Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress

Yang, Xinyu; Kang, Yichen; Liu, Yuhui; Shi, Mingfu; Zhang, Weina; Fan, Yanling; Yan-hong, Yao; Li, Hong; Qin, Shuhao

doi:10.1016/j.ecoenv.2021.112682

Cited by 30 publications

(13 citation statements)

References 75 publications

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“…Glutathione is converted to r-s-glutathione via glutathione s-transferase ( Noctor et al, 2012 ; Kapoor et al, 2019 ). The results of this study are consistent with the study results of potatoes ( Solanum tuberosum ) under cadmium stress ( Yang et al, 2021 ). Herein, miR169 negatively regulated GST under Pi starvation, inducing a negative effect on glutathione in alfalfa.…”

Section: Discussionsupporting

confidence: 92%

“…The correlation between miRNA and mRNA expression was analyzed using Pearson correlation to further determine the regulatory relationship between miRNAs and their target genes (Bylesjo et al, 2007). Negatively co-expressed miRNA-target gene pairs were obtained using the value of miRNA-mRNA at a threshold of correlation < −0.8 and p < 0.05 (Fan et al, 2021). Cytoscape (version 3.9.1) was used to selectively construct the miRNA-mRNA regulatory network (Shannon et al, 2003).…”

Section: Construction Of Mirna-mrna Regulatory Networkmentioning

confidence: 99%

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Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

Tong

et al. 2022

Front. Plant Sci.

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The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.

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Section: Discussionsupporting

confidence: 92%

Section: Construction Of Mirna-mrna Regulatory Networkmentioning

confidence: 99%

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

Tong

et al. 2022

Front. Plant Sci.

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“…miRNAs expression is affected by different stresses in plants which would regulate mRNA levels to respond to environmental alteration and affect plant development and growth [44,[51][52][53]. To clarify the targeted regulatory relationship between miRNAs and mRNAs, single miRNA to mRNA analysis or miRNA-mRNA integrated analysis are widely conducted [54,55]. In this study, we examined the miRNA expression alteration and its impact on target gene expression in the RL plants compared to the WT doner plants of rice cv.…”

Section: Discussionmentioning

confidence: 99%

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

Wang

Zhang

et al. 2022

Agronomy

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Tissue culture is an important experimental technique widely used for plant transformation and can induce somaclonal variation that is shown to be associated with genetic and epigenetic changes. However, the molecular basis of somaclonal variation and plant cell response to tissue culture has yet to be fully understood. In this study, we investigated gene expression, DNA methylation, and small RNA changes in regenerated lines (RL) compared with the wild-type progenitor plants (WT) of rice cv. Hitomebore. Using microarray, we identified many genes that were differentially expressed in the shoot-tip tissue and showed that TEs were generally activated in RL. Methylation Sensitive Amplification Polymorphism (MSAP) analysis of 5′CCGG sites combined with bisulfite sequencing detected a generally reduced DNA methylation in the RL lines. Small RNA sequencing analysis detected widespread changes in small RNA accumulation between RL and WT. In particular, repeat and TE-associated 24-nt size class of small RNAs, the inducer of RNA-directed DNA methylation, was in general down-regulated in RL, consistent with reduced CHG and CHH methylation at some of the differentially methylated TE loci. A large number of differentially expressed miRNAs were identified in RL and WT lines, including known and novel miRNAs. The expression of some of these miRNAs exhibited inverse correlation with the predicted target genes, suggesting a regulatory function. The RL plants looked similar to WT plants under normal conditions but showed significant phenotypic alterations under abiotic stress conditions. The widespread changes in DNA methylation, small RNA accumulation and gene expression in regenerated plants supports the role of epigenetic changes in tissue culture-induced somaclonal variation.

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“…Peroxidase activity was measured using the guaiacol method ( Jiao et al., 2022b ), and lignin content was determined in strict accordance with the operation process specified for testing kits from Suzhou Michy Biomedical Technology Co., Ltd. Reduced glutathione (GSH) and trehalose content were determined by UV spectrophotometry ( Yang et al., 2021a ; Kang et al., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…MiRNA-mRNA regulatory network plays a key role in plant responses to abiotic stresses Kang et al (2021) and Yang et al (2021a) demonstrated that combined analysis of miRNA-mRNA can reveal relevant regulatory mechanisms with important roles in plant responses to abiotic stress. Here, we conducted combined analysis of miRNAs and mRNAs related to maize root system drought stress responses, detected correlations between a series of DEMIRs and DEMRs, and constructed a regulatory network map.…”

Section: Mirna Sequencing Analysis and Drought Stress Responsementioning

confidence: 99%

Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

Jiao

Ma²,

Wang³

et al. 2022

Front. Plant Sci.

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Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA–mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety “M8186” at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA–mRNA analysis, 16 miRNA–target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, “plant hormone signal transduction”, “phenylpropane biosynthesis”, “glutathione metabolism”, and “starch and sucrose metabolism”, were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.

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Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress

Cited by 30 publications

References 75 publications

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

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