Evidences for differential expression of miR167d-5p, target, positional nucleotide preference, and its role in somatic and different stages of regenerating calli of Oryza sativa

Sinha, Anshika; Solanki, Manish; Shukla, Lata I.

doi:10.1007/s11240-018-01535-w

Cited by 13 publications

(10 citation statements)

References 42 publications

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“…The importance of miR167-ARF6/ARF8 in the acquisition of embryogenic competence during SE has also been indicated in cotton by a decrease in the miR167 activity, which led to enhanced callogenesis and an increased production of somatic embryos [ 154 ], while an overexpression of MIR167 genes inhibited the formation of somatic embryos in Arabidopsis, which showed that miR167 negatively regulates SE induction [ 112 ]. Moreover, Lin et al identified the expression of two endogenous TM transcripts that modulate the miR167 activity during SE in D. longan , which resulted in increased expression of ARF6 and ARF8 , thus indicating the important role of miR167-ARF6/ARF8 in the development of somatic embryos [ 155 ], which is in line with previous analyses that were carried out using other available functional genomics tools ([ 75 , 156 , 157 ] reviewed in [ 94 ]). Moreover, the TM approach has been successfully used for the functional analysis of miR156, miR160, miR166, miR393, miR396, miR398, and miR1432, thereby indicating their importance in regulating sexual and asexual embryogenesis in barley [ 102 ], tomato [ 158 , 159 ], rice [ 160 , 161 ], and Arabidopsis [ 115 , 126 , 162 , 163 ].…”

Section: Available Plant Mirna-dedicated Research Toolssupporting

confidence: 69%

“…The RT product can then be amplified and monitored in a qPCR reaction using a miRNA-specific forward primer and a universal reverse primer. The developed protocols enable the profiling of mature miRNA accumulation and high-throughput analysis of the miRNA expression, which has been successfully used in the functional analysis of miRNA during ZE and SE [ 35 , 73 , 74 , 75 , 76 , 77 ].…”

Section: Available Plant Mirna-dedicated Research Toolsmentioning

confidence: 99%

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Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Wójcik

2020

IJMS

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During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.

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Section: Available Plant Mirna-dedicated Research Toolssupporting

confidence: 69%

Section: Available Plant Mirna-dedicated Research Toolsmentioning

confidence: 99%

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Wójcik

2020

IJMS

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“…The miRNA molecules involved in auxin perception, signaling, and biosynthesis expressed in the SE transcriptomes of different plants[85][86][87][88][89][90]. x, transcriptomic analysis; •, functional analysis.…”

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confidence: 99%

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.

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“…The ratio of phytohormones auxin and cytokinins in regeneration media is a key factor for shoot differentiation in indica rice (Abiri et al 2017). The regeneration in Navara shows a preference for 6-benzylaminopurine (BAP) than kinetin as seen earlier in indica rice varieties CR1009 (Anshika and Shukla 2015;Sinha et al 2019). Also, minor concentration 0.1-0.5 mg/l of 1-naphthaleneacetic acid (NAA) along with BAP improved regeneration efficiency earlier (Lin and Qifa 2005).…”

Section: Discussionmentioning

confidence: 99%

“…The correlation between calli fresh weight, size, CIF (callus induction frequency), browning, white/yellow/cream colour (WYC) and green spot frequency (GSF) was analysed using "The Unscramble X", a tool for multiple variant analyses (Sinha et al 2019) where the PC-1 (Y-axis) and PC-2 (X-axis) show the level of confidence by which we can say data are reliable. If it is more than 80% (cumulative), then it is more reliable and reproducible.…”

Section: The Unscramble X Softwarementioning

confidence: 99%

Optimization of in vitro culture media for improvement in yield of Navara ancient Indian medicinal rice

2019

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Medicinally important ancient Navara rice (GI Kerala, India 2007) is a very short duration (60-70 days) variety with a yield of only 0.5 tonnes/hectare costing ~ Rs. 400/kg. It is used for indigenous treatment for chronic diseases by local and oral consumption. In this study, scutellum-derived calli were generated from mature Navara seeds and these were inoculated on different CIM-1 to CIM-5 media supplemented with 2.5 mg/l 2,4-dichlorophenoxyacetic acid. Regeneration of calli on different regeneration media RI, RII and RIII media were performed. Regeneration of 30-day-old calli on RI media showed 30%, for RII it showed no regeneration and on RIII media only 12% regeneration was obtained. The addition of glutamine and proline showed a 30-40% improvement in somatic embryogenesis. The 74-88% callus induction frequency was obtained on CIM-1 to CIM-5. The fresh weight (mg) of 30-day-old calli is CIM-2 < CIM-3 < CIM-4 < CIM-1 << CIM-5 and corresponding size shows CIM-2-CIM-3 < CIM-5 < CIM-1 < CIM-4. A negative correlation between the callus fresh weight and the regeneration efficiency was observed. In CIM-5, 20-25 days 3.4-fold increase and 25-30 days a 1.7-fold increase in fresh weight of calli is noted. The 20-day-old calli transfer to RI media shows 80% regeneration frequency and 6-7 plantlets/callus, which are twofold higher as compared with 30-day-old calli. The somatic embryogenesis and its regeneration on synthetic media provide an alternative for biotechnological intervention for yield improvement, in turn cost reduction for Navara rice.

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Evidences for differential expression of miR167d-5p, target, positional nucleotide preference, and its role in somatic and different stages of regenerating calli of Oryza sativa

Cited by 13 publications

References 42 publications

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Optimization of in vitro culture media for improvement in yield of Navara ancient Indian medicinal rice

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