Genome-wide transcriptome profiling of ROS scavenging and signal transduction pathways in rice (Oryza sativa L.) in response to different types of ionizing radiation

Reactive oxygen species may be involved in the distinctive biological effects of different doses of 12C6+ ion beams on Arabidopsis

Introduction

Heavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated by an increase in root and biomass, while 200 Gy irradiation significantly inhibited the growth of seedlings, causing a visible decrease in plant growth.

Methods

The Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels.

Results and discussion

Monte Carlo simulations revealed that high-dose irradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170 DEGs were present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cell wall homeostasis. Further GO enrichment of DEGs unique to 50 Gy and 200 Gy revealed 58 50Gy-exclusive DEGs were enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advances our insight into the biological effects of heavy ion irradiation and the underlying mechanisms.

Effect of low-dose ionizing radiation on spatiotemporal parameters of functional responses induced by electrical signals in tobacco plants

Plants growing under an increased radiation background may be exposed to additional stressors. Plant acclimatization is formed with the participation of stress signals that cause systemic responses-a change in the activity of physiological processes. In this work, we studied the mechanisms of the effect of ionizing radiation (IR) on the systemic functional responses induced by electrical signals. Chronic β-irradiation (31.3 μGy/h) have a positive effect on the morphometric parameters and photosynthetic activity of tobacco plants (Nicotiana tabacum L.) at rest. An additional stressor causes an electrical signal, which, when propagated, causes a temporary change in chlorophyll fluorescence parameters, reflecting a decrease in photosynthesis activity. Irradiation did not significantly affect the electrical signals. At the same time, more pronounced photosynthesis responses are observed in irradiated plants: both the amplitude and the leaf area covered by the reaction increase. The formation of such responses is associated with changes in pH and stomatal conductance, the role of which was analyzed under IR. Using tobacco plants expressing the fluorescent pH-sensitive protein Pt-GFP, it was shown that IR enhances signal-induced cytoplasmic acidification. It was noted that irradiation also disrupts the correlation between the amplitudes of the electrical signal, pH shifts, changes in chlorophyll fluorescence parameters. Also stronger inhibition of stomatal conductance by the signal was shown in irradiated plants. It was concluded that the effect of IR on the systemic response induced by the electrical signal is mainly due to its effect on the stage of signal transformation into the response.

Ionizing Radiation: Effective Physical Agents for Economic Crop Seed Priming and the Underlying Physiological Mechanisms

To overcome various factors that limit crop production and to meet the growing demand for food by the increasing world population. Seed priming technology has been proposed, and it is considered to be a promising strategy for agricultural sciences and food technology. This technology helps to curtail the germination time, increase the seed vigor, improve the seedling establishment, and enhance the stress tolerance, all of which are conducive to improving the crop yield. Meanwhile, it can be used to reduce seed infection for better physiological or phytosanitary quality. Compared to conventional methods, such as the use of water or chemical-based agents, X-rays, gamma rays, electron beams, proton beams, and heavy ion beams have emerged as promising physics strategies for seed priming as they are time-saving, more effective, environmentally friendly, and there is a greater certainty for yield improvement. Ionizing radiation (IR) has certain biological advantages over other seed priming methods since it generates charged ions while penetrating through the target organisms, and it has enough energy to cause biological effects. However, before the wide utilization of ionizing priming methods in agriculture, extensive research is needed to explore their effects on seed priming and to focus on the underlying mechanism of them. Overall, this review aims to highlight the current understanding of ionizing priming methods and their applicability for promoting agroecological resilience and meeting the challenges of food crises nowadays.

Molecular and Biochemical Analysis of Duplicated Cytosolic CuZn Superoxide Dismutases of Rice and in silico Analysis in Plants

Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous antioxidant metalloenzymes important for oxidative stress tolerance and cellular redox environment. Multiple factors have contributed toward the origin and diversity of SOD isoforms among different organisms. In plants, the genome duplication events, responsible for the generation of multiple gene copies/gene families, have also contributed toward the SOD diversity. However, the importance of such molecular events on the characteristics of SODs has not been studied well. This study investigated the effects of divergence on important characteristics of two block-duplicated rice cytosolic CuZn SODs (OsCSD1, OsCSD4), along with in silico assessment of similar events in other plants. The analysis revealed heterogeneity in gene length, regulatory regions, untranslated regions (UTRs), and coding regions of two OsCSDs. An inconsistency in the database-predicted OsCSD1 gene structure was also identified and validated experimentally. Transcript analysis showed differences in the basal levels and stress responsiveness of OsCSD1 and OsCSD4, and indicated the presence of two transcription start sites in the OsCSD1. At the amino acid level, the two OsCSDs showed differences at 18 sites; however, both exist as a homodimer, displaying typical CuZn SOD characteristics, and enhancing the oxidative stress tolerance of Escherichia coli cells. However, OsCSD4 showed higher specific activity as well as stability. The comparison of the two OsCSDs with reported thermostable CSDs from other plants identified regions likely to be associated with stability, while the homology modeling and superposition highlighted structural differences. The two OsCSDs displayed heteromeric interaction capability and forms an enzymatically active heterodimer (OsCSD1:OsCSD4) on co-expression, which may have significance as both are cytosolic. In silico analysis of 74 plant genomes revealed the prevalence of block duplications for multiple CSD copies (mostly cytosolic). The divergence and clustering analysis of CSDs suggested the possibility of an ancestral duplication event in monocots. Conserved SOD features indicating retention of SOD function among CSD duplicates were evident in few monocots and dicots. In most other species, the CSD copies lacked critical features and may not harbor SOD function; however, other feature-associated functions or novel functions might be present. These aspects of divergent CSD copies encoding co-localized CSDs may have implications in plant SOD functions in the cytosol and other organelles.

Biological Effect of Gamma Rays According to Exposure Time on Germination and Plant Growth in Wheat

Gamma rays as a type of ionizing radiation constitute a physical mutagen that induces mutations and could be effectively used in plant breeding. To compare the effects of gamma and ionizing irradiation according to exposure time in common wheat (Keumgang, IT 213100), seeds were exposed to 60Co gamma rays at different dose rates. To evaluate the amount of free radical content, we used electron spin resonance spectroscopy. Significantly more free radicals were generated in the case of long-term compared with short-term gamma-ray exposure at the same dose of radiation. Under short-term exposure, shoot and root lengths were slightly reduced compared with those of the controls, whereas long-term exposure caused severe growth inhibition. The expression of antioxidant-related and DNA-repair-related genes was significantly decreased under long-term gamma-ray exposure. Long-term exposure caused higher radiosensitivity than short-term exposure. The results of this study could help plant breeders select an effective mutagenic induction dose rate in wheat.

Responses of genes of DNA repair, alternative oxidase, and pro-/antioxidant state in Arabidopsis thaliana with altered expression of AOX1a to gamma irradiation

PURPOSE

High doses of gamma (γ) irradiation cause oxidative stress and DNA damage. Alternative oxidase (AOX) catalyzes the energy-dissipating cyanide-resistant alternative pathway in plant mitochondria and is an important part of the cellular defense network under stress conditions. In this study, Arabidopsis thaliana plants with an altered expression of the AOX1a gene were exposed by high dose-rate ionizing radiation to assess the expression of genes of DNA repair and pro-/antioxidant states to elucidate the functional significance of AOX in plant stress response.

MATERIALS AND METHODS

Five-week-old A. thaliana plants, either with basal AOX1a gene expression (wild-type Colombia-0 (Col-0)), antisense silencing of AOX1a (AS-12), and overexpression of the gene (XX-2), were γ-irradiated at a dose of 200 Gy. Gene expression and biochemical analyses were performed 12 h after irradiation.

RESULTS

Acute γ-irradiation caused different responses between the genotypes. XX-2 plants, either control or irradiated, showed the highest expression of AOX1a gene and AOX protein, and the lowest expression of DNA repair genes. Wild type and AS-12 plants exposed to γ-irradiation upregulated another stress-induced gene, AOX1d, and DNA repair genes. Furthermore, a higher activity of Mn-dependent superoxide dismutase (Mn-SOD) was observed in the irradiated AS-12 plants than in the untreated plants of this line. However, AS-12 plants were less effective than Col-0 plants in controlling the accumulation of the superoxide anion. XX-2 plants had the lowest reactive oxygen species (ROS) levels among the genotypes.

CONCLUSIONS

AS-12 plants display a compensatory mechanism by increasing the expression of AOX1d and the synthesis of the AOX protein, as well as by Mn-SOD activation. However, these were insufficient to maintain the background level of embryonic lethal mutations, and thereby the reproductive capacity. These results highlight the importance of AOX in the successful adaptation of plants to acute γ-irradiation, and indicate that AOX1a plays a key role in the regulation of the stress response.

Protective role of fat hen (Chenopodium album L.) extract and gamma irradiation treatments against fusarium root rot disease in sunflower plants

One of the most drastic diseases causing economic losses in sunflower crops is fusarium root rot caused by Fusarium solani. Plant extracts and ionizing radiation provide alternative environmentally safe control agents that have a significant role in controlling and overcoming this fungal plant pathogen. In the present study, the effect of different concentrations of aqueous Chenopodium album extract (2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5 and 6.0%) and gamma radiation at a dose of 6 Gy were examined for their efficacy in inducing resistance of sunflower plants against fusarium root rot caused by F. solani MG-3 by evaluation of some physiological and biochemical parameters of infected and healthy plants under greenhouse conditions. The pre-treatment of sunflower seeds with 6% C. album extract and 6 Gy gamma radiation reduced fusarium incidence from 47.49% to 28.25%. Also, nucleic acid content, ascorbic acid, α-tocopherol, anthocyanin, total flavonoids, proline, glycine betaine and lipid components significantly increased in irradiated infected plants treated with C. album extract, while H₂ O₂ content and lipid peroxidation markedly decreased as compared with healthy control plants. Moreover, treatment with gamma radiation reduced the amount of unsaturated fatty acids through accumulation of saturated fatty acids compared with non-irradiated plants; treatment with C. album extract also enhanced the content of unsaturated fatty acids, with a noticeable decrease in saturated fatty acid content. Hence, C. album extract and gamma radiation can be used to enhance biological control of fusarium root rot of sunflower plants.

Gamma radiation negatively impacted seed germination, seedling growth and antioxidant enzymes activities in tall fescue infected with Epichloë endophyte

Plants and their accompanying microorganisms growing in contaminated sites with long-lived gamma-emitting radionuclides may be affected by radiation stress. The present study aimed to investigate the effects of gamma radiation on symbiotic relationship between Epichloë endophyte and Festuca arundinacea plant along with the radio-sensitivity of a pair of clones of tall fescue with (E+) and without (E-) symbiotic Epichloë endophyte exposed to different doses of gamma radiation including 25, 50, 75, 100, 150, 200, 300, and 400 Gray (Gy) from a Cobalt-60 source. Both irradiated and non-irradiated seeds of each status were grown under controlled conditions. Seed germination indices, seedling growth and certain physiological criteria associated with plant responses to oxidative stress were examined. The results revealed that low doses (up to 75 Gy) of gamma radiation stimulated seed germination indices and seedling growth. However, high doses (100-400 Gy) significantly reduced the final germination percentage, germination rate index, coefficient of velocity of germination, and the seed reserve depletion percentage, and enhanced the mean germination time. Further, high doses of radiation reduced root and shoot lengths, root and shoot fresh weights, and activities of antioxidant enzymes (especially catalase and superoxide dismutase), and increased the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) of the seedlings. The results showed that the endophyte was present in seeds after gamma ray irradiation. However, the presence of endophyte in seedlings started to be reduced significantly (18.45% reduction rather than the control) at 50 Gy of gamma radiation. High doses (100 Gy and above) dramatically declined the presence of endophyte down to zero in seedlings compared to the control. In this study, the E- clone had higher seed germination and seedling growth as well as lower H2O2 and MDA contents under radiation stress as compared with the E+ clone. Additionally, shoot tolerance index (STI) indicated more radiation tolerance in the E- clone. According to the results of the present study, it is concluded that biological impacts of gamma radiation stress and the harmful effects on endophyte viability may cause more radio-sensitivity and changes in the growth and physio-biochemical aspects of the host plant.

A Comparison of the Transcriptomes of Cowpeas in Response to Two Different Ionizing Radiations

In this study, gene expression changes in cowpea plants irradiated by two different types of radiation: proton-beams and gamma-rays were investigated. Seeds of the Okdang cultivar were exposed to 100, 200, and 300 Gy of gamma-rays and proton-beams. In transcriptome analysis, the 32, 75, and 69 differentially expressed genes (DEGs) at each dose of gamma-ray irradiation compared with that of the control were identified. A total of eight genes were commonly up-regulated for all gamma-ray doses. However, there were no down-regulated genes. In contrast, 168, 434, and 387 DEGs were identified for each dose of proton-beam irradiation compared with that of the control. A total of 61 DEGs were commonly up-regulated for all proton-beam doses. As a result of GO and KEGG analysis, the ranks of functional categories according to the number of DEGs were not the same in both treatments and were more diverse in terms of pathways in the proton-beam treatments than gamma-ray treatments. The number of genes related to defense, photosynthesis, reactive oxygen species (ROS), plant hormones, and transcription factors (TF) that were up-/down-regulated was higher in the proton beam treatment than that in gamma ray treatment. Proton-beam treatment had a distinct mutation spectrum and gene expression pattern compared to that of gamma-ray treatment. These results provide important information on the mechanism for gene regulation in response to two ionizing radiations in cowpeas.

Integrated RNA-seq and Proteomic Studies Reveal Resource Reallocation towards Energy Metabolism and Defense in Skeletonema marinoi in Response to CO2 Increase

Rising atmospheric CO2 concentrations are causing ocean acidification (OA) with significant consequences for marine organisms. Because CO2 is essential for photosynthesis, the effect of elevated CO2 on phytoplankton is more complex and the mechanism is poorly understood. Here we applied RNA-seq and iTRAQ proteomics to investigate the impacts of CO2 increase (from ∼400 to 1000 ppm) on the temperate coastal marine diatom Skeletonema marinoi We identified 32,389 differentially expressed genes (DEGs) and 1,826 differentially expressed proteins (DEPs) from elevated CO2 conditions, accounting for 48.5% of total genes and 25.9% of total proteins we detected, respectively. Elevated pCO2 significantly inhibited the growth of S marinoi, and the 'omic' data suggested that this might be due to compromised photosynthesis in the chloroplast and raised mitochondrial energy metabolism. Furthermore, many genes/proteins associated with nitrogen metabolism, transcriptional regulation, and translational regulation were markedly up-regulated, suggesting enhanced protein synthesis. In addition, S marinoi exhibited higher capacity of ROS production and resistance to oxidative stress. Overall, elevated pCO2 seems to repress photosynthesis and growth of S marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.Importance Rising atmospheric CO2 concentrations are causing ocean acidification with significant consequences for marine organisms. Chain-forming centric diatoms of Skeletonema is one of the most successful groups of eukaryotic primary producers with widespread geographic distribution. Among the recognized 28 species, S. marinoi can be a useful model for investigating the ecological, genetic, physiological, and biochemical characteristics of diatoms in temperate coastal regions. In this study, we found that the elevated pCO2 seems to repress photosynthesis and growth of S. marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.

Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil-root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities or the composition of the rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to reverse any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impact on the investigated processes should be conducted.

Impact of Proton Beam Irradiation on the Growth and Biochemical Indexes of Barley (Hordeum vulgare L.) Seedlings Grown under Salt Stress

The present paper examines the effects of salt stress on the growth, pigments, lipid peroxidation and antioxidant ability of barley (Hordeum vulgare L.) seedlings raised from proton beam irradiated caryopses. In order to assess the effects of radiation on the early stages of plant growth and analyze its possible influence on the alleviation of salinity, 3 and 5 Gy doses were used on dried barley seeds and germination occurred in the presence/absence of NaCl (100 mM and 200 mM). After treatment, photosynthetic pigments increased in the 5 Gy variant, which registered a higher value than the control. Among the antioxidant enzymes studied (SOD, CAT, and POD) only CAT activity increased in proton beam irradiated seeds germinated under salinity conditions, which indicates the activation of antioxidant defense. The malondialdehyde (MDA) content declined with the increase of irradiation doses on seeds germinated at 200 mM NaCl. On the other hand, the concentration of 200 mM NaCl applied alone or combined with radiation revealed an increase in soluble protein content. The growth rate suggests that 3 Gy proton beam irradiation of barley seeds can alleviate the harmful effects of 100 mM NaCl salinity, given that seedlings' growth rate increased by 1.95% compared to the control.

Transcriptome Analysis Reveals Complex Defensive Mechanisms in Salt-Tolerant and Salt-Sensitive Shrub Willow Genotypes under Salinity Stress

Salinity stress is one of the most devastating abiotic stresses limiting plant growth and productivity. As a moderately salt-tolerant crop, shrub willow (Salix spp.) is widely distributed over the world and can provide multiple bioenergy product and environmental benefits. To delve into the salt tolerance mechanism and screen out salt-tolerant genes, two shrub willow cultivars (a salt-sensitive genotype JW9-6 and a salt-tolerant genotype JW2372) at three time points (0, 2, and 12 h) after NaCl treatments were used for RNA sequencing. A comparative analysis between genotypes and time points showed 1,706 differentially expressed genes (DEGs), of which 1,029 and 431 DEGs were only found in the JW9-6 and JW2372, respectively. Gene Ontology (GO) and MapMan annotations suggested that many DEGs were involved in various defense-related biological pathways, including cell wall integrity, hormone signaling, antioxidant system, heat shock proteins, and transcription factors. Compared to JW9-6, JW2372 contained more DEGs involved in the maintenance of the cell wall integrity, ABA, and ethylene signal transduction pathways. In addition, more DEGs encoding heat shock proteins were found in JW2372. Instead, transcription factors including ERF, MYB, NAC, and WRKY were found to be more differentially expressed in JW9-6 under salinity stress. Furthermore, expressions of nine randomly selected DEGs were verified by qRT-PCR analysis. This study contributes in new perspicacity into underlying the salt tolerance mechanism of a shrub willow at the transcriptome level and also provides numerous salt-tolerant genes for further genetic engineering and breeding purposes in the future.

Rocket Science: The Effect of Spaceflight on Germination Physiology, Ageing, and Transcriptome of Eruca sativa Seeds

In the 'Rocket Science' project, storage of Eruca sativa (salad rocket) seeds for six months on board the International Space Station resulted in delayed seedling establishment. Here we investigated the physiological and molecular mechanisms underpinning the spaceflight effects on dry seeds. We found that 'Space' seed germination vigor was reduced, and ageing sensitivity increased, but the spaceflight did not compromise seed viability and the development of normal seedlings. Comparative analysis of the transcriptomes (using RNAseq) in dry seeds and upon controlled artificial ageing treatment (CAAT) revealed differentially expressed genes (DEGs) associated with spaceflight and ageing. DEG categories enriched by spaceflight and CAAT included transcription and translation with reduced transcript abundances for 40S and 60S ribosomal subunit genes. Among the 'spaceflight-up' DEGs were heat shock proteins (HSPs), DNAJ-related chaperones, a heat shock factor (HSFA7a-like), and components of several DNA repair pathways (e.g., ATM, DNA ligase 1). The 'response to radiation' category was especially enriched in 'spaceflight-up' DEGs including HSPs, catalases, and the transcription factor HY5. The major finding from the physiological and transcriptome analysis is that spaceflight causes vigor loss and partial ageing during air-dry seed storage, for which space environmental factors and consequences for seed storage during spaceflights are discussed.

Mutagenesis in Rice: The Basis for Breeding a New Super Plant

The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.

Physiological consequences of gamma ray irradiation in tall fescue with elimination potential of Epichloë fungal endophyte

Perennial plants and their associated microorganisms grow in the areas that may be contaminated with long-lived gamma-emitting radionuclides. This will induce gamma stress response in plants and their accompanying microorganisms. The present work investigated the growth and physiological responses of Epichloe endophyte infected tall fescue to gamma radiation, as well as whether the endophyte could persist and infect the host plant once exposed to gamma radiation. Seeds of Iranian native genotype of 75B⁺ of tall fescue were exposed to different doses, including 5.0, 10.0, 15.0, 20.0, 30.0 and 40.0 krad of gamma ray from a ⁶⁰Co source. Irradiated and unirradiated seeds were sown in pots and grown under controlled conditions in the greenhouse. The growth and physiological parameters associated with plant tolerance to oxidative stress of host plants, as well as endophytic infection frequency (% of plants infected) and intensity (mean number of endophytic hyphae per the field of view), were examined in 3 months-old seedlings. The results indicated that all gamma radiation doses (except 5.0 kr) significantly reduced the height and survival percentage of the host plant. Days to the emergence of seedling increased gradually as gamma doses rose. A dose-rate dependent induction was seen for photosynthetic pigments and proline content. Malondialdehyde (MDA) content grew with elevation of irradiation doses. Depending on the dose and time, the activities of antioxidant enzymes in the host plant responded differently to gamma radiation. Gamma radiation altered the enzyme activities with sever decline in SOD and CAT activities. However, it had barely any effect on in APX and POD activities. The results also revealed that the persistence and intensity of endophyte were affected after gamma-ray irradiation. The initial percentage of tall fescue seeds infected with the endophyte was 91% in un-irradiated seeds. Presence of the viable endophyte started to decline significantly (23%) at 5.0 kr of gamma radiation. A dramatic reduction in the presence and intensity of endophyte occurred at 10.0 to 40.0 kr intensities. Gamma radiation × trait (GT)-biplot analysis indicated positive correlations between the endophyte symbiosis and antioxidant enzyme activities. Also, negative correlations were observed between the endophyte and MDA content in the host plant. Our results suggest that radiation stress (doses over 5.0 kr) caused reduction in the growth and antioxidant enzyme activities of the host plant that accompanied by a dramatic reduction in the persistence and intensity of endophyte fungi. Our findings have provided the basic information for future studies on the effect of gamma irradiation on the interaction between endophytic fungi and its host plant.

Effect of ionizing radiation on physiological and molecular processes in plants

The study of effects of ionizing radiation (IR) on plants is important in relation to several problems: (I) the existence of zones where background radiation - either natural or technogenic - is increased; (II) the problems of space biology; (III) the use of IR in agricultural selection; (IV) general biological problems related to the fundamental patterns and specifics of the effects of IR on various living organisms. By now, researchers have accumulated and systematized a large body of data on the effects of IR on the growth and reproduction of plants, as well as on the changes induced by IR at the genetic level. At the same time, there is a large gap in understanding the mechanisms of IR influence on the biochemical and physiological processes - despite the fact that these processes form the basis determining the manifestation of IR effects at the level of the whole organism. On the one hand, the activity of physiological processes determines the growth of plants; on the other, it is determined by changes at the genetic level. Thus, it is the study of IR effects at the physiological and biochemical levels that can give the most detailed and complex picture of IR action in plants. The review focuses on the effects of radiation on the essential physiological processes, including photosynthesis, respiration, long-distance transport, the functioning of the hormonal system, and various biosynthetic processes. On the basis of a large body of experimental data, we analyze dose and time dependences of the IR-induced effects - which are qualitatively similar - on various physiological and biochemical processes. We also consider the sequence of stages in the development of those effects and discuss their mechanisms, as well as the cause-effect relationships between them. The primary IR-induced physicochemical reactions include the formation of various forms of reactive oxygen species (ROS) and are the cause of the observed changes in the functional activity of plants. The review emphasizes the role of hydrogen peroxide, a long-lived ROS, not only as a damaging agent, but also as a mediator - a universal intracellular messenger, which provides for the mechanism of long-distance signaling. A supposition is made that IR affects physiological processes mainly by violating the regulation of their activity. The violation seems to become possible due to the fact that there exists a crosstalk between different signaling systems of plants, such as ROS, calcium, hormonal and electrical systems. As a result of both acute and chronic irradiation, an increase in the level of ROS can influence the activity of a wide range of physiological processes - by regulating them both at the genetic and physiological levels. To understand the ways, by which IR affects plant growth and development, one needs detailed knowledge about the mechanisms of the processes that occur at the (i) genetic and (ii) physiological levels, as well as their interplay and (iii) knowledge about regulation of these processes at different levels.

Regulation through MicroRNAs in Response to Low-Energy N+ Ion Irradiation in Oryza sativa

MicroRNAs (miRNAs) are a non-coding regulatory RNAs that play significant roles in plant growth and development, especially in the stress response. Low-energy ion radiation, a type of environmental stress, can cause multiple biological effects. To understand the roles of miRNAs in response to low-energy N⁺ ion radiation in Oryza sativa, high-throughput sequencing of small RNAs was carried out to detect the expression of miRNAs in the shoots of the rice after 2 × 10¹⁷ N+/cm² irradiation. The differentially expressed 28 known miRNAs were identified, 17 of these identified miRNAs were validated by real-time quantitative fluorescent PCR (q-PCR), including 9 up-regulated miRNAs (miR1320-3p, miR1320-5p, miR156b-3p, miR156c-5p, miR156c-3p/g-3p, miR1561-5p, miR398b and miR6250) and 8 down-regulated miRNAs (miR156a/e/i, miR156k, miR160f-5p, miR166j-5p, miR1846e and miR399d). In addition, 45 novel radiationresponsive miRNAs were predicted, and 8 of them were verified by q-PCR. The target genes of radiation-responsive miRNAs were predicted and gene function enrichment analysis was performed with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of 9 targets of 4 known miRNA families (miR156, miR399, miR1320 and miR398) and 2 targets of 2 novel miRNAs were quantified by q-PCR, and a strong negative regulation relation between miRNAs and their targets were observed. Those targets including SQUAMOSA promoterbinding-like protein (SPL) genes, copper/zinc superoxide dismutase (Cu/Zn-SOD), copper chaperone for SOD (CCS1) and electron transporter/ heat-shock protein binding protein (HSP), which are involved in growth and defense against various stresses, especially associated with reactive oxygen species (ROS) scavenging. This work provides important information for understanding the ROS generation and elimination mechanisms closely related to miRNAs in rice seedlings after low-energy N⁺ radiation exposure.

Biochemical and functional characterization of OsCSD3, a novel CuZn superoxide dismutase from rice

Superoxide dismutases (SODs, EC 1.15.1.1) belong to an important group of antioxidant metalloenzymes. Multiple SODs exist for scavenging of reactive oxygen species (ROS) in different cellular compartments to maintain an intricate ROS balance. The present study deals with molecular and biochemical characterization of CuZn SOD encoded by LOC_Os03g11960 (referred to as OsCSD3), which is the least studied among the four rice isozymes. The OsCSD3 showed higher similarity to peroxisomal SODs in plants. The OsCSD3 transcript was up-regulated in response to salinity, drought, and oxidative stress. Full-length cDNA encoding OsCSD3 was cloned and expressed in Escherichia coli and analyzed for spectral characteristics. UV (ultraviolet)–visible spectroscopic analysis showed evidences of d–d transitions, while circular dichroism analysis indicated high β-sheet content in the protein. The OsCSD3 existed as homodimer (∼36 kDa) with both Cu2+ and Zn2+ metal cofactors and was substantially active over a wide pH range (7.0–10.8), with optimum pH of 9.0. The enzyme was sensitive to diethyldithiocarbamate but insensitive to sodium azide, which are the characteristics features of CuZn SODs. The enzyme also exhibited bicarbonate-dependent peroxidase activity. Unlike several other known CuZn SODs, OsCSD3 showed higher tolerance to hydrogen peroxide and thermal inactivation. Heterologous overexpression of OsCSD3 enhanced tolerance of E. coli sod double-knockout (ΔsodA ΔsodB) mutant and wild-type strain against methyl viologen-induced oxidative stress, indicating the in vivo function of this enzyme. The results show that the locus LOC_Os03g11960 of rice encodes a functional CuZn SOD with biochemical characteristics similar to the peroxisomal isozymes.

ATM signals to AMPK to promote autophagy and positively regulate DNA damage in response to cadmium-induced ROS in mouse spermatocytes

Cadmium (Cd) is a toxic heavy metal and harmful to human health due to its ability to accumulate in organs. Previous studies have shown that Cd can induce DNA damage and autophagy. Autophagy can stabilize genetic material and DNA integrity. The aim of the present study was to determine the exact mechanism and role of autophagy induced by Cd in spermatozoa cells. Mouse spermatocyte-derived cells (GC-2) were treated with 20 μM Cd chloride for 24 h. The level of reactive oxygen species (ROS), DNA damage, autophagy and the expression of the molecular signaling pathway ATM/AMP-activated protein kinase (AMPK)/mTOR were determined. The results showed that Cd induced autophagy and DNA damage in GC-2 cells via ROS generation, and the autophagy signal pathway AMPK/mTOR was activated by ATM which is a DNA damage sensor. Melatonin, a well-known antioxidant, ameliorated DNA damage, and inhibited autophagy via the AMPK/mTOR signal pathway. Furthermore, after inhibition of autophagy by knockdown of AMPKα, increased DNA damage by Cd treatment was observed in GC-2 cells. These findings demonstrated the protective role of autophagy in DNA damage and suggested that the mechanism of autophagy induced by Cd was through the ATM/AMPK/mTOR signal pathway in spermatozoa cells.

Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies

Ecotoxicological research provides knowledge on ionising radiation-induced responses in different plant species. However, the sparse data currently available are mainly extracted from acute exposure treatments. To provide a better understanding of environmental exposure scenarios, the response to stress in plants must be followed in more natural relevant chronic conditions. We previously showed morphological and biochemical responses in Lemna minor plants continuously exposed for 7days in a dose-rate dependent manner. In this study responses on molecular (gene expression) and physiological (photosynthetic) level are evaluated in L. minor plants exposed to ionising radiation. To enable this, we examined the gene expression profiles of irradiated L. minor plants by using an RNA-seq approach. The gene expression data reveal indications that L. minor plants exposed at lower dose rates, can tolerate the exposure by triggering acclimation responses. In contrast, at the highest dose rate tested, a high number of genes related to antioxidative defense systems, DNA repair and cell cycle were differentially expressed suggesting that only high dose rates of ionising radiation drive L. minor plants into survival strategies. Notably, the photosynthetic process seems to be unaffected in L. minor plants among the tested dose rates. This study, supported by our earlier work, clearly indicates that plants shift from acclimation responses towards survival responses at increasing dose rates of ionising radiation.

Knocking down mitochondrial iron transporter (MIT) reprograms primary and secondary metabolism in rice plants

Iron (Fe) is an essential micronutrient for plant growth and development, and its reduced bioavailability strongly impairs mitochondrial functionality. In this work, the metabolic adjustment in the rice (Oryza sativa) mitochondrial Fe transporter knockdown mutant (mit-2) was analysed. Biochemical characterization of purified mitochondria from rice roots showed alteration in the respiratory chain of mit-2 compared with wild-type (WT) plants. In particular, proteins belonging to the type II alternative NAD(P)H dehydrogenases accumulated strongly in mit-2 plants, indicating that alternative pathways were activated to keep the respiratory chain working. Additionally, large-scale changes in the transcriptome and metabolome were observed in mit-2 rice plants. In particular, a strong alteration (up-/down-regulation) in the expression of genes encoding enzymes of both primary and secondary metabolism was found in mutant plants. This was reflected by changes in the metabolic profiles in both roots and shoots of mit-2 plants. Significant alterations in the levels of amino acids belonging to the aspartic acid-related pathways (aspartic acid, lysine, and threonine in roots, and aspartic acid and ornithine in shoots) were found that are strictly connected to the Krebs cycle. Furthermore, some metabolites (e.g. pyruvic acid, fumaric acid, ornithine, and oligosaccharides of the raffinose family) accumulated only in the shoot of mit-2 plants, indicating possible hypoxic responses. These findings suggest that the induction of local Fe deficiency in the mitochondrial compartment of mit-2 plants differentially affects the transcript as well as the metabolic profiles in root and shoot tissues.

Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis

In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.

Transcriptome analysis reveals that distinct metabolic pathways operate in salt-tolerant and salt-sensitive upland cotton varieties subjected to salinity stress

Salinity stress is one of the most devastating abiotic stresses in crop plants. As a moderately salt-tolerant crop, upland cotton (Gossypium hirsutum L.) is a major cash crop in saline areas and a suitable model for salt stress tolerance research. In this study, we compared the transcriptome changes between the salt-tolerant upland cotton cultivar Zhong 07 and salt-sensitive cultivar Zhong G5 in response to NaCl treatments. Transcriptional regulation, signal transduction and secondary metabolism in two varieties showed significant differences, all of which might be related to mechanisms underlying salt stress tolerance. The transcriptional profiles presented here provide a foundation for deciphering the mechanism underlying salt tolerance. Based on our findings, we proposed several candidate genes that might be used to improve salt tolerance in upland cotton.

Rice RING E3 ligase may negatively regulate gamma-ray response to mediate the degradation of photosynthesis-related proteins

In this study, our findings regarding the regulation of GA irradiation-induced OsGIRP1 in relation to the levels of photosynthesis-related proteins such as OsrbcL1 and OsrbcS1 and hypersensitive responses of overexpressing plants to GR irradiation provide insight into the molecular functions of OsGIRP1 as a negative regulator in response to the stress of radiation. The RING (Really Interesting New Gene) finger proteins are known to play crucial roles in various abiotic stresses in plants. Here, we report on RING finger E3 ligase, Oryza sativa gamma rays-induced RING finger protein1 gene (OsGIRP1), which is highly induced by gamma rays (GR) irradiation. In vitro ubiquitination assay demonstrated that a single amino acid substitution (OsGIRP1(C196A)) of the RING domain showed no E3 ligase activity, supporting the notion that the activity of most E3s is specified by a RING domain. We isolated at least 6 substrate proteins of OsGIRP1, including 2 Rubisco subunits, OsrbcL1 and OsrbcSl, via yeast two-hybridization and bimolecular fluorescence complementation assays. OsGIRP1 and its partner proteins were targeted to the cytosol and the cytosol or chloroplasts, respectively; however, florescence signals of the complexes with OsGIPR1 were observed in the cytosol. Protein degradation in cell extracts showed that OsGIRP1 mediates proteolysis of 2 substrates, OsrbcS1 and OsrbcL1, via the 26S proteasome degradation pathway. The Arabidopsis plants overexpressing OsGIRP1 clearly exhibited increased sensitivity to GR irradiation. These results might suggest that OsGIRP1 acts as a negative regulator of GR response to mediate the degradation of photosynthesis-related proteins.

Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Plants are exposed to a wide range of abiotic stresses (AS), which often occur in combination. Because physiological investigations typically focus on one stress, our understanding of unspecific stress responses remains limited. The plant redox homeostasis, i.e., the production and removal of reactive oxygen species (ROS), may be involved in many environmental stress conditions. Therefore, this study intended to identify genes, which are activated in diverse AS, focusing on ROS-related pathways. We conducted a meta-analysis (MA) of microarray experiments, focusing on rice. Transcriptome data were mined from public databases and fellow researchers, which represented 36 different experiments and investigated diverse AS, including ozone stress, drought, heat, cold, salinity, and mineral deficiencies/toxicities. To overcome the inherent artifacts of different MA methods, data were processed using Fisher, rOP, REM, and product of rank (GeneSelector), and genes identified by most approaches were considered as shared differentially expressed genes (DEGs). Two MA strategies were adopted: first, datasets were separated into shoot, root, and seedling experiments, and these tissues were analyzed separately to identify shared DEGs. Second, shoot and seedling experiments were classed into oxidative stress (OS), i.e., ozone and hydrogen peroxide treatments directly producing ROS in plant tissue, and other AS, in which ROS production is indirect. In all tissues and stress conditions, genes a priori considered as ROS-related were overrepresented among the DEGs, as they represented 4% of all expressed genes but 7-10% of the DEGs. The combined MA approach was substantially more conservative than individual MA methods and identified 1001 shared DEGs in shoots, 837 shared DEGs in root, and 1172 shared DEGs in seedlings. Within the OS and AS groups, 990 and 1727 shared DEGs were identified, respectively. In total, 311 genes were shared between OS and AS, including many regulatory genes. Combined co-expression analysis identified among those a cluster of 42 genes, many involved in the photosynthetic apparatus and responsive to drought, iron deficiency, arsenic toxicity, and ozone. Our data demonstrate the importance of redox homeostasis in plant stress responses and the power of MA to identify candidate genes underlying unspecific signaling pathways.

Transcriptome profiling of the spl5 mutant reveals that SPL5 has a negative role in the biosynthesis of serotonin for rice disease resistance

BACKGROUND

Rice mutant, spl5 (spotted leaf 5), has spontaneous hypersensitive-like lesions on its leaves and shows enhanced resistance to pathogens, indicating that SPL5 plays a role in programmed cell death (PCD) and disease resistance. To understand the molecular mechanism of SPL5 gene, we investigated the transcriptome profiles of the spl5 mutant leaves with few lesions (FL) and leaves with many lesions (ML) compared to the wild-type (WT) leaves respectively by microarray.

RESULTS

The data from microarray revealed that 243 and 896 candidate genes (Fold change ≥ 3.0) were up- or down-regulated in the spl5-FL and spl5-ML, respectively, and a large number of these genes involved in biotic defense responses or reactive oxygen species (ROS) metabolism. Interestingly, according to our microarray and real-time PCR assays, the expressions of a transcription factor OsWRKY14 and genes responsible for the biosynthesis of serotonin, anthranilate synthase (AS), indole-3-glycerolphosphate synthase (IGPS), tryptophan synthase (TS) and tryptophan decarboxylase (TDC) were significantly up-regulated in the spl5 mutant. It has been reported previously that TS and TDC expressions are regulated by OsWRKY14 in rice, which raises the possibility that OsWRKY14 regulates serotonin production through the up-regulation of TS and TDC. Our HPLC analysis further confirmed that serotonin levels were higher in the leaves of spl5 mutant than that in WT.

CONCLUSIONS

Since the serotonin plays a critical role in inducing disease-resistance, the increased serotonin level may contribute, at least partly, to the disease resistance in spl5. The SPL5 gene may act as a negative regulatory factor activating the serotonin metabolic pathway, and these results might provide a new insight into the spl5-induced defense response mechanisms in plants.

Transcriptomic analysis of rice in response to iron deficiency and excess

BACKGROUND

Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe.

RESULTS

We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots.

CONCLUSION

These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.

Physiological changes and anti-oxidative responses of Arabidopsis plants after acute and chronic γ-irradiation

To identify the effects of acute and chronic γ-irradiation in Arabidopsis plants, physiological responses and antioxidant-related gene expression were investigated. Seedlings were exposed to 200 Gy of γ-irradiation in acute manner for 1 or 24 h (A1 and A24) or in chronic manner for 1, 2, or 3 weeks (C1 W, C2 W, and C3 W). Plant height, silique number, and silique length in A1 and A24 irradiated plants were significantly reduced when compared to non-irradiated plants. Silique number decreased in response to both acute and chronic irradiation, except with the C3 W treatment, and the number of trichomes dramatically increased in A1 and C1 W. Electron spin resonance signal intensities increased in A1 and in all chronically irradiated plants, but decreased in the A24-treated plant. To investigate the effects of acute and chronic γ-irradiation on antioxidant enzymes, we examined activity of four antioxidant enzymes: catalase (CAT), peroxidase (POD), ascorbate peroxidase, and superoxide dismutase. In general, POD and CAT activities decreased in response to acute and chronic γ-irradiation. Oligonucleotide microarrays were used to investigate transcriptional changes after irradiation. Several genes related to reactive oxygen species signaling were up-regulated after acute and chronic exposure, including genes encoding heat shock factors, zinc finger proteins, NADPH oxidase, WRKY DNA-binding proteins, and calcium binding proteins. Taken together, our data indicate that the responses and activation of antioxidant systems prompted by irradiation exposure are dependent upon the γ-ray dose rate.

Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica)

Radiation has been efficiently used for rice germplasm innovation. However, the molecular mechanisms by which radiation induces mutations are still unclear. In this study, we performed whole genome sequencing to reveal the comprehensive mutations in rice treated with radiation. Red-1 (a rice rich in beneficial ingredients for human health) was derived from rice 9311 after γ-radiation. Solexa sequencing technology was applied to uncover the mutations. Compared with the 9311 genome, 9.19% of genome sequences were altered in the Red-1 genome. Among these alterations, there were 381,403 SNPs, 50,116 1-5 bp Indels, 1279 copy number variations, and 10,026 presence/absence variations. These alterations were located in 14,493 genes, the majority of which contained a kinase domain, leucine rich repeats, or Cyt_P450. Point mutations were the main type of variation in the Red-1 genome. Gene ontology clustering revealed that genes that are associated with cell components, binding function, catalytic activity and metabolic processes were susceptible to γ-radiation. It was also predicted that 8 mutated genes were involved in the biosynthetic pathways of beneficial products or pigment accumulation. We conclude that genome-wide analysis of mutations provides novel insights into the mechanisms by which radiation improves the beneficial ingredients in rice Red-1.

Is gene transcription involved in seed dry after-ripening?

Orthodox seeds are living organisms that survive anhydrobiosis and may display dormancy, an inability to germinate at harvest. Seed germination potential can be acquired during a prolonged period of dry storage called after-ripening. The aim of this work was to determine if gene transcription is an underlying regulatory mechanism for dormancy alleviation during after-ripening. To identify changes in gene transcription strictly associated with the acquisition of germination potential but not with storage, we used seed storage at low relative humidity that maintains dormancy as control. Transcriptome profiling was performed using DNA microarray to compare change in gene transcript abundance between dormant (D), after-ripened non-dormant (ND) and after-ripened dormant seeds (control, C). Quantitative real-time polymerase chain reaction (qPCR) was used to confirm gene expression. Comparison between D and ND showed the differential expression of 115 probesets at cut-off values of two-fold change (p<0.05). Comparisons between both D and C with ND in transcript abundance showed that only 13 transcripts, among 115, could be specific to dormancy alleviation. qPCR confirms the expression pattern of these transcripts but without significant variation between conditions. Here we show that sunflower seed dormancy alleviation in the dry state is not related to regulated changes in gene expression.

Synergistic exposure of rice seeds to different doses of γ-ray and salinity stress resulted in increased antioxidant enzyme activities and gene-specific modulation of TC-NER pathway

Recent reports have underlined the potential of gamma (γ)-rays as tools for seed priming, a process used in seed industry to increase seed vigor and to enhance plant tolerance to biotic/abiotic stresses. However, the impact of γ -rays on key aspects of plant metabolism still needs to be carefully evaluated. In the present study, rice seeds were challenged with different doses of γ -rays and grown in absence/presence of NaCl to assess the impact of these treatments on the early stages of plant life. Enhanced germination efficiency associated with increase in radicle and hypocotyl length was observed, while at later stages no increase in plant tolerance to salinity stress was evident. APX, CAT, and GR were enhanced at transcriptional level and in terms of enzyme activity, indicating the activation of antioxidant defence. The profiles of DNA damage accumulation were obtained using SCGE and the implication of TC-NER pathway in DNA damage sensing and repair mechanisms is discussed. OsXPB2, OsXPD, OsTFIIS, and OsTFIIS-like genes showed differential modulation in seedlings and plantlets in response to γ -irradiation and salinity stress. Altogether, the synergistic exposure to γ -rays and NaCl resulted in enhanced oxidative stress and proper activation of antioxidant mechanisms, thus being compatible with plant survival.

The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.