Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers

Tyagi, Sandhya; Sharma, Shobha; Ganie, Showkat Ahmad; Tahir, Mohd; Mir, Reyazul Rouf; Pandey, Renu

doi:10.1007/s13205-019-1942-y

Cited by 37 publications

(22 citation statements)

References 89 publications

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“…2c). [40,19,3] and their sequences have been deposited in a publicly-available miRNA database, miRBase (http://www.sanger.ac.uk/cgibin/Rfam/mirna/browse.pl). Several miRNAs that have been identified and characterised in crop plants have been found involved in development, phyto-hormone signalling, flowering and sex determination and responses to biotic and abiotic stresses [40].…”

Section: Cluster Analysis Of 37 Wheat Genotypesmentioning

confidence: 99%

“…In addition, miRNAs play a major role in growth, development, and response to various biotic and abiotic stresses. The pace of discovery of small miRNAs have increased over the years due to the advances made in the area of next-generation high-throughput sequencing technologies that open up possibilities of exploring small RNA (sRNA) populations in economically important crop species like wheat [2,3].…”

Section: Introductionmentioning

confidence: 99%

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Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivumL.)

Tyagi

Kumar

Gautam³

et al. 2020

Preprint

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Wheat is one of the most important cereal crop in the world. Heat stress is an important abiotic stress limiting wheat production and productivity in the world including south-east Asia. The importance of miRNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, especially SSR markers, plays an important role for the success in molecular plant breeding programs. The discovery of SSRs from non-coding regions has been a challenging task. Therefore, development of novel miRNA-based SSRs from the conserved portions of the genome will prove useful for the study of genetic diversity of heat-responsive miRNA-genes in wheat. In the present study, efforts are made to mine SSR markers from 96 members of heat-responsive miRNA-genes of wheat followed by their validation using 37 contrasting (heat tolerance/susceptible) wheat genotypes. Among a set of 13 miRNA-SSRs used,7SSRs were found polymorphic. Among these polymorphic SSR markers, three found to be very informative SSRs (HT-169j, HT-160a and HT-160b) and could largely discriminate heat tolerant genotypes from the heat susceptible ones. Further analysis based on Polymorphism Information Content (PIC) revealed that miRNA genes were more diverse in susceptible genotypes compared to tolerant genotypes. Ours is the first report that the genic/miRNA markers could be successfully used to study wheat diversity, population structure and characterization of trait specific germplasm. The important and useful miRNA-based SSRs, therefore, would serve as best markers in the marker-assisted breeding programs aimed at enhancing heat tolerance of Indian wheat.

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Section: Cluster Analysis Of 37 Wheat Genotypesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivumL.)

Tyagi

Kumar

Gautam³

et al. 2020

Preprint

Self Cite

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“…The miRNA-linked AGO protein in the RISC complex examines mRNA molecules for perfect base complementarity in coding regions of target molecules, and subsequently, takes different actions. For example, miRNA cause protein repression by using ( Figure 2) three different molecular mechanisms during or after transcription via (1) degradation of mRNA transcripts, regulated by RISC or AGO1 [21,92] ; (2) suppression of the translational process; and (3) inhibition of transcription by methylation of nitrogenous (epigenetic changes) via recruiting the additional cofactors like General Control Nonrepressed Protein 5 (GCN5) which acetylates to H3K14 that further controls expression of MIR156a and MIR156c genes [21,[95][96][97]. It also reported that miRNAs [98,99] further lead to the synthesis of secondary siRNAs called phasiRNAs and/or easiRNAs.…”

Section: Biogenesis and Action Of The Mir156mentioning

confidence: 99%

“…Moreover, phosphorylation and dephosphorylation of HYL1 by both Mitogen-Activated Protein Kinase 3 (MPK3) and SNF1-related Protein Kinase 2 (SnRK2) in the response of light affect its transport from the nucleus to the cytoplasm. But finer points related to miRNAs based signal cascades are still poorly understood [21,87,92,96,102,105]. Currently, several good review articles describe the recent developments in the area of miRNA biogenesis, and its related newly discovered proteins, enzymes, transporters, and small nuclear RNAs (tasiRNAs and phasiRNAs).…”

Section: Biogenesis and Action Of The Mir156mentioning

confidence: 99%

“…Since, plant miRNAs are implicated in virtually all biological functions in plants especially, to control growth and development under adverse environmental conditions [14]. Recently hundreds of miRNAs families have been identified in various crop plants [19][20][21] that deposited in various microRNAs repositories [22,23]. These databases provide a great wealth of knowledge related to miRNAs, and their biogenesis, structures, functions, and evolutionary origins.…”

Section: Introductionmentioning

confidence: 99%

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The miR156: A Master Regulator to Harmonize Complex Biofuel Traits in Lignocellulosic Biomass Crops

Singh¹

2020

Preprint

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Currently, energy security and environmental degradation are the two biggest challenges before humanity that can be surmounted with the use of green and sustainable biofuels produced from lignocellulosic crops. In the future, to ensure adequate and cost-effective supply of biofuels, it requires a sufficient amount of amenable and quality lignocellulosic feedstocks. Therefore, agricultural yields of lignocellulosic biomass crops should be substantially increased by intense genetic maneuvering of key gene regulatory mechanisms and signaling pathways that control plant biomass yield. Recently, numerous miRNAs families are identified, characterized, and validated across the plant kingdom. Plant microRNAs (miRNAs) are 21 to 24 nucleotides long, non-coding small RNAs, act as regulators of their target genes via inducing modifications in transcription, translation, and epigenome. MiRNAs represent many hallmark characteristics like sequence-specific regulation, tissue, and species-specific expression, evolutionary conservation, and functional diversity. They coordinate well physiological and life cycle processes in plants under adverse environmental conditions. Hence, miRNAs offer accurate, precise, and efficient regulatory switches in the miRNA-targeted genetic networks. It is evident from the study of the miR156 family and its target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes network that controls highly significant agronomic traits in crop plants. The miR156/SPL module acts as a master circuit that synchronizes many intricate complex biological functions such as growth and development, and metabolic processes by sensing internal and external environmental signals in plants. Therefore, miR156 can prove a potential target for miRNAs based plant biotechnology to harmonize complex biofuel traits and improve biomass yield in lignocellulosic biomass crops.

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Regulatory Role of Micro-RNAs in Plants Under Challenging Environmental Conditions with Special Focus on Drought and Salinity

Kumar¹,

Kaur

Rajam

2021

Harsh Environment and Plant Resilience

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Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers

Cited by 37 publications

References 89 publications

Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivumL.)

Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivumL.)

The miR156: A Master Regulator to Harmonize Complex Biofuel Traits in Lignocellulosic Biomass Crops

Regulatory Role of Micro-RNAs in Plants Under Challenging Environmental Conditions with Special Focus on Drought and Salinity

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