Exploring plant tolerance to biotic and abiotic stresses

Plants are exposed to many stress factors, such as drought, high salinity or pathogens, which reduce the yield of the cultivated plants or affect the quality of the harvested products. Arabidopsis thaliana was used as a model plant to study the responses of plants to different sources of stress. With Agrobacterium T-DNA mediated promoter tagging, a novel di-/tripeptide transporter gene AtPTR3 was identified as a wound-induced gene. This gene was found to be induced by mechanical wounding, high salt concentrations, bacterial infection and senescence, and also in response to several plant hormones and signalling compounds, such as salicylic acid, jasmonic acid, ethylene and abscisic acid. Atptr3 mutants of two Arabidopsis ecotypes, C24 and Col-0, were impaired in germination on media containing a high salt concentration, which indicates that AtPTR3 is involved in seed germination under salt stress. Wounding caused local expression of the AtPTR3 gene, whereas inoculation with the plant pathogenic bacterium Erwinia carotovora subsp. carotovora caused both local and systemic expression of the gene. Atptr3 mutants showed increased susceptibility to infection caused by bacterial phytopathogens, E carotovora and Pseudomonas syringae pv. tomato, and the P. syringae type III secretion system was shown to be involved in suppression of the AtPTR3 expression in inoculated plants. Moreover, the Atptr3 mutation was found to reduce the expression of the marker gene for systemic acquired resistance, PR1 and the mutants accumulated reactive oxygen species (ROS) following the treatment of the plants with ROS generating substances. Overall results and observations suggest that the AtPTR3 is a novel and versatile stress responsive gene needed for defence reactions against many stresses. In a second part of the study, the yeast (Saccharomyces cerevisiae) trehalose-6-phosphate synthase gene (ScTPS1) was utilized to improve the drought tolerance of Arabidopsis. This gene codes for the first enzyme in the trehalose biosynthesis pathway of yeast, and expression in plants leads to improved drought tolerance but also growth aberrations. In this study, the ScTps1 protein was expressed in Arabidopsis using the constructs containing chloroplast targeting transit peptide sequence that facilitated the import of the ScTps1 into the chloroplast. The drought tolerance and growth phenotypes of Arabidopsis transgenics transformed with ScTPS1 with or without transit peptide, were characterized. The plants with cytosolic localization of the ScTps1 protein showed aberrant root phenotype, but the plants with the chloroplast targeted ScTps1 protein caused no aberration in root morphology. Even though both the transgenic lines showed enhanced drought tolerance, the relative water content of the lines was found to be similar to the wild type control. Moreover, both the transgenic lines showed slightly better water holding capacity or reduced water loss over time compared to wild type plants. The overall results indicated that the growth aberrations caused by cytosolic localization of ScTps1 could be uncoupled from the enhanced drought tolerance in the transgenic plants when the ScTps1 was targeted to chloroplast

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño.

BackgroundGene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.MethodsAllele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.ResultsA total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.DiscussionPrior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation

Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice

長崎大学学位論文 [学位記番号]博（医歯薬）甲第1168号 [学位授与年月日]令和元年6月5

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p><it>Arabidopsis thaliana </it>is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (<it>Oryza sativa</it>). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.</p> <p>Results</p> <p>Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of <it>cis</it>-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis.</p> <p>Conclusions</p> <p>These results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.</p

Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways

Sugarcane interacts with particular types of beneficial nitrogen-fixing bacteria that provide fixed-nitrogen and plant growth hormones to host plants, promoting an increase in plant biomass. Other benefits, as enhanced tolerance to abiotic stresses have been reported to some diazotrophs. Here we aim to study the effects of the association between the diazotroph Gluconacetobacter diazotrophicus PAL5 and sugarcane cv. SP70-1143 during water depletion by characterizing differential transcriptome profiles of sugarcane. RNA-seq libraries were generated from roots and shoots of sugarcane plants free of endophytes that were inoculated with G. diazotrophicus and subjected to water depletion for 3 days. A sugarcane reference transcriptome was constructed and used for the identification of differentially expressed transcripts. The differential profile of non-inoculated SP70-1143 suggests that it responds to water deficit stress by the activation of drought-responsive markers and hormone pathways, as ABA and Ethylene. qRT-PCR revealed that root samples had higher levels of G. diazotrophicus 3 days after water deficit, compared to roots of inoculated plants watered normally. With prolonged drought only inoculated plants survived, indicating that SP70-1143 plants colonized with G. diazotrophicus become more tolerant to drought stress than non-inoculated plants. Strengthening this hypothesis, several gene expression responses to drought were inactivated or regulated in an opposite manner, especially in roots, when plants were colonized by the bacteria. The data suggests that colonized roots would not be suffering from stress in the same way as non-inoculated plants. On the other hand, shoots specifically activate ABA-dependent signaling genes, which could act as key elements in the drought resistance conferred by G. diazotrophicus to SP70-1143. This work reports for the first time the involvement of G. diazotrophicus in the promotion of drought-tolerance to sugarcane cv. SP70-1143, and it describes the initial molecular events that may trigger the increased drought tolerance in the host plant

Root Involvement in Plant Responses to Adverse Environmental Conditions

limate change is altering the environment in which plants grow and survive. An increase in worldwide Earth surface temperatures has been already observed, together with an increase in the intensity of other abiotic stress conditions such as water deficit, high salinity, heavy metal intoxication, etc., generating harmful conditions that destabilize agricultural systems. Stress conditions deeply affect physiological, metabolic and morphological traits of plant roots, essential organs for plant survival as they provide physical anchorage to the soil, water and nutrient uptake, mechanisms for stress avoidance, specific signals to the aerial part and to the biome in the soil, etc. However, most of the work performed until now has been mainly focused on aerial organs and tissues. In this review, we summarize the current knowledge about the effects of different abiotic stress conditions on root molecular and physiological responses. First, we revise the methods used to study these responses (omics and phenotyping techniques). Then, we will outline how environmental stress conditions trigger various signals in roots for allowing plant cells to sense and activate the adaptative responses. Later, we discuss on some of the main regulatory mechanisms controlling root adaptation to stress conditions, the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will present recent advances on how the root system integrates all these signals to generate different physiological responses, including changes in morphology, long distance signaling and root exudation. Finally, we will discuss the new prospects and challenges in this field

DISSECTION OF STRESS RESPONSE NETWORKS REGULATING MULTIPLE STRESSES IN RICE

Important food crops like rice are constantly exposed to various stresses that can have devastating effect on their survival and productivity. Being sessile, these highly evolved organisms have developed elaborate molecular machineries to sense a mixture of stress signals and elicit a precise response to minimize the damage. However, recent discoveries revealed that the interplay of these stress regulatory and signaling molecules is highly complex and remains largely unknown. In this work, we conducted large scale analysis of differential gene expression using advanced computational methods to dissect regulation of stress response which is at the heart of all molecular changes leading to the observed phenotypic susceptibility. One of the most important stress conditions in terms of loss of productivity is drought. We performed genomic and proteomic analysis of epigenetic and miRNA mechanisms in regulation of drought responsive genes in rice and found subsets of genes with striking properties. Overexpressed genesets included higher number of epigenetic marks, miRNA targets and transcription factors which regulate drought tolerance. On the other hand, underexpressed genesets were poor in above features but were rich in number of metabolic genes with multiple co-expression partners contributing majorly towards drought resistance. Identification and characterization of the patterns exhibited by differentially expressed genes hold key to uncover the synergistic and antagonistic components of the cross talk between stress response mechanisms. We performed meta-analysis on drought and bacterial stresses in rice and Arabidopsis, and identified hundreds of shared genes. We found high level of conservation of gene expression between these stresses. Weighted co-expression network analysis detected two tight clusters of genes made up of master transcription factors and signaling genes showing strikingly opposite expression status. To comprehensively identify the shared stress responsive genes between multiple abiotic and biotic stresses in rice, we performed meta-analyses of microarray studies from seven different abiotic and six biotic stresses separately and found more than thirteen hundred shared stress responsive genes. Various machine learning techniques utilizing these genes classified the stresses into two major classes\u27 namely abiotic and biotic stresses and multiple classes of individual stresses with high accuracy and identified the top genes showing distinct patterns of expression. Functional enrichment and co-expression network analysis revealed the different roles of plant hormones, transcription factors in conserved and non-conserved genesets in regulation of stress response

Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots

Published by CSIRO Publishing. This is the Author Accepted Manuscript. This article may be used for personal use only.Abiotic stresses such as heat, drought or salinity have been widely studied individually. Nevertheless, in the nature and in the field, plants and crops are commonly exposed to a different combination of stresses, which often result in a synergistic response mediated by the activation of several molecular pathways that cannot be inferred from the response to each individual stress. By screening microarray data obtained from different plant species and under different stresses, we identified several conserved stress-responsive genes whose expression was differentially regulated in tomato (Solanum lycopersicum L.) roots in response to one or several stresses. We validated 10 of these genes as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. In addition, the genes identified in this work could be used as general salt-stress biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available