Abiotic metaDEGs responsive to ABA, auxin, JA and SA were more up-regulated than expected by random chance as determined by the 2 goodness of fit test (p0.05, Fig. Change 1, 42 (2011). Annu. Kawahara, Y. et al. The effects of salinity on vegetable growth and how management practices (irrigation, drainage, and fertilization) can prevent soil and water salinization and mitigate the adverse effects of Salinity are discussed. (d) MetaDEGs identified from meta-analyses. Huang, H. et al. This book provides a valuable insight into how the area of plant adaptation to abiotic stresses has progressed through the application of the new technologies. PubMed Xu, J. et al. Taken together, these results indicate that rice utilizes ACGT-bZIP TF to regulate response to both abiotic and biotic stress, and identify bZIP elements as key nodes for further studies. Occurrence of abiotic stresses can alter plant-pest interactions by enhancing host plant susceptibility to pathogenic organisms, insects, and by reducing competitive ability with weeds. Zhang, Z.-F., Li, Y.-Y. 8, 1427 (2017). Ghosh, S., Kanwar, P. & Jha, G. Alterations in rice chloroplast integrity, photosynthesis and metabolome associated with pathogenesis of Rhizoctonia solani. PubMed Central The authors thank Vamsi J. Nalam (Colorado State University) for important discussion and Alvaro L. Prez-Quintero (Colorado State University) for critical reading of the manuscript. Cite this article. Sah, S. K., Reddy, K. R. & Li, J. Abscisic acid and abiotic stress tolerance in crop plants. 5a,b, TableS7). Bioch. 148, 19381952, https://doi.org/10.1104/pp.108.128199 (2008). Antagonistic interaction between systemic acquired resistance and the abscisic acidmediated abiotic stress response in Arabidopsis. Temporal and spatial changes in gene expression, metabolite accumulation and phytohormone content in rice seedlings grown under drought stress conditions. You are using a browser version with limited support for CSS. ABA is also important to inter-kingdom signaling among pathogens and plants. Fast Download speed and no annoying ads. As knowledge generated by molecular plant researchers often does not reach plant breeders and decision-makers, we discussed with our colleagues the idea of editing a Special Issue about Biotic and Abiotic Stress Responses in Plants in the journal Agronomy, with the goal of contributing to lling this gap and additionally highlighting this . Bidzinski, P. et al. 14, e1007092 (2018). This study provides a valid approach to ask additional questions with respect to how plants respond to stress, including but not limited to (1) how tolerant rice varieties respond to stress and (2) how other plants respond to stress. Other plant responses to pathogens include production of toxic compounds, including phytoalexins and reactive oxygen species, and induction of localized cell death13. Genes responsive to JA and/or SA, but not responsive to ABA, were still up-regulated more than expected by random chance (TableS5). This chapter has emphasized on the contribution made by genomics and proteomics approaches to gain further insights in understanding the molecular mechanisms of plants responses against stress. Ding, Y., Dommel, M. & Mou, Z. Abscisic acid promotes proteasomemediated degradation of the transcription coactivator NPR 1 in Arabidopsis thaliana. 4, Supplementary DataS1). 81, 128134 (2014). That is, of the metaDEGs responsive to JA and SA, most were also responsive to ABA (Fig. Biotic and abiotic stress factors can adversely affect the agricultural productivity leading to physiological and biochemical damage to crops. By submitting a comment you agree to abide by our Terms and Community Guidelines. This article aims to evaluate and review the reported modes of ABA action on pathogen defense and highlight recent advances in deciphering the complex role of A BA in plant-pathogen interactions. Fu, J. et al. Abiotic stress is defined as the negative impact of non-living factors on living organisms in a specific environment. However, this was a much smaller proportion of metaDEGs (1.4 and 3.5% of abiotic and biotic metaDEGs, respectively). While our results show that both ABA and SA are induced during response to biotic stress, ABA-induced susceptibility to Xoo is due to ABA suppressing SA-mediated defense26. The resources and approach provided with this work will allow for a deeper understanding of rice strategies for overcoming stresses. The data reveal a previously uncharacterized connection between ABA, Na(+) homeostasis, oxidative stress and pathogen response, and shed light on the genetic control of crosstalk between plant responses to pathogens and abiotic stress. The expression of these genes indicate that during either stress type, JA and SA signaling are increased (Fig. Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. Bot. 16, 8288 (2017). The role of ABA in response to abiotic stress at the molecular level and ABA signaling is discussed and the effect of A BA in respect to gene expression is dealt with. Lu, G., Gao, C., Zheng, X. Rev. The enrichment of ABRE-like motifs in the promoters of biotic stress-induced metaDEGs suggests that even though there are fewer bZIP TFs responsive to biotic stresses than abiotic stresses, bZIP TFs may still act as critical regulators of response to biotic stress. 26, 14391458 (1994). R: A Language and Environment for Statistical Computing, (2016). Rice also generally up-regulates hormone-responsive genes during stress response, most notably genes in the abscisic acid, jasmonic acid and salicylic acid pathways. USA 92, 41144119 (1995). Plants growing under field conditions are constantly exposed, either sequentially or simultaneously, to many abiotic or biotic stress factors. Ghosh, T. K. et al. Although the reference genome is annotated with only 45 BP GO terms, we identified several BPs that were altered by stress, including catabolic process, cell communication, embryo development, reproduction, and response to extracellular stimulus, which were all up-regulated by stress, and photosynthesis, protein modification process, and response to external stimulus, which were all down-regulated by stress. Therefore, this approach was valid for investigating rice core responses to abiotic and biotic stress. For single analyses, genes were considered differentially expressed if the FDR-adjusted p-values were 0.01. Abiotic and biotic stresses induce a core transcriptome response in rice, https://doi.org/10.1038/s41598-019-42731-8. The topics, addressed in up-to-date specific chapters, include effects and responses of plants to stresses caused by such factors as: 1) high temperature, 2) low temperature (chilling and freezing), 3) salt, 4) drought, 5) flooding, 6) heavy metals, 7) elevated carbon dioxide, 8) ozone. Sci. n.s. Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acidinducible mitogen-activated protein kinase. Int. Pre-processed gene expression studies were acquired from NCBI Gene Expression Omnibus. A range of biotic stresses, including bacterial, viral, and fungal pathogens, also inhibit photosynthesis in plants61,62,63,64,65. Information is summarized about the involvement of polyamines as antioxidants against the potential abiotic stress-derived oxidative damage and other types of abiotic stresses, such as mineral deficiencies, chilling, wounding, heavy metals, UV, ozone and paraquat, where polyamine metabolism is also modified. Gomez-Porras, J. L., Riano-Pachon, D. M., Dreyer, I., Mayer, J. E. & Mueller-Roeber, B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 8, 260, https://doi.org/10.1186/1471-2164-8-260 (2007). Numerous genetic, biochemical and molecular studies have identified many of the factors that regulate abiotic stress responses, and it is now clear that abiotic stress elicits multilevel. Anders, S., Pyl, P. T. & Huber, W. HTSeqa Python framework to work with high-throughput sequencing data. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Article Sci. 15, 10 (2015). We cannot guarantee that every ebooks is available! Plant Growth Regul. Plant Physiol. et al. Article Hypersensitive Response (HR): On being attacked by insects or a pathogenic microorganism, typically a plant responds with: (i) Formation of pathogenesis-related (PR) proteins, ADVERTISEMENTS . Klessig, D. F. & Malamy, J. A variety of environmental stresses affect plants in the field and can limit crop yield. Deciphering the combined actions of these different signaling pathways in plants would greatly enhance the ability of breeders to develop food crops that can thrive in deteriorating environmental conditions under climate change, and that can maintain or even increase crop yield. Xiang, Y., Tang, N., Du, H., Ye, H. & Xiong, L. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. This paper provides a comprehensive review of major research advances on biochemical, physiological, and molecular mechanisms regulating plant adaptation and tolerance to salinity stress. Over 8,000 fungal species are known to cause plant disease. Transcriptional basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae. Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. These results validate our meta-analysis approach to finding the rice core stress response. Cell 126, 969980 (2006). Abscisic acid interacts antagonistically with salicylic acid signaling pathway in riceMagnaporthe grisea. To investigate the rice biological processes (BP) altered during stress, we evaluated the enrichment patterns of the 45 BP gene ontology (GO) terms in abiotic and biotic up- and down-regulated metaDEGs (TableS4). Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. Plant Sci. We identified several promoter motifs that are likely involved in stress-responsive regulatory mechanisms in rice. In addition to Ca 2+, ABA also induces the second messengers NO (nitric oxide), and PA (phosphatidic acid) and other phospholipids. Adapter sequences and low quality reads were removed with Trimmomatic v0.3673. 6, 1082 (2015). In this scenario, the current most accepted opinion of scientists is that both biotic and abiotic factors in nature and agroecosystems are affected by climate change, which may lead to significant crop yield decreases worldwide. Front. Most of the data relates to changes in free polyamines and it is suggested that future research on polyamines in hostpathogen interactions should include careful examination of polyamine conjugates. (a) Analysis pipeline used to conduct differential gene expression analysis and meta-analysis on publicly available data sets. Abiotic stress signaling and responses in plants - PMC Published in final edited form as: signal activates CPKs and CBLs-CIPKs that also phosphorylate effector proteins such as SLAC1. For the 2 tests, the expected number of up- and down-regulated genes was proportional to the total number of up- and down-regulated genes in the background set. This Special Issue provides a useful overview of the topic, including basic information on the mechanisms of abiotic stress tolerance as well as practical aspects such as the alleviation of the deleterious effects of stress by different means, or the use of local landraces as a source of genetic material adapted to combined stresses. The development of metabolomics, along with other -omics technologies, allowed in depth analysis of the reactive processes characterizing plant stress as the result of the alteration of metabolites and gene expressions. BMC Genomics 14, 216 (2013). Fishers exact test with a p-value threshold of 0.01 was used to determine whether motifs were enriched in metaDEG sets. With climate change, more extreme weather events are occurring, increasing the likelihood that plants experience multiple stresses in the field, including additional pressure from plant diseases9. All selected studies used stress-sensitive rice varieties. 2, TableS5). Both the basal and the resistance (R) gene-mediated defense responses to Pseudomonas syringae are found to be inhibited by a moderately high temperature, and hypersensitive responses induced by R genes against two viruses are also reduced by an increase of temperature, indicating that temperature modulation ofdefense responses to biotrophic and hemibiotrophic pathogens might be a general phenomenon. Rep. 1, 66 (2011). Trends Plant Sci. 30, 1627 (2017). This chapter aims at the stresses related to water and the expression 'drought' which is derived from the agricultural context, is used as equal to water stress throughout the article. For immunity to pathogens, plants primarily rely on salicylic acid (SA), JA and ethylene signaling. PeskanBerghfer, T. et al. Todaka, D. et al. Plant Sci. CAS While the first is considered the damage done to an organism by other living organisms, the latter occurs as a result of a negative impact of non-living factors on the organisms. Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci. 1e, TableS3). drought, salinity, pathogen, etc.) Garg, R., Chevala, V. N., Shankar, R. & Jain, M. Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. This book is based to a great extent on the biochemical and molecular mechanisms of tolerance of commonly encountered abiotic stresses in nature. Nat. Plant Sci. This book is useful for under-graduate and post-graduate students in Entomology, Plant Pathology, Agronomy, Horticulture, other cognate disciplines of agriculture and allied sciences and other research workers. 3). Bioinformatics 30, 21142120, https://doi.org/10.1093/bioinformatics/btu170 (2014). Spence, C. A., Lakshmanan, V., Donofrio, N. & Bais, H. P. Crucial roles of abscisic acid biogenesis in virulence of rice blast fungus Magnaporthe oryzae. Understanding abiotic stress factors such as temperature and drought tolerance and biotic stress tolerance traits such as insect pest and pathogen resistance in combination with high yield in plants is of paramount importance to counter climate change related adverse effects on the productivity of crops. 39, 19821993 (2016). In the meantime, to ensure continued support, we are displaying the site without styles Garg, R., Tyagi, A. K. & Jain, M. Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice. Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. 1a). Under the supervision of J.E.L., S.P.C. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. Our results open the path to future avenues of research, including both in silico and in planta studies. Several chemical compounds, known as plant growth regulators (PGRs), modulate plant responses to biotic and abiotic stresses at the cellular, tissue, and organ levels. In systems with few or no publicly available transcriptome studies, the analysis we describe enables researchers to design transcriptome studies from the ground up to study stress response in their systems. This book is a printed edition of the Special Issue "Biotic and Abiotic Stress Responses in Crop Plants" that was published in Agronomy. CAMTA 1 regulates drought responses in Arabidopsis thaliana. Bioinformatics 26, 139140, https://doi.org/10.1093/bioinformatics/btp616 (2010). Drought, salinity, extreme temperatures (cold and heat) and oxidative stress are often interrelated; these conditions singularly or in combination induce cellular damage. Also, multiple abiotic stress tolerance in banana had been reported by the over-expression of MusaWRKY71 gene, which is a very potential abiotic stress-responsive WRKY TF gene, cloned from Musa species cv. chopin; impromptu imslp. Previous studies have explored broad plant stress response by analyzing microarray data31,32. 171, 28102825 (2016). Commun. oryzae lipopolysaccharide and extracellular polysaccharide in modulation of defense responses during infection. Even while limited by the available rice stress-responsive transcriptome data, with multiple tissue types, host cultivars, and few replicates per treatment (Table2), real trends were identified, indicating it is possible to design experiments in less well-studied plant systems to use with our approach. Biotic stress which is often called decay is caused by infectious diseases that develop in harvested fruit and is usually caused by bacteria, fungi, or yeasts. Download Citation | Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance | Main conclusion Application of the recently developed CRISPR/Cas tools might . Photoinhibition and photoinhibition-like damage to the photosynthetic apparatus in tobacco leaves induced by Pseudomonas syringae pv. This book deals with an array of topics in the broad area of biotic stress responses in plants focusing problems and their management by selecting some of the widely investigated themes. The 2nd section deals with three major stresses - temperature, water and salinity and the metabolic changes and protective adjustments in plants for withstanding these stresses. GO term analysis revealed six motifs that are likely to be involved in stress-responsive pathways (Fig. Plants are subjected to numerous environmental stresses, which can be classified into two broad areas: abiotic and biotic stresses. Our results confirm that rice universally down-regulates photosynthesis in response to both abiotic and biotic stress. J. Saudi Soc. This is likely a protective mechanism against plant photooxidative damage during stress56,57. Tran, T. T. et al. this book serves as a complete package on the basics and applications for abiotic stress response sensing and genetic and metabolic response pathways in plants; it is designed for use by advanced undergraduate students, graduate students and beginning researchers in the area of stress biology, plant molecular biology, plant physiology, We present this work as a proof of concept: meta-analysis of diverse transcriptomic data sets is a valid and robust approach to develop hypotheses for how plants respond to stress in general. By clicking accept or continuing to use the site, you agree to the terms outlined in our. 90, 6178 (2017). This review focuses on the responses of plants to simultaneous biotic and abiotic stresses at the molecular level and the importance of studying plant stress factors in combination. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice. Analysis of the whole-genome transcriptional profiles from Arabidopsis thaliana indicated that cell rescue/defense/virulence, energy, and metabolism functional classes were overrepresented, providing novel insight into the functional basis of multiple stress tolerance inArabidopsis. PLOS One 11, e0146946 (2016). the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in It is hypothesized that the photosynthesis pathway is a hub of cross-talk in growth and defense trade-offs during plant-pathogen interactions66. These stresses include drought33, salt34, high and low temperature35,36, and infection with Xanthomonas oryzae pathovars oryzicola (Xoc) and oryzae (Xoo)37,38, Magnaporthe oryzae39, and Rice Stripe (RSV) and Dwarf (RDV) viruses40,41 (Table1). For example, synthesis of ABA by the fungal pathogen M. oryzae during interactions with rice is necessary for pathogen virulence71. Sci. Global warming leads to the concurrence of a number of abiotic and biotic stresses, thus affecting agricultural productivity. Most metaDEGs were uniquely regulated by either abiotic or biotic stress. Defense responses during infection defined as the negative impact of non-living factors on living organisms in a specific environment plants. Work with high-throughput sequencing data involved in stress-responsive regulatory mechanisms in rice seedlings grown under drought stress adaptation in rice... 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