Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana

Functions of nitric oxide-mediated post-translational modifications under abiotic stress

Environmental conditions greatly impact plant growth and development. In the current context of both global climate change and land degradation, abiotic stresses usually lead to growth restriction limiting crop production. Plants have evolved to sense and respond to maximize adaptation and survival; therefore, understanding the mechanisms involved in the different converging signaling networks becomes critical for improving plant tolerance. In the last few years, several studies have shown the plant responses against drought and salinity, high and low temperatures, mechanical wounding, heavy metals, hypoxia, UV radiation, or ozone stresses. These threats lead the plant to coordinate a crosstalk among different pathways, highlighting the role of phytohormones and reactive oxygen and nitrogen species (RONS). In particular, plants sense these reactive species through post-translational modification (PTM) of macromolecules such as nucleic acids, proteins, and fatty acids, hence triggering antioxidant responses with molecular implications in the plant welfare. Here, this review compiles the state of the art about how plant systems sense and transduce this crosstalk through PTMs of biological molecules, highlighting the S-nitrosylation of protein targets. These molecular mechanisms finally impact at a physiological level facing the abiotic stressful traits that could lead to establishing molecular patterns underlying stress responses and adaptation strategies.

Coordinated regulation of the mitochondrial retrograde response by circadian clock regulators and ANAC017

Mitochondrial retrograde signaling (MRS) supports photosynthetic function under a variety of conditions. Induction of mitochondrial dysfunction with myxothiazol (a specific inhibitor of the mitochondrial bc₁ complex) or antimycin A (an inhibitor of the mitochondrial bc₁ complex and cyclic electron transport in the chloroplast under light conditions) in the light and dark revealed diurnal control of MRS. This was evidenced by (1) significantly enhanced binding of ANAC017 to promoters in the light compared with the dark in Arabidopsis plants treated with myxothiazol (but not antimycin A), (2) overlap in the experimentally determined binding sites for ANAC017 and circadian clock regulators in the promoters of ANAC013 and AOX1a, (3) a diurnal expression pattern for ANAC017 and transcription factors it regulates, (4) altered expression of ANAC017-regulated genes in circadian clock mutants with and without myxothiazol treatment, and (5) a decrease in the magnitude of LHY and CCA1 expression in an ANAC017-overexpressing line and protein-protein interaction between ANAC017 and PIF4. This study also shows a large difference in transcriptome responses to antimycin A and myxothiazol in the dark: these responses are ANAC017 independent, observed in shoots and roots, similar to biotic challenge and salicylic acid responses, and involve ERF and ZAT transcription factors. This suggests that antimycin A treatment stimulates a second MRS pathway that is mediated or converges with salicylic acid signaling and provides a merging point with chloroplast retrograde signaling.

High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis

Callus induction, which results in fate transition in plant cells, is considered as the first and key step for plant regeneration. This process can be stimulated in different tissues by a callus-inducing medium (CIM), which contains a high concentration of phytohormone auxin. Although a few key regulators for callus induction have been identified, the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation. Here, we find that high auxin induces callus through a H3K36 histone methylation-dependent mechanism, which requires the methyltransferase SET DOMAIN GROUP 8 (SDG8). During callus induction, the increased auxin accumulates SDG8 expression through a TIR1/AFBs-based transcriptional regulation. SDG8 then deposits H3K36me3 modifications on the loci of callus-related genes, including a master regulator WOX5 and the cell proliferation-related genes, such as CYCB1.1. This epigenetic regulation in turn is required for the transcriptional activation of these genes during callus formation. These findings suggest that the massive transcriptional reprogramming for cell fate transition by auxin during callus formation requires epigenetic modifications including SDG8-mediated histone H3K36 methylation. Our results provide insight into the coordination between auxin signaling and epigenetic regulation during fundamental processes in plant development.

Ozone and nitrogen dioxide regulate similar gene expression responses in Arabidopsis but natural variation in the extent of cell death is likely controlled by different genetic loci

High doses of ozone (O3) and nitrogen dioxide (NO2) cause damage and cell death in plants. These two gases are among the most harmful air pollutants for ecosystems and therefore it is important to understand how plant resistance or sensitivity to these gases work at the molecular level and its genetic control. We compared transcriptome data from O3 and NO2 fumigations to other cell death related treatments, as well as individual marker gene transcript level in different Arabidopsis thaliana accessions. Our analysis revealed that O3 and NO2 trigger very similar gene expression responses that include genes involved in pathogen resistance, cell death and ethylene signaling. However, we also identified exceptions, for example RBOHF encoding a reactive oxygen species producing RESPIRATORY BURST OXIDASE PROTEIN F. This gene had increased transcript levels by O3 but decreased transcript levels by NO2, showing that plants can identify each of the gases separately and activate distinct signaling pathways. To understand the genetics, we conducted a genome wide association study (GWAS) on O3 and NO2 tolerance of natural Arabidopsis accessions. Sensitivity to both gases seem to be controlled by several independent small effect loci and we did not find an overlap in the significantly associated regions. Further characterization of the GWAS candidate loci identified new regulators of O3 and NO2 induced cell death including ABH1, a protein that functions in abscisic acid signaling, mRNA splicing and miRNA processing. The GWAS results will facilitate further characterization of the control of programmed cell death and differences between oxidative and nitrosative stress in plants.

Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines

We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, and NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73-Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the nested association mapping pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long-term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.

Simultaneous Ozone and High Light Treatments Reveal an Important Role for the Chloroplast in Co-ordination of Defense Signaling

Plants live in a world of changing environments, where they are continuously challenged by alternating biotic and abiotic stresses. To transfer information from the environment to appropriate protective responses, plants use many different signaling molecules and pathways. Reactive oxygen species (ROS) are critical signaling molecules in the regulation of plant stress responses, both inside and between cells. In natural environments, plants can experience multiple stresses simultaneously. Laboratory studies on stress interaction and crosstalk at regulation of gene expression, imply that plant responses to multiple stresses are distinctly different from single treatments. We analyzed the expression of selected marker genes and reassessed publicly available datasets to find signaling pathways regulated by ozone, which produces apoplastic ROS, and high light treatment, which produces chloroplastic ROS. Genes related to cell death regulation were differentially regulated by ozone versus high light. In a combined ozone + high light treatment, the light treatment enhanced ozone-induced cell death in leaves. The distinct responses from ozone versus high light treatments show that plants can activate stress signaling pathways in a highly precise manner.

Ozone responses in Arabidopsis: beyond stomatal conductance

Tropospheric ozone (O3) is a major air pollutant that decreases yield of important crops worldwide. Despite long-lasting research of its negative effects on plants, there are many gaps in our knowledge on how plants respond to O3. In this study, we used natural variation in the model plant Arabidopsis (Arabidopsis thaliana) to characterize molecular and physiological mechanisms underlying O3 sensitivity. A key parameter in models for O3 damage is stomatal uptake. Here we show that the extent of O3 damage in the sensitive Arabidopsis accession Shahdara (Sha) does not correspond with O3 uptake, pointing toward stomata-independent mechanisms for the development of O3 damage. We compared tolerant (Col-0) versus sensitive accessions (Sha, Cvi-0) in assays related to photosynthesis, cell death, antioxidants, and transcriptional regulation. Acute O3 exposure increased cell death, development of lesions in the leaves, and decreased photosynthesis in sensitive accessions. In both Sha and Cvi-0, O3-induced lesions were associated with decreased maximal chlorophyll fluorescence and low quantum yield of electron transfer from Photosystem II to plastoquinone. However, O3-induced repression of photosynthesis in these two O3-sensitive accessions developed in different ways. We demonstrate that O3 sensitivity in Arabidopsis is influenced by genetic diversity given that Sha and Cvi-0 developed accession-specific transcriptional responses to O3. Our findings advance the understanding of plant responses to O3 and set a framework for future studies to characterize molecular and physiological mechanisms allowing plants to respond to high O3 levels in the atmosphere as a result of high air pollution and climate change.

Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce

Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

Effects of ozone treatment on the antioxidant capacity of postharvest strawberry

Strawberries are highly popular around the world because of their juicy flesh and unique taste. However, they are delicate and extremely susceptible to peroxidation of their membrane lipids during storage, which induces water loss and rotting of the fruit. This study investigated the effects of ozone treatment on the physiological traits, active oxygen metabolism, and the antioxidant properties of postharvest strawberry. The results revealed that the weight loss (WL) and respiration rate (RR) of strawberry were inhibited by ozone treatment (OT), while the decline of firmness (FIR) and total soluble solids (TSS) were delayed. Ozone also reduced the generation rate of superoxide radical anions , and the content of hydrogen peroxide (H₂O₂) enhanced the activity of superoxidase (SOD), catalase (CAT), ascorbate peroxidase (APX), and monodehydroascorbate reductase (MDHAR), as well as promoted the accumulation of ascorbic acid (ASA), glutathione (GSH), and ferric reducing/antioxidant power (FRAP). In addition, a total of 29 antioxidant-related proteins were changed between the OT group and control (CK) group as detected by label-free proteomics during the storage time, and the abundance associated with ASA–GSH cycle was higher in the OT group at the later stage of storage, and the qRT-PCR results were consistent with those of proteomics. The improvement of the antioxidant capacity of postharvest strawberry treated with ozone may be achieved by enhancing the activity of the antioxidant enzymes and increasing the expression of the antioxidant proteins related to the ascorbic acid–glutathione (ASA–GSH) cycle.

Strawberries are highly popular around the world because of their juicy flesh and unique taste.

How does Malus crabapple resist ozone? Transcriptomics and metabolomics analyses

Ozone (O₃), an oxidizing toxic air pollutant, is ubiquitous in industrialized and developing countries. To understand the effects of O₃ exposure on apple (Malus) and to explore its defense mechanisms, we exposed 'Hongjiu' crabapple to O₃ and monitored its responses using physiological, transcriptomics, and metabolomics analyses. Exposure to 300 nL L^-1 O₃ for 3 h caused obvious damage to the leaves of Malus crabapple, affected chlorophyll and anthocyanin contents, and activated antioxidant enzymes. The gene encoding phospholipase A was highly responsive to O₃ in Malus crabapple. McWRKY75 is a key transcription factor in the response to O₃ stress, and its transcript levels were positively correlated with those of flavonoid-related structural genes (McC4H, McDFR, and McANR). The ethylene response factors McERF019 and McERF109-like were also up-regulated by O₃. Exogenous methyl jasmonate (MeJA) decreased the damaging effects of O₃ on crabapple and was most effective at 200 μmol L ^-1. Treatments with MeJA altered the metabolic pathways of crabapple under O₃ stress. In particular, MeJA activated the flavonoid metabolic pathway in Malus, which improved its resistance to O₃ stress.

Genetic controls of short- and long-term stomatal CO2 responses in Arabidopsis thaliana

BACKGROUND AND AIMS

The stomatal conductance (gs) of most plant species decreases in response to elevated atmospheric CO2 concentration. This response could have a significant impact on plant water use in a future climate. However, the regulation of the CO2-induced stomatal closure response is not fully understood. Moreover, the potential genetic links between short-term (within minutes to hours) and long-term (within weeks to months) responses of gs to increased atmospheric CO2 have not been explored.

METHODS

We used Arabidopsis thaliana recombinant inbred lines originating from accessions Col-0 (strong CO2 response) and C24 (weak CO2 response) to study short- and long-term controls of gs. Quantitative trait locus (QTL) mapping was used to identify loci controlling short- and long-term gs responses to elevated CO2, as well as other stomata-related traits.

KEY RESULTS

Short- and long-term stomatal responses to elevated CO2 were significantly correlated. Both short- and long-term responses were associated with a QTL at the end of chromosome 2. The location of this QTL was confirmed using near-isogenic lines and it was fine-mapped to a 410-kb region. The QTL did not correspond to any known gene involved in stomatal closure and had no effect on the responsiveness to abscisic acid. Additionally, we identified numerous other loci associated with stomatal regulation.

CONCLUSIONS

We identified and confirmed the effect of a strong QTL corresponding to a yet unknown regulator of stomatal closure in response to elevated CO2 concentration. The correlation between short- and long-term stomatal CO2 responses and the genetic link between these traits highlight the importance of understanding guard cell CO2 signalling to predict and manipulate plant water use in a world with increasing atmospheric CO2 concentration. This study demonstrates the power of using natural variation to unravel the genetic regulation of complex traits.

Transcriptome profiles of Quercus rubra responding to increased O3 stress

BACKGROUND

Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression.

RESULTS

RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.

CONCLUSION

This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.

Differential role of MAX2 and strigolactones in pathogen, ozone, and stomatal responses

Strigolactones are a group of phytohormones that control developmental processes including shoot branching and various plant-environment interactions in plants. We previously showed that the strigolactone perception mutant more axillary branches 2 (max2) has increased susceptibility to plant pathogenic bacteria. Here we show that both strigolactone biosynthesis (max3 and max4) and perception mutants (max2 and dwarf14) are significantly more sensitive to Pseudomonas syringae DC3000. Moreover, in response to P. syringae infection, high levels of SA accumulated in max2 and this mutant was ozone sensitive. Further analysis of gene expression revealed no major role for strigolactone in regulation of defense gene expression. In contrast, guard cell function was clearly impaired in max2 and depending on the assay used, also in max3, max4, and d14 mutants. We analyzed stomatal responses to stimuli that cause stomatal closure. While the response to abscisic acid (ABA) was not impaired in any of the mutants, the response to darkness and high CO2 was impaired in max2 and d14-1 mutants, and to CO2 also in strigolactone synthesis (max3, max4) mutants. To position the role of MAX2 in the guard cell signaling network, max2 was crossed with mutants defective in ABA biosynthesis or signaling. This revealed that MAX2 acts in a signaling pathway that functions in parallel to the guard cell ABA signaling pathway. We propose that the impaired defense responses of max2 are related to higher stomatal conductance that allows increased entry of bacteria or air pollutants like ozone. Furthermore, as MAX2 appears to act in a specific branch of guard cell signaling (related to CO2 signaling), this protein could be one of the components that allow guard cells to distinguish between different environmental conditions.

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.

Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana

This research was undertaken to investigate the global role of the plant inositol phosphorylceramide synthase (IPCS), a non-mammalian enzyme previously shown to be associated with the pathogen response. RNA-Seq analyses demonstrated that over-expression of inositol phosphorylceramide synthase isoforms AtIPCS1, 2 or 3 in Arabidopsis thaliana resulted in the down-regulation of genes involved in plant response to pathogens. In addition, genes associated with the abiotic stress response to salinity, cold and drought were found to be similarly down-regulated. Detailed analyses of transgenic lines over-expressing AtIPCS1-3 at various levels revealed that the degree of down-regulation is specifically correlated with the level of IPCS expression. Singular enrichment analysis of these down-regulated genes showed that AtIPCS1-3 expression affects biological signaling pathways involved in plant response to biotic and abiotic stress. The up-regulation of genes involved in photosynthesis and lipid localization was also observed in the over-expressing lines.

To defend or to grow: lessons from Arabidopsis C24

The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.

Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation

Auxin-induced callus formation represents an important cell reprogramming process during in vitro regeneration of plants, in which the pericycle or pericycle-like cells within plant organs are reprogrammed into the pluripotent cell mass termed callus that is generally required for subsequent regeneration of root or shoot. However, the molecular events behind cell reprogramming during auxin-induced callus formation are largely elusive. We previously identified that auxin-induced LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors act as the master regulators to trigger auxin-induced callus formation. Here, by ChIP-seq (chromatin immunoprecipitation-based sequencing) and RNA sequencing approaches, we identified the potential LBD29 target genes at the genome-wide level and outlined the molecular events of LBD-triggered cell reprogramming during callus formation. We showed that LBD29 preferentially bound to the G-box (CACGTG) and TGGGC[C/T] motifs and potentially targeted >350 genes, among which the genes related to methylation, reactive oxygen species (ROS) metabolism, cell wall hydrolysis and lipid metabolism were rapidly activated, while most of the light-responsive genes were suppressed by LBD29. Further examination of a few representative genes validated that they were targeted by LBD29 and participated in the regulation of cell reprogramming during callus formation. Our data not only outline a framework of the early molecular events behind auxin-induced cell reprogramming of callus formation, but also provide a valuable resource for identification of genes that regulate cell fate switch during in vitro regeneration of plants.

Interaction points in plant stress signaling pathways

Plants live in a world where they are challenged by abiotic and biotic stresses. In response to unfavorable conditions or an acute challenge like a pathogen attack, plants use various signaling pathways that regulate expression of defense genes and other mechanisms to provide resistance or stress adaptation. Identification of the regulatory steps in defense signaling has seen much progress in recent years. Many of the identified signaling pathways show interactions with each other, exemplified by the modulation of the jasmonic acid response by salicylic acid. Accordingly, defense regulation is more appropriately thought of as a web of interactions, rather than linear pathways. Here we describe various regulatory components and how they interact to provide an appropriate defense response. One of the common assays to monitor the output of defense signaling, as well as interaction between signaling pathways, is the measurement of altered gene expression. We illustrate that, while this is a suitable assay to monitor defense regulation, it can also inadvertently provide overstated conclusions about interaction among signaling pathways.

Natural variation of life-history traits, water use, and drought responses in Arabidopsis

The ability of plants to acquire and use water is critical in determining life-history traits such as growth, flowering, and allocation of biomass into reproduction. In this context, a combination of functionally linked traits is essential for plants to respond to environmental changes in a coordinated fashion to maximize resource use efficiency. We analyzed different water-use traits in Arabidopsis ecotypes to identify functionally linked traits that determine water use and plant growth performance. Water-use traits measured were (i) leaf-level water-use efficiency (WUE i ) to evaluate the amount of CO 2 fixed relative to water loss per leaf area and (ii) short-term plant water use at the vegetative stage (VWU) as a measure of whole-plant transpiration. Previously observed phenotypic variance in VWU, WUE i and life-history parameters, highlighted C24 as a valuable ecotype that combined drought tolerance, preferential reproductive biomass allocation, high WUE i , and reduced water use. We therefore screened 35 Arabidopsis ecotypes for these parameters, in order to assess whether the phenotypic combinations observed in C24 existed more widely within Arabidopsis ecotypes. All parameters were measured on a short dehydration cycle. A segmented regression analysis was carried out to evaluate the plasticity of the drought response and identified the breakpoint as a reliable measure of drought sensitivity. VWU was largely dependent on rosette area, but importantly the drought sensitivity and plasticity measures were independent of the transpiring leaf surface. A breakpoint at high rSWC indicated a more drought-sensitive plant that closed stomata early during the dehydration cycle and consequently showed stronger plasticity in leaf-level WUE i parameters. None of the sensitivity, plasticity, or water-use measurements were able to predict the overall growth performance; however, there was a general trade-off between vegetative and reproductive biomass. PCA and hierarchical clustering revealed that C24 was unique among the 35 ecotypes in uniting all the beneficial water use and stress tolerance traits, while also maintaining above average plant growth. We propose that a short dehydration cycle, measuring drought sensitivity and VWU is a fast and reliable screen for plant water use and drought response strategies.

Transcriptomic analysis of Pak Choi under acute ozone exposure revealed regulatory mechanism against ozone stress

BACKGROUND

Ground-level ozone (O3) is one of the major air pollutants, which cause oxidative injury to plants. The physiological and biochemical mechanisms underlying the responses of plants to O3 stress have been well investigated. However, there are limited reports about the molecular basis of plant responses to O3. In this study, a comparative transcriptomic analysis of Pak Choi (Brassica campestris ssp. chinensis) exposed to different O3 concentrations was conducted for the first time.

RESULTS

Seedlings of Pak Choi with five leaves were exposed to non-filtered air (NF, 31 ppb) or elevated O3 (E-O3, 252 ppb) for 2 days (8 h per day, from 9:00-17:00). Compared with plants in the NF, a total of 675 differentially expressed genes (DEGs) were identified in plants under E-O3, including 219 DEGs with decreased expressions and 456 DEGs with increased expressions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that O3 stress invoked multiple cellular defense pathways to mitigate the impaired cellular integrity and metabolism, including 'glutathione metabolism', 'phenylpropanoid biosynthesis', 'sulfur metabolism', 'glucosinolate biosynthesis', 'cutin, suberine and wax biosynthesis' and others. Transcription factors potentially involved in this cellular regulation were also found, such as AP2-ERF, WRKY, JAZ, MYB etc. Based on the RNA-Seq data and previous studies, a working model was proposed integrating O3 caused reactive oxygen burst, oxidation-reduction regulation, jasmonic acid and downstream functional genes for the regulation of cellular homeostasis after acute O3 stress.

CONCLUSION

The present results provide a valuable insight into the molecular responses of Pak Choi to acute O3 stress and the specific DEGs revealed in this study could be used for further functional identification of key allelic genes determining the O3 sensitivity of Pak Choi.

Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress

Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.

Current and future ozone risks to global terrestrial biodiversity and ecosystem processes

Risks associated with exposure of individual plant species to ozone (O3) are well documented, but implications for terrestrial biodiversity and ecosystem processes have received insufficient attention. This is an important gap because feedbacks to the atmosphere may change as future O3 levels increase or decrease, depending on air quality and climate policies. Global simulation of O3 using the Community Earth System Model (CESM) revealed that in 2000, about 40% of the Global 200 terrestrial ecoregions (ER) were exposed to O3 above thresholds for ecological risks, with highest exposures in North America and Southern Europe, where there is field evidence of adverse effects of O3, and in central Asia. Experimental studies show that O3 can adversely affect the growth and flowering of plants and alter species composition and richness, although some communities can be resilient. Additional effects include changes in water flux regulation, pollination efficiency, and plant pathogen development. Recent research is unraveling a range of effects belowground, including changes in soil invertebrates, plant litter quantity and quality, decomposition, and nutrient cycling and carbon pools. Changes are likely slow and may take decades to become detectable. CESM simulations for 2050 show that O3 exposure under emission scenario RCP8.5 increases in all major biomes and that policies represented in scenario RCP4.5 do not lead to a general reduction in O3 risks; rather, 50% of ERs still show an increase in exposure. Although a conceptual model is lacking to extrapolate documented effects to ERs with limited or no local information, and there is uncertainty about interactions with nitrogen input and climate change, the analysis suggests that in many ERs, O3 risks will persist for biodiversity at different trophic levels, and for a range of ecosystem processes and feedbacks, which deserves more attention when assessing ecological implications of future atmospheric pollution and climate change.

Dissecting Abscisic Acid Signaling Pathways Involved in Cuticle Formation

The cuticle is the outer physical barrier of aerial plant surfaces and an important interaction point between plants and the environment. Many environmental stresses affect cuticle formation, yet the regulatory pathways involved remain undefined. We used a genetics and gene expression analysis in Arabidopsis thaliana to define an abscisic acid (ABA) signaling loop that positively regulates cuticle formation via the core ABA signaling pathway, including the PYR/PYL receptors, PP2C phosphatase, and SNF1-Related Protein Kinase (SnRK) 2.2/SnRK2.3/SnRK2.6. Downstream of the SnRK2 kinases, cuticle formation was not regulated by the ABA-responsive element-binding transcription factors but rather by DEWAX, MYB16, MYB94, and MYB96. Additionally, low air humidity increased cuticle formation independent of the core ABA pathway and cell death/reactive oxygen species signaling attenuated expression of cuticle-biosynthesis genes. In Physcomitrella patens, exogenous ABA suppressed expression of cuticle-related genes, whose Arabidopsis orthologs were ABA-induced. Hence, the mechanisms regulating cuticle formation are conserved but sophisticated in land plants. Signaling specifically related to cuticle deficiency was identified to play a major role in the adaptation of ABA signaling pathway mutants to increased humidity and in modulating their immunity to Botrytis cinerea in Arabidopsis. These results define a cuticle-specific downstream branch in the ABA signaling pathway that regulates responses to the external environment.

Roles of Defense Hormones in the Regulation of Ozone-Induced Changes in Gene Expression and Cell Death

Apoplast, the diffusional space between plant cell plasma membranes, is an important medium for signaling within and between the cells. Apoplastic reactive oxygen species (ROS) are crucial signaling molecules in various biological processes. ROS signaling is interconnected with the response to several hormones, including jasmonic acid (JA), salicylic acid (SA) and ethylene. Using ozone (O3) to activate apoplastic ROS signaling, we performed global and targeted analysis of transcriptional changes and cell death assays to dissect the contribution of hormone signaling and various transcription factors (TFs) in the regulation of gene expression and cell death. The contributions of SA, JA, and ethylene were assessed through analysis of single, double, and triple mutants deficient in biosynthesis or signaling for all three hormones. Even in the triple mutant, the global gene expression responses to O3 were mostly similar to the wild-type. Cell death in the JA receptor mutant coi1-16 was suppressed by impairment of the NADPH oxidase RBOHF, suggesting a role for a ROS signal in limiting the spread of cell death. In response to apoplastic ROS, there is not a single signaling pathway that regulates gene expression or cell death. Instead, several pathways regulate the apoplastic ROS response via combinatorial or overlapping mechanisms.