Role of miRNAs in root development of model plant Arabidopsis thaliana

Gautam, Vibhav; Singh, Archita; Verma, Swati; Kumar, Ashutosh; Kumar, Pramod; Mahima, Mahima; Singh, Sharmila; Mishra, Vishnu; Sarkar, Ananda K.

doi:10.1007/s40502-017-0334-8

Cited by 22 publications

(8 citation statements)

References 93 publications

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“…The present study identified hormone signaling pathway-related miRNAs and their target genes [ 73 ]. A number of miRNAs have been recognized to regulate root growth by targeting various genes during AR root formation [ 33 , 74 ]. For example, miR156 is necessary for lateral root growth by targeting its target genes SPL9 and SPL10 [ 75 ], whereas miR160 modulates root development by the negative regulation of its target genes ARF10 , ARF16 , and ARF17 [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.

Uddin

Munir

Gull

et al. 2022

Genes

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Tetraploid Robinia pseudoacacia L. is a difficult-to-root species, and is vegetatively propagated through stem cuttings. Limited information is available regarding the adventitious root (AR) formation of dark-pretreated micro-shoot cuttings. Moreover, the role of specific miRNAs and their targeted genes during dark-pretreated AR formation under in vitro conditions has never been revealed. The dark pretreatment has successfully promoted and stimulated adventitious rooting signaling-related genes in tissue-cultured stem cuttings with the application of auxin (0.2 mg L−1 IBA). Histological analysis was performed for AR formation at 0, 12, 36, 48, and 72 h after excision (HAE) of the cuttings. The first histological events were observed at 36 HAE in the dark-pretreated cuttings; however, no cellular activities were observed in the control cuttings. In addition, the present study aimed to uncover the role of differentially expressed (DE) microRNAs (miRNAs) and their targeted genes during adventitious root formation using the lower portion (1–1.5 cm) of tetraploid R. pseudoacacia L. micro-shoot cuttings. The samples were analyzed using Illumina high-throughput sequencing technology for the identification of miRNAs at the mentioned time points. Seven DE miRNA libraries were constructed and sequenced. The DE number of 81, 162, 153, 154, 41, 9, and 77 miRNAs were upregulated, whereas 67, 98, 84, 116, 19, 16, and 93 miRNAs were downregulated in the following comparisons of the libraries: 0-vs-12, 0-vs-36, 0-vs-48, 0-vs-72, 12-vs-36, 36-vs-48, and 48-vs-72, respectively. Furthermore, we depicted an association between ten miRNAs (novel-m0778-3p, miR6135e.2-5p, miR477-3p, miR4416c-5p, miR946d, miR398b, miR389a-3p, novel m0068-5p, novel-m0650-3p, and novel-m0560-3p) and important target genes (auxin response factor-3, gretchen hagen-9, scarecrow-like-1, squamosa promoter-binding protein-like-12, small auxin upregulated RNA-70, binding protein-9, vacuolar invertase-1, starch synthase-3, sucrose synthase-3, probable starch synthase-3, cell wall invertase-4, and trehalose phosphatase synthase-5), all of which play a role in plant hormone signaling and starch and sucrose metabolism pathways. The quantitative polymerase chain reaction (qRT-PCR) was used to validate the relative expression of these miRNAs and their targeted genes. These results provide novel insights and a foundation for further studies to elucidate the molecular factors and processes controlling AR formation in woody plants.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.

Uddin

Munir

Gull

et al. 2022

Genes

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“…The development and validation of SSR markers from SSR-bearing "pre-miRNA candidates" were recently achieved in several crop species, including rice [45], Arabidopsis thaliana [46], Brassica [47], Medicago truncatula [48], pomegranate [49], Melilotus albus [50], and wheat [51,52]. Despite the many SSR-bearing "pre-miRNA candidates" from a wide range of plant species, these candidates were not explored for marker development.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Biswas

Bagchi

et al. 2021

Agronomy

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Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.

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“…miRNA sequence specificity with its corresponding target gene is necessary for regulating their expression in both plants and animals [ 20 ]. Earlier reports suggest that most animal and plant miRNAs regulate the expression of their corresponding target genes by triggering translational repression and mRNA cleavage, respectively [ 21 , 22 ].…”

Section: Biogenesis Of Mirnas: Mirna Transcription and Maturationmentioning

confidence: 99%

“…The PmiREN v.2.0 latest release contains 38,186 known miRNAs belonging to 7,838 families with a predicted 141, 327 miRNA-targets pairs in 179 plant species [ 15 ]. These miRNAs can control a broad range of biological processes by modulating their corresponding target genes expression [ 16 , 17 ], involved in a vast range of plant functions, including leaf morphogenesis [ 18 ], root development [ 19 , 20 ], growth transition [ 21 ], reproductive stage [ 22 ], disease resistance [ 23 , 24 ], etc.…”

Section: Introductionmentioning

confidence: 99%

Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant’s disease response

2022

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In the recent past, cross-kingdom movement of miRNAs, small (20–25 bases), and endogenous regulatory RNA molecules has emerged as one of the major research areas to understand the potential implications in modulating the plant’s biotic stress response. The current review discussed the recent developments in the mechanism of cross-kingdom movement (long and short distance) and critical cross-talk between host’s miRNAs in regulating gene function in bacteria, fungi, viruses, insects, and nematodes, and vice-versa during host-pathogen interaction and their potential implications in crop protection. Moreover, cross-kingdom movement during symbiotic interaction, the emerging role of plant’s miRNAs in modulating animal’s gene function, and feasibility of spray-induced gene silencing (SIGS) in combating biotic stresses in plants are also critically evaluated. The current review article analysed the horizontal transfer of miRNAs among plants, animals, and microbes that regulates gene expression in the host or pathogenic organisms, contributing to crop protection. Further, it highlighted the challenges and opportunities to harness the full potential of this emerging approach to mitigate biotic stress efficiently.

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Role of miRNAs in root development of model plant Arabidopsis thaliana

Cited by 22 publications

References 93 publications

Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.

Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.

A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant’s disease response

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