Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related ...parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
•This review contains all available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice.•The miRNA nodes that are associated with this process are described•The impact of abiotic stress induced alterations on the levels of the miRNAs related to grain yield is discussed.•The role of miR156-SPL node has been discussed in details.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The regulatory role of small non-coding RNAs that are 20–24 nucleotides in length has become the foremost area of research for biologists. A major class of small RNAs represented by the microRNAs ...(miRNAs), has been implicated in various aspects of plant development including leaf pattering, meristem function, root patterning etc. Recent findings support that miRNAs are regulated by drought and other abiotic stresses in various plant species. In this study, were report the expression profiling of 8 known abiotic stress deregulated miRNAs in 11 elite sorghum genotypes, under watered and drought conditions. Significant deregulation was observed with miR396, miR393, miR397-5p, miR166, miR167 and miR168. Among these, the expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes. The expression of sbi-miR396 was maximum in the grain sorghum HSD3226 under well-watered conditions and the profile shifted towards HSD3221 under drought stress. Forage accessions, N98 and Atlas, showed an opposite behavior in expression patterns of miR397-5p in drought physiologies. Such dynamic expression patterns could be indicative of prevailing drought tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRNAs which may have potential use in improving drought tolerance in sorghum and other cereal crops.
•Expression analysis of 8 conserved sorghum miRNAs across 11 gentoypes in response to drought.•The expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes.•Absence of regular pattern suggests differential intrinsic capabilities of various sorghum genotypes.•The study emphasizes need for miR-target based characterization of sorghum for developing drought tolerant varieties.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Indica
rice varieties especially from North East India show a broad variation in drought tolerance due to the rich biodiversity of the region. In this study, genome-wide analysis of ...drought-responsive regulons was performed by comparing the stress-tolerant, Tampha and stress-sensitive, Chandan,
indica
rice genotypes. The results showed that drought stress induces greater number of differentially expressed transcripts in the Tampha as compared to Chandan. Sixty-one drought-regulated transcripts showed higher expression level in Tampha and these included dehydrins, glycosyltransferases, DnaK molecular chaperones and several transcription factors. The drought-responsive transcripts formed co-expression gene modules and were majorly associated with redox pathways and carbohydrate metabolism. The gene regulation was coordinated by transcription factors and miRNAs. The Tampha transcriptome also exhibited significant changes in ASE under drought stress. Therefore, the results demonstrate that substantial differences in both transcriptional variations and post-transcriptional regulations determine the transcriptome profiles to regulate the plant response to drought stress in varieties.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Artificial microRNAs (amiRNA) provide a new feature in the gene silencing era. Concomitantly, reducing the amount of lignin in fiber-yielding plants such as jute holds significant commercial and ...environmental potential, since this amount is inversely proportional to the quality of the fiber. The present study aimed at reducing the lignin content in jute, by introducing amiRNA based vectors for down-regulation of two monolignoid biosynthetic genes of jute, coumarate 3-hydroxylase (C3H) and ferulate 5-hydroxylase (F5H). The transgenic lines of F5H–amiRNA and C3H–amiRNA showed a reduced level of gene expression, which resulted in about 25 % reduction in acid insoluble lignin content for whole stem and 12–15 % reduction in fiber lignin as compared to the non-transgenic plants. The results indicate successful F5H–amiRNA and C3H–amiRNA transgenesis for lignin reduction in jute. This is likely to have far-reaching commercial implications and economic acceleration for jute producing countries.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Abstract RNA silencing refers to a conserved RNA-directed gene regulatory mechanism in a wide range of eukaryotes. It plays an important role in many processes including growth, development, genome ...stability, and antiviral defense in the plants. Geminivirus encoded AC2 is identified as an RNA silencing suppressor protein, however, the mechanism of action has not been characterized. In this paper, we elucidate another mechanism of AC2-mediated suppression activity of Mungbean Yellow Mosaic India Virus (MYMIV). The AC2 protein, unlike many other suppressors, does not bind to siRNA or dsRNA species and its suppression activity is mediated through interaction with key components of the RNA silencing pathway, viz., RDR6 and AGO1. AC2 interaction inhibits the RDR6 activity, an essential component of siRNA and tasi-RNA biogenesis and AGO1, the major slicing factor of RISC. Thus the study identifies dual sites of MYMIV-AC2 interference and probably accounts for its strong RNA silencing suppression activity.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Pokkali is one of the rice varieties that have adapted to grow under highly saline conditions. Several studies have shown that plant’s response to salt stress is a multigenic trait involving the ...coordinated action of signaling molecules, ion transporters, enzymes, and transcription factors. In earlier studies, we have reported that the adaptability of Pokkali rice to excess salt involves genetic regulations by a panel of microRNAs (miRNAs). The miRNAs are crucial primary regulators of gene expression that may act at the transcriptional or post-transcriptional levels in a sequence-specific manner. In this study, we have analyzed and compared the small RNA and transcriptome datasets of roots and leaves of Pokkali plants grown in the presence of salt. The expression profiles in the absence of salt, in both roots and leaves, were used for comparative controls. The miRNA nodes involved in root–leaf synergism were identified and validated. The analysis highlighted the role of osa-miR156a, osa-miR164a, osa-miR167a, osa-miR169a,b, osa-miR396a,b, osa-miR398b, and osa-miR399d. These miRNAs operated in stringently regulated genetic networks. The analysis also revealed that osa-miR167a and osa-miR399d are important part of synergistically interacting nodes to regulate growth of Pokkali plants in the presence of salt.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Construct encoding self-complementary ‘hairpin’ RNA (hpRNA) has been shown as an effective trigger of post-translational gene silencing. Gene silencing can be effectively inhibited by virus-encoded ...silencing suppressors that have been acquired evolutionarily to surmount silencing and allow infection. Here, we show that AC2, the silencing suppressor protein of Mungbean Yellow Mosaic India Virus (MYMIV), can inhibit the hpRNA-induced gene silencing in planta. Phytoene desaturase (PDS)-silenced transgenic lines were generated using PDS-hairpin gene-silencing construct in Nicotiana. The photobleach phenotype was observed in different T1 and T2 PDS-silenced lines indicating that the hairpin gene-silencing construct can efficiently down-regulate or silence the endogenous gene activity, and that the silencing is stably inherited over generations. The analysis of abundance of the PDS transcripts showed that the degree of silencing ranged from 20 to 70 % in different T0 and T1 transgenic lines. Upon introduction of MYMIV-AC2 in the silenced PDS transgenic lines, by genetic hybridization, the PDS expression was restored in F1 hybrids. The F1 lines (♀PDS X ♂MYMIV-AC2) showed the normal green phenotype instead of the photobleached phenotype indicating that introgression of MYMIV-AC2 in PDS silenced T0 lines, suppresses the hairpin gene-silencing. Our findings suggest that hpRNA vector can efficiently and stably induce gene silencing in plants and that MYMIV-AC2 can inhibit this silencing. This is the first report where we put forward that the dual system of hpRNA and MYMIV-AC2 suppressor can serve as an efficient switch for turning off and turning on gene expression, with potential applications in gene function analysis.
High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular ...genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
RNAi pathway is an antiviral defence mechanism employed by insects that result in degradation of viral RNA thereby curbing infection. Several viruses including flaviviruses encode viral suppressors ...of RNAi (VSRs) to counteract the antiviral RNAi pathway. Till date, no VSR has been reported in alphaviruses. The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay. Two non-structural proteins, namely, nsP2 and nsP3 were found to exhibit RNAi suppressor activity. We further validated the findings in natural hosts, namely in Aedes and in mammalian cell lines and further through EMSA and Agrobacterium infiltration in GFP silenced transgenic tobacco plants. Domains responsible for maximum RNAi suppressor activity were also identified within these proteins. RNA binding motifs in these domains were identified and their participation in RNAi suppression evaluated using site directed mutagenesis. Sequence alignment of these motifs across all species of known alphaviruses revealed conservation of these motifs emphasizing on a similar role of action in other species of alphaviruses as well. Further validation of RNAi suppressor activity of these proteins awaits establishment of specific virus infection models.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Seed germination paves the way for the dormant embryo to establish itself as a new plant marking the first critical step in postembryonic plant growth and development. Germination starts with the ...uptake of water (imbibition), followed by induction of transcription, translation, energy metabolism, and cell division processes. Although small RNAs have been implicated in many developmental processes, their role during seed germination stages and conditions remained elusive. Here we show that seed germination conditions, like imbibition and temperature, dynamically regulate the expression of many developmentally important miRNAs and their targets. We have identified 58 miRNAs belonging to 30 different families at different seed germination conditions. Amongst these, 15 miRNAs and their targets were significantly differentially expressed in Arabidopsis seeds in dry and 12 h, 24 h and 48 h of imbibition. Interestingly, differential expression of miR390, which targets trans-acting siRNA locus (TAS3) derived transcripts, resulted in alteration of tasiR-ARF mediated regulation of expression of target AUXIN RESPONSE FACTORs (ARF2/3/4). Our results suggest that the dynamic expression of several miRNAs, their targets, and a crosstalk between miRNA and ta-siRNA pathways contribute to the regulation of seed germination in Arabidopsis thaliana.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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