Plant miRNAome: Cross Talk in Abiotic Stressful Times

Patel, Prashanti; Yadav, Karuna; Ganapathi, T. R.; Suprasanna, Penna

doi:10.1007/978-3-319-91956-0_2

Cited by 11 publications

(6 citation statements)

References 176 publications

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“…miRNA-396 targets cell cycle regulators, as well as those that control plant growth and differentiation. miRNA-396 is increased under stress and represses cell multiplication ( Patel et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

et al. 2021

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Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

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Section: Discussionmentioning

confidence: 99%

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

et al. 2021

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“…miRNA-396 contributes to leaf and flower shape control and axillary meristem maintenance as it balances differentiation and proliferation of cell masses and hence morphogenesis. Stress induction of miRNA-396 represses cell multiplication under unfavourable conditions 20 . www.nature.com/scientificreports www.nature.com/scientificreports/ Supervised prediction of plant stress by having the plant miRnAs' concentration.…”

Section: Resultsmentioning

confidence: 99%

Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses

Vakilian

2020

Sci Rep

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During the last two decades, human has increased his knowledge about the role of miRNAs and their target genes in plant stress response. Biotic and abiotic stresses result in simultaneous tissue-specific up/down-regulation of several miRNAs. In this study, for the first time, feature selection algorithms have been used to investigate the contribution of individual plant miRnAs in Arabidopsis thaliana response towards different levels of several abiotic stresses including drought, salinity, cold, and heat. Results of information theory-based feature selection revealed that miRNA-169, miRNA-159, miRNA-396, and miRNA-393 had the highest contributions to plant response towards drought, salinity, cold, and heat, respectively. Furthermore, regression models, i.e., decision tree (DT), support vector machines (SVMs), and Naïve Bayes (NB) were used to predict the plant stress by having the plant miRNAs' concentration. SVM with Gaussian kernel was capable of predicting plant stress (R 2 = 0.96) considering miRnA concentrations as input features. findings of this study prove the performance of machine learning as a promising tool to investigate some aspects of miRnAs' contribution to plant stress responses that have been undiscovered until today. microRNAs (miRNAs) are small single-stranded RNAs with low protein-coding potential 1. Although plant miR-NAs target only a small number of mRNAs (<1%) 2 , the role of miRNA-controlled gene regulation in plants cannot be neglected because most of the target mRNAs participate in most plant developmental processes 3,4. Furthermore, there are evidences showing the relationships between plant stress responses and changes in miR-NAs' expression 5,6. miRNAs are known as negative post-transcription regulators since they exert specific binding to their target mRNAs or repressing target mRNA translation 7-9. Among the major plant abiotic stress sources, drought, salinity, cold, heat, ultraviolet irradiation, carbon dioxide, and heavy metal pollution have significant effects on plant morphological, physiological, and biochemical characteristics 10,11. To adapt and survive under stress conditions, plants exert miRNA up/down-regulation which results in gene expression reprogramming to restore cellular homeostasis 12,13. Plant miRNA expression towards stress is generally spatial (plant tissue) and temporal (developmental/growth stage) specific 4,14. With the identification of stress-responsive miRNAs, useful information on their role in improving the stress tolerance mechanism of plants can be obtained. A search in bibliographic resources reveals that hundreds of research studies have been dedicated to the changes in plant miRNA expression in response to biotic and abiotic stresses. A large part of these studies has focused on Arabidopsis thaliana, Brachypodium distachyon, Glycine max, Hordeum vulgare, Medicago truncatula, Manihot esculenta, Phaseolus vulgaris, Populus euphratica, Populus trichocarpa, Populus tremula, Triticum turgidum, Oryza sativa, Vigna unguiculate, and Zea mays 15. Studies ...

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“…The present study and our previous one (Salgado et al, 2021) used plants with the same genetic background (clones from the same plant), the same age (young oil palm plants), almost similar duration of stress (12 and 14 days, respectively for salinity and drought stress), same omics platform (transcriptome of mRNAs and smallRNAs), and the same group of analytical tools. All these commonalities between these two studies allowed us analyze the similarities and dissimilarities regarding expression analysis of miRNAs and their putative target genes, what it a valuable set of information to help us in the search for genes that can be used to promote future attempts to horizontally transfer tolerance at once to both stresses; not only to oil palm, but also other plant species (Patel et al, 2019;Chaudhary et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

The early response of oil palm (Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress

et al. 2022

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Oil palm (Elaeis guineensis Jacq.) is a oilseed crop of great economic importance drastically affected by abiotic stresses. MicroRNAs (miRNAs) play crucial roles in transcription and post-transcription regulation of gene expression, being essential molecules in the response of plants to abiotic stress. To better understand the molecular mechanisms behind the response of young oil palm plants to drought stress, this study reports on the prediction and characterization of miRNAs and their putative target genes in the apical leaf of plants subjected to 14 days of water deprivation. Then, the data from this study were compared to the data from a similar study that focused on salinity stress. Both, the drought-and salt-responsive miRNAs and their putative target genes underwent correlation analysis to identify similarities and dissimilarities among them. Among the 81 identified miRNAs, 29 are specific for oil palm, including two (egu-miR28ds and egu-miR29ds) new ones – described for the first time. As for the expression profile, 62 miRNAs were significantly differentially expressed under drought stress, being five up-regulated (miR396e, miR159b, miR529b, egu-miR19sds, and egu-miR29ds) and 57 down-regulated. Transcription factors, such as MYBs, HOXs, and NF-Ys, were predicted as putative miRNA-target genes in oil palm under water deprivation; making them the most predominant group of such genes. Finally, the correlation analysis study revealed a group of putative target genes with similar behavior under salt and drought stresses. Those genes that are upregulated by these two abiotic stresses encode lncRNAs and proteins linked to stress tolerance, stress memory, modulation of ROS signaling, and defense response regulation to abiotic and biotic stresses. In summary, this study provides molecular evidence for the possible involvement of miRNAs in the drought stress response in oil palm. Besides, it shows that, at the molecular level, there are many similarities in the response of young oil palm plants to these two abiotic stresses.

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Plant miRNAome: Cross Talk in Abiotic Stressful Times

Cited by 11 publications

References 176 publications

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses

The early response of oil palm (Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress

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