Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat

Pan, Yan; Li, Mengqi; Huang, Jun; Pan, Wenqiu; Shi, Tingrui; Guo, Qifan; Yang, Guang; Nie, Xiaojun

doi:10.3390/ijms23031405

Cited by 5 publications

(3 citation statements)

References 51 publications

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“…In contrast, reports of A-to-G editing in plants appear to be based solely on sequencing-based approaches that would report inosines incorrectly as guanines (Pan et al, 2022), with A-to-I editing apparently first proposed by Meng et al (2010) on the basis of A-to-”G” mRNA editing discovered by sequencing plant transcriptomes. In contrast, A-to-G editing does not appear to be a verified biological phenomenon in any taxon.…”

Section: Discussionmentioning

confidence: 99%

Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation betweenMimulus luteusvar.luteusandM. l. variegatus

Orr

Kim

Raj

et al. 2022

Preprint

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Phenotypic transitions in related taxa often share a common genetic basis, which suggests that there are constraints that shape the process of evolution at the genetic level. For example, noncoding changes in a gene may be favored relative to coding changes. Non-coding changes, which can alter context-specific gene expression, tend to have fewer pleiotropic consequences than coding changes, which affect the function of a gene product in all contexts. In this study, we evaluate the importance of protein-coding versus non-coding changes to the recent evolution of a novel anthocyanin pigmentation trait in the monkeyflower genus Mimulus. The magenta-flowered Mimulus luteus var. variegatus recently gained petal lobe anthocyanin pigmentation via a single-locus Mendelian difference from its sister taxon, the yellow-flowered M. l. luteus. Mapping and functional tests previously showed that transcription factor MYB5a/NEGAN is the single gene responsible for this difference. Further characterization of M. l. variegatus MYB5a, presented here, suggests post-transcriptional editing of two sites in the mRNA. We overexpressed the genomically encoded protein-coding sequences of MYB5a, from both M. l. luteus and M. l. variegatus, in Nicotiana tabacum leaves, in order to test their efficacy as anthocyanin-pigment activators. Quantitative image analysis of transfected tobacco leaves revealed robust anthocyanin production driven by both types of transgenes, compared to a negative control, and overall functional equivalency between the luteus and variegatus alleles. This finding supports the hypothesis that petal pigment was not gained by protein-coding changes in M. l. variegatus, but instead via non-coding cis-regulatory evolution.

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Section: Discussionmentioning

confidence: 99%

Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation betweenMimulus luteusvar.luteusandM. l. variegatus

Orr

Kim

Raj

et al. 2022

Preprint

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“…Drought-responsive miRNAs have been investigated in wheat (Singroha et al, 2021). The mutation led to the loss of tae-miR9657b-5p targeting, and lost the binding of tae-miR9657b-5p, which caused increased expression of tae-miR9657b-5p under the drought conditions, indicating that post-transcriptional RNA modification might mediate miRNA to response the drought stress (Pan et al, 2022). Moreover, according to the first durum wheat degradome report, some new miRNA-target regulatory pairs were discovered.…”

Section: Mirnas Response To Drought Stress In Plantsmentioning

confidence: 99%

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

Zhang

Yang²,

Zhang³

et al. 2022

Front. Plant Sci.

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MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20–24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

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“…The wheat NAC gene ( TaNAC071-A ) is recently reported as showing one of the strongest associations with drought stress. They experimented with the knockout technique and found that the TaNAC071-A gene is a positive regulator of plant dehydration response [ 15 , 16 ]; Zinc finger protein ( ZFP ) consists of various member proteins constituting a family [ 17 ], apart from the RNA/DNA difference (RDD) during central dogma confer resistance to drought stress in plants [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)

Aqeel¹,

Ajmal²,

Mujahid

et al. 2022

Genes

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Plant cell metabolism inevitably forms an important drought-responsive mechanism, which halts crop productivity. Globally, more than 30% of the total harvested area was affected by dehydration. RNA-seq technology has enabled biologists to identify stress-responsive genes in relatively quick times. However, one shortcoming of this technology is the inconsistent data generation compared to other parts of the world. So, we have tried, here, to generate a consensus by analyzing meta-transcriptomic data available in the public microarray database GEO NCBI. In this way, the aim was set, here, to identify stress genes commonly identified as differentially expressed (p < 0.05) then followed by downstream analyses. The search term “Drought in wheat” resulted in 233 microarray experiments from the GEO NCBI database. After discarding empty datasets containing no expression data, the large-scale meta-transcriptome analytics and one sample proportional test were carried out (Bonferroni adjusted p < 0.05) to reveal a set of 11 drought-responsive genes on a global scale. The annotation of these genes revealed that the transcription factor activity of RNA polymerase II and sequence-specific DNA-binding mechanism had a significant role during the drought response in wheat. Similarly, the primary root differentiation zone annotations, controlled by TraesCS5A02G456300 and TraesCS7B02G243600 genes, were found as top-enriched terms (p < 0.05 and Q < 0.05). The resultant standard drought genes, glycosyltransferase; Arabidopsis thaliana KNOTTED-like; bHLH family protein; Probable helicase MAGATAMA 3; SBP family protein; Cytochrome c oxidase subunit 2; Trihelix family protein; Mic1 domain-containing protein; ERF family protein; HD-ZIP I protein; and ERF family protein, are important in terms of their worldwide proved link with stress. From a future perspective, this study could be important in a breeding program contributing to increased crop yield. Moreover, the wheat varieties could be identified as drought-resistant/sensitive based on the nature of gene expression levels.

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Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat

Cited by 5 publications

References 51 publications

Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation betweenMimulus luteusvar.luteusandM. l. variegatus

Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation betweenMimulus luteusvar.luteusandM. l. variegatus

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)

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