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Plant, Abiotic Stress and Responses to Climate Change. Edited by: Violeta Andjelkovic. ISBN , eISBN
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Only three small clusters identified within abiotic metaDEGs Fig. Interestingly, in the Xoo study used for this validation, the expression of JA- and SA-responsive genes was generally opposite of all other biotic stress responses. JA and SA response were a larger component of the biotic stress response However, this was a much smaller proportion of metaDEGs 1.

Taken together, these results indicate that in responses to any stress, rice orchestrates responses via phytohormones. Signaling downstream of JA and SA is increased during stress.

Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive

Gene expression log 2 fold changes of JA- and SA-responsive metaDEGs for a abiotic stress and b biotic stresses relative to controls columns are shown on the right in yellow down-regulated , black not regulated and cyan up-regulated. Hormone regulatory patterns of JA- and SA-responsive metaDEGs are shown on the left in magenta down-regulated , black not regulated; n. Clusters of genes regulated oppositely of hormone pathways are indicated by the orange squares C1 through C5.

We performed d e novo promoter motif enrichment analysis to identify potential stress-responsive regulatory elements. GO term analysis revealed six motifs that are likely to be involved in stress-responsive pathways Fig. De novo discovered promoter motifs. With one exception, all studies fit the expected trends; i.

The study that did not fit the expected trend GSE drought had two time-points, with the earlier time-point 1 d after stress not fitting the expected trend in down-regulated metaDEGs.

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As in the meta-analysis, photosynthesis genes were mostly down-regulated Fig. In the later time-point of the latter study GSE drought 3d , plants down-regulated photosynthesis-annotated genes, suggesting there may be some temporal effects of drought on altered regulation of photosynthesis, particularly as leaves dehydrate after continued drought. In study GSE, rice strongly down-regulated photosynthesis-annotated genes in response to Xoo Fig.

These results validate our meta-analysis approach to finding the rice core stress response. Publicly available gene expression studies validated meta-analysis results. A variety of environmental stresses affect plants in the field and can limit crop yield. To endure these stresses, plants respond with coordinated changes to their transcriptome. While these changes are dependent on the specific stress experienced, our results indicate that there is a rice core response to all stresses. With our meta-analysis of publicly available RNA-Seq data of rice experiencing various abiotic and biotic stresses, we identified 5, and 2, genes that are differentially regulated by abiotic stress and biotic stress, respectively Fig.

A different study utilized differential expression analysis of rice microarray data to identify genes commonly regulated by abiotic and biotic stresses, and found 40 rice genes that were responsive to both abiotic and biotic stresses Our meta-analysis of RNA-Seq data identified more of the rice core stress response than this previous comparative microarray analysis. We also validated our meta-analysis approach using additional publicly available studies not used in the training sets; through this validation, we identified sets of stress-responsive genes similar to those found in the meta-analysis Fig.

Photosynthesis is known to be down-regulated by abiotic stresses such as drought, cold, and heat stress 53 , 54 , 55 , This is likely a protective mechanism against plant photooxidative damage during stress 56 , In stress tolerant varieties of rice, photosynthetic efficiency is restored, and up-regulation of photosynthesis is physiologically important for yield stability 58 , Consistent with these findings, overexpression of a master regulator of photosynthesis enhanced rice tolerance to drought A range of biotic stresses, including bacterial, viral, and fungal pathogens, also inhibit photosynthesis in plants 61 , 62 , 63 , 64 , It is hypothesized that the photosynthesis pathway is a hub of cross-talk in growth and defense trade-offs during plant-pathogen interactions Studying the roles of the photosynthesis-regulated metaDEGs identified in this study may facilitate the development of stress tolerant varieties of rice.

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Various stresses positively induced phytohormone pathways Fig. Abiotic stress up-regulated genes responsive to ABA, auxin, JA, and SA, while biotic stress up-regulated genes responsive to the same hormones plus cytokinin and ethylene. ABA is also important to inter-kingdom signaling among pathogens and plants. For example, synthesis of ABA by the fungal pathogen M.

Plant-synthesized ABA promotes rice susceptibility to the bacterial pathogen X. We previously hypothesized that ABA is a node of cross-talk in the rice response to simultaneous high temperature stress and X. The results from our current study show that cross-talk among ABA, JA and SA response pathways makes the contribution of each hormone to the rice transcriptome unclear Fig. Notably, ABA-regulated genes appear to dominate the hormone response during stress. These intertwined pathways are critical to plant stress responses, which frequently occur simultaneously, emphasizing that additional study of hormonal cross-talk is needed to provide insights into how to improve plant health.

Our results open the path to future avenues of research, including both in silico and in planta studies. We immediately provide candidate genes for studying multiple stress responses in rice. Our analysis only used studies with rice plants that were sensitive susceptible to the different stresses. Future researchers can expand on this work by analyzing the regulation of metaDEGs in studies with stress-tolerant rice varieties.

We only found 88 oppositely regulated metaDEGs between abiotic and biotic stresses, but it is likely that stress tolerance and sensitivity oppositely regulate many more genes. The resources and approach provided with this work will allow for a deeper understanding of rice strategies for overcoming stresses. 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.

It is also possible to expand our approach into other systems. For example, with the wealth of publicly available Arabidopsis transcriptome data, researchers can repeat this analysis to identify candidate regulators of Arabidopsis stress response. 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.

To summarize, publicly available rice transcriptome data were used to identify genes and pathways regulated by abiotic stress, biotic stress, and both stress types.

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  5. We confirmed that photosynthesis is a generally down-regulated pathway in response to all stress types. With this work, we provide a list of candidate genes to study for improving rice stress tolerance, and thus yield, in light of environmental stresses. 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. Adapter sequences and low quality reads were removed with Trimmomatic v0.

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    Identification of plant genes for abiotic stress resistance

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    Function, structure and regulation of membrane transporters involved in abiotic stress

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