toxic concentrations lead to less resilient offspring, while conditioning doses that induced a pronounced hormetic effect in F0 plants had a sensitivity-reducing and hormesis-promoting effect on the offspring. The observed reduction in sensitivity in F1 plants compared to unconditioned F1 plants was up to 2.2-fold.

CONCLUSIONS

This study demonstrates that hormetic herbicide treatments have the ability to prime weeds for enhanced tolerance to subsequent treatments in the next generation. Effects proved dose sensitive and may act in concert with other stimulatory adaptations in plant populations. This is relevant for weed control and herbicide resistance evolution, but also for herbicide side-effects that go beyond the exposed area. © 2020 The Author. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus

Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (Oryza sativa L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified in CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. Additionally, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 102 genes with positive correlation and 71 genes with negative correlation between methylation level at promoter regions and gene expression. Key genes associated with maintaining DNA methylation in rice were analyzed by RT-qPCR and indicated that OsDMT702 might be responsible for the global increase of DNA methylation level in rice under RBSDV stress. Our results suggest important roles of rice DNA methylation in response to RBSDV and provide potential target genes for rice antiviral immunity.

OsNHAD is a chloroplast membrane-located transporter required for resistance to salt stress in rice (Oryza sativa)

Salt stress is one of the major environmental factors limiting crop productivity. Although physiological and molecular characterization of salt stress response in plants has been the focus for many years, research on transporters for sodium ion (Na⁺) uptake, translocation and accumulation in plants, particularly in food crops like rice is limited. In this study, we functionally identified an uncharacterized sodium ion transporter named OsNHAD which encodes a putative Na⁺ ⁄ H⁺ antiporter in rice. Homology search shows its close relation to the Arabidopsis Na⁺/H⁺ antiporter AtNHD1 with 72.74% identity of amino acids. OsNHAD transcripts mainly express in leaves and are induced by Na⁺ stress. Confocal laser scanning microscopy analysis of OsNHAD::GFP fusion in tobacco leaves shows that OsNHAD resides in the chloroplast envelop. Knock-down of OsNHAD by RNA interference led to increased rice sensitivity to Na⁺, manifested by stunted plant growth, enhanced cellular damage, reduced PSII activity and changed chloroplast morphology. Mutation of OsNHAD also resulted in accumulation of more Na⁺ in chloroplasts and in shoots as well, suggesting that OsNHAD is involved in mediating efflux and detoxification of Na⁺ but does not affect K⁺ accumulation in plant cells. Complementation test reveals that OsNHAD was able to functionally restore the Arabidopsis mutant atnhd1-1 growth phenotype. These results suggest that OsNHAD possibly mediates homeostasis of sodium ions in the subcellular compartments and tissues of the plants when challenged to salt stress.

Identification of epigenetic mechanisms in paddy crop associated with lowering environmentally related cadmium risks to food safety

Cadmium (Cd) is a toxic metal that contributes to human diseases such as pediatric cancer and cardiovascular dysfunction. Epigenetic modification caused by Cd exposure is the major factor in etiology of environmentally-relevant diseases. However, the underlying epigenetic mechanism for Cd uptake and accumulation in food crops, particularly those growing in Cd-contaminated environments, is largely unknown. This study investigated uncharacterized regulatory mechanisms and biological functions of global DNA hypomethylation at CG sites that are associated with gene expression for Cd detoxification and accumulation in the food crop rice. Mutation of the CG maintenance enzyme OsMET1 confers rice tolerance to Cd exposure. Genome-wide analysis of OsMET1 loss of function mutant Osmet1 and its wild type shows numerous loci differentially methylated and upregulated genes for Cd detoxification, transport and accumulation. We functionally identified a new locus for a putative cadmium tolerance factor (here termed as OsCTF) and demonstrated that Cd-induced DNA demethylation is the drive of OsCTF expression. The 3'-UTR of OsCTF is the primary site of DNA and histone (H3K9me2) demethylation, which is associated with higher levels of OsCTF transcripts detected in the Osmet1 and Ossdg714 mutant lines. Mutation of OsCTF in rice led to hypersensitivity to Cd and the Osctf line accumulated more Cd, whereas transfer of OsCTF back to the Osctf mutant completely restored the normal phenotype. Our work unveiled an important epigenetic mechanism and will help develop breeding crops that contribute to food security and better human health.

Uptake of atrazine in a paddy crop activates an epigenetic mechanism for degrading the pesticide in plants and environment

There is a rising public concern on accumulation of harmful pesticides in environment and crops. Epigenetic alteration caused by environmental contaminants is one of the key factors in the etiology of environmentally-associated diseases. Growing evidence shows that harmful pesticide atrazine (ATZ) has a profound effect on DNA methylation in human genome, however, little is known about the epigenetic mechanism underlying ATZ accumulation and degradation in plants, particularly in edible plants growing in the ATZ-contaminated areas. This study investigated the atrazine elimination that was mediated by DNA methylation and histone modification in the food crop rice. Studies with two mutant Osmet1-1/2 defective in the genomic CG DNA methylation show significantly lower accumulation of atrazine than its wild-types. Profiling methylome and transcriptome of ATZ-exposed Osmet1 and wild-type identified many differentially methylated loci (≥2 fold change, p < 0.05), which were associated with activation of genes responsible for atrazine degradation in plants. Three demethylated loci OsGTF, OsHPL1 and OsGLH were expressed in eukaryotic yeast cells and found to eliminate a marked proportion of ATZ in growth environments by 48%, 43% and 32%, respectively, whereas the increased ATZ-degraded products were characterized using UPLC/Q-TOF-MS/MS. These results suggest that activation of the loci mediated by ATZ-induced hypomethylation could be responsible for the removal of ATZ in rice. Our work helps understand a new regulatory mechanism underlying the atrazine degradation in crops which may potentially reduce the environmental risks to human health through food chain.

Dynamics and function of DNA methylation in plants

DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions.

Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice

Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.

Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance

Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool to unveil potential connections between specific epigenetic modifications and stress tolerance capacity. We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity. We hypothesize that short regions as DMRs can shape the chromatin landscape of specific genomic regions and, therefore, may modulate the function of several genes. In this sense, the identification of DMRs represents one step towards to uncover new players in the regulation of stress-responsive genes and new target genes with potential application in enhancement of plant salinity-tolerance.

Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression

The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.

Degrading and Phytoextracting Atrazine Residues in Rice (Oryza sativa) and Growth Media Intensified by a Phase II Mechanism Modulator

Atrazine (ATZ) residue in farmland is one of the environmental contaminants seriously affecting crop production and food safety. Understanding the regulatory mechanism for ATZ metabolism and degradation in plants is important to help reduce ATZ potential toxicity to both plants and human health. Here, we report our newly developed engineered rice overexpressing a novel Phase II metabolic enzyme glycosyltransfearse1 (ARGT1) responsible for transformation of ATZ residues in rice. Our results showed that transformed lines, when exposed to environmentally realistic ATZ concentration (0.2-0.8 mg/L), displayed significantly high tolerance, with 8-27% biomass and 36-56% chlorophyll content higher, but 37-69% plasma membrane injury lower than untransformed lines. Such results were well confirmed by ARGT1 expression in Arabidopsis. ARGT1-transformed rice took up 1.6-2.7 fold ATZ from its growth medium compared to its wild type (WT) and accumulated ATZ 10%-43% less than that of WT. A long-term study also showed that ATZ in the grains of ARGT1-transformed rice was reduced by 30-40% compared to WT. The ATZ-degraded products were characterized by UPLC/Q-TOF-MS/MS. More ATZ metabolites and conjugates accumulated in ARGT1-transformed rice than in WT. Eight ATZ metabolites for Phase I reaction and 10 conjugates for Phase II reaction in rice were identified, with three ATZ-glycosylated conjugates that have never been reported before. These results indicate that ARGT1 expression can facilitate uptake of ATZ from environment and metabolism in rice plants.

Herbicide injury induces DNA methylome alterations in Arabidopsis

The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic changes, such as alterations in DNA methylation, are potential additional adaptive mechanisms for herbicide resistance. We performed methylC sequencing of Arabidopsis thaliana leaves that developed after either mock treatment or two different sub-lethal doses of the herbicide glyphosate, the most-used herbicide in the history of agriculture. The herbicide injury resulted in 9,205 differentially methylated regions (DMRs) across the genome. In total, 5,914 of these DMRs were induced in a dose-dependent manner, wherein the methylation levels were positively correlated to the severity of the herbicide injury, suggesting that plants can modulate the magnitude of methylation changes based on the severity of the stress. Of the 3,680 genes associated with glyphosate-induced DMRs, only 7% were also implicated in methylation changes following biotic or salinity stress. These results demonstrate that plants respond to herbicide stress through changes in methylation patterns that are, in general, dose-sensitive and, at least partially, stress-specific.

Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice

Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.

Potential biomarkers for monitoring the toxicity of long-term exposure to atrazine in rat by metabonomic analysis

1. Herbicide atrazine (ATR) poses harmful effects on human health. The purpose of this study is to study potential biomarkers used for monitoring the toxic effects after chronic exposure to ATR by studying urine metabolites. 2. Rats were assigned into clinical chemistry and metabonomics arms, and each arm was divided into low-dose, high-dose and control groups. ATR was administered to rats along with their feed. At the end of 16, 20 and 24 weeks, clinical parameters and histopathologic changes was assessed to monitor the toxic effects. Twenty-four hour urine samples was analyzed by UPLC-MS, to find the significant alterations in metabolic profiling. 3. The body weight of rats in ATR group was lower than that of control starting from 12th week; abnormal levels of serum biochemistry and histopathologic alterations of organs were found initially from 16th and 20th week, respectively. Five exogenous and five endogenous metabolites were found which showed significant differences between ATR groups and control group at above-mentioned time points. 4. These metabolites may be used as potential indicators to monitor ATR toxicity, and also may provide some clues for understanding the mechanism of toxicity of ATR. The exact relationship between endogenous metabolites and ATR toxicity needs further investigation.

Enhanced detoxification and degradation of herbicide atrazine by a group of O-methyltransferases in rice

Atrazine (ATR) as a toxic herbicide has become one of the seriously environmental contaminants worldwide due to its long-term intensive use in crop production. This study identified novel methyltransferases (MTs) involved in detoxification and degradation of ATR residues in rice plants. From a subset of MTs differentially expressed in ATR-exposed rice, forty-four O-methyltransferase genes were investigated. Total activities were significantly enhanced by ATR in rice tissues. To prove detoxifying capacity of the MTs in rice plants, two rice O-MTs (LOC_Os04g09604 and LOC_Os11g15040) were selected and transformed into yeast cells (Pichia pastoris X-33). The positive transformants accumulated less ATR and showed less toxicity. Using UPLC-TOF-MS/MS, ATR-degraded products in rice and yeast cells were characterized. A novel O-methylated-modified metabolite (atraton) and six other ATR-derivatives were detected. The topological interaction between LOC_Os04g09604 enzyme and its substrate was specially analyzed by homology modeling programs, which was well confirmed by the molecular docking analysis. The significance of the study is to provide a better understanding of mechanisms for the specific detoxification and degradation of ATR residues in rice growing in environmentally relevant ATR-contaminated soils and may hold a potential engineering perspective for generating ATR-resistant rice that helps to minimize ATR residues in crops.

Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence an epigenetic mechanism that regulates the expression of unique genes responsible for drought stress tolerance.

Epigenetic regulation and epigenomic landscape in rice

Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

The epigenetic events imposed during germline reprogramming and affected by harmful exposure can be inherited and transferred to subsequent generations via gametes inheritance. In this study, we examine the transgenerational effects promoted by widely used herbicide atrazine (ATZ). We exposed pregnant outbred CD1 female mice and the male progeny was crossed for three generations with untreated females. We demonstrate here that exposure to ATZ affects meiosis, spermiogenesis and reduces the spermatozoa number in the third generation (F3) male mice. We suggest that changes in testis cell types originate from modified transcriptional network in undifferentiated spermatogonia. Importantly, exposure to ATZ dramatically increases the number of transcripts with novel transcription initiation sites, spliced variants and alternative polyadenylation sites. We found the global decrease in H3K4me3 occupancy in the third generation males. The regions with altered H3K4me3 occupancy in F3 ATZ-derived males correspond to altered H3K4me3 occupancy of F1 generation and 74% of changed peaks in F3 generation are associated with enhancers. The regions with altered H3K4me3 occupancy are enriched in SP family and WT1 transcription factor binding sites. Our data suggest that the embryonic exposure to ATZ affects the development and the changes induced by ATZ are transferred up to three generations.

Rice (Oryza sativa) Laccases Involved in Modification and Detoxification of Herbicides Atrazine and Isoproturon Residues in Plants

Atrazine (ATR) and isoproturon (IPU) as herbicides have become serious environmental contaminants due to their overuse in crop production. Although ATR and IPU in soils are easily absorbed by many crops, the mechanisms for their degradation or detoxification in plants are poorly understood. This study identified a group of novel genes encoding laccases (EC 1.10.3.2) that are possibly involved in catabolism or detoxification of ATR and IPU residues in rice. Transcriptome profiling shows at least 22 differentially expressed laccase genes in ATR/IPU-exposed rice. Some of the laccase genes were validated by RT-PCR analysis. The biochemical properties of the laccases were analyzed, and their activities in rice were induced under ATR/IPU exposure. To investigate the roles of laccases in degrading or detoxifying ATR/IPU in rice, transgenic yeast cells (Pichia pastoris X-33) expressing two rice laccase genes (LOC_Os01g63180 and LOC_Os12g15680) were generated. Both transformants were found to accumulate less ATR/IPU compared to the control. The ATR/IPU-degraded products in the transformed yeast cells using UPLC-TOF-MS/MS were further characterized. Two metabolites, hydroxy-dehydrogenated atrazine (HDHA) and 2-OH-isopropyl-IPU, catalyzed by laccases were detected in the eukaryotic cells. These results indicate that the laccase-coding genes identified here could confer degradation or detoxification of the herbicides and suggest that the laccases could be one of the important enzymatic pathways responsible for ATR/IPU degradation/detoxification in rice.