Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice.

Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.

Red Light and Glucose Enhance Cytokinin-Mediated Bud Initial Formation in Physcomitrium patens.

Growth and development of Physcomitrium patens is endogenously regulated by phytohormones such as auxin and cytokinin. Auxin induces the transition of chloronema to caulonema. This transition is also regulated by additional factors such as quantity and quality of light, carbon supply, and other phytohormones such as strigolactones and precursors of gibberrelic acid. On the other hand, cytokinins induce the formation of bud initials following caulonema differentiation. However, the influence of external factors such as light or nutrient supply on cytokinin-mediated bud initial formation has not been demonstrated in Physcomitrium patens. This study deals with the effect of light quality and nutrient supply on cytokinin-mediated bud initial formation. Bud initial formation has been observed in wild type plants in different light conditions such as white, red, and blue light in response to exogenously supplied cytokinin as well as glucose. In addition, budding assay has been demonstrated in the cry1a mutant of Physcomitrium in different light conditions. The results indicate that carbon supply and red light enhance the cytokinin response, while blue light inhibits this process in Physcomitrium.

MicroRNAs modulate ethylene induced retrograde signal for rice endosperm starch biosynthesis by default expression of transcriptome.

Control of stage specific spike in ethylene production at anthesis has been a vauable route to potentially enhance genetic ceiling for grain filling of rice spikelet. A number of genes controlling ethylene homeostasis and starch synthesis have been identified so long, but lack of credible information on master modulation of gene expression by miRNAs and their target genes associated with hormonal dynamics obfuscate mechanisms controlling genotype difference in quantum of grain filling. The confusion accounts for consequent shrinkage of options for yield manipulation. In a two by two factorial design, miRNA regulation of spikelet specific grain development in low against high sterile recombinant inbred lines of rice Oryza sativa L. namely CR 3856-62-11-3-1-1-1-1-1-1 (SR 157) and CR 3856-63-1-1-1-1-1-1-1 (SR 159) respectively, and inferior verses superior spikelets were compared during first 10 days after anthesis. Grain filling was poorer in SR159 than SR157 and inferior spikelets in the former were most vulnerable. Between the cultivars, overall expression of unique miRNAs with targets on ethylene pathway genes was higher in SR159 than SR157 and the situation was opposite for auxin pathway genes. Precision analysis in psTarget server database identified up-regulation of MIR2877 and MIR530-5p having Os11t0141000-02 and Os07t0239400-01 (PP2A regulatory subunit-like protein and ethylene-responsive small GTP-binding proteins) and MIR396h having Os01t0643300-02 (an auxin efflux carrier protein) and Os01t0643300-01 (a PIN1-like auxin transport protein), as targets with highest probability at anthesis and 5 days after anthesis respectively, in the inferior spikelet and the fold change values of DGE matched with pattern of gene expression (relative transcript level) in the qRT-PCR studies conducted for relevant miRNAs and protein factors for ethylene and auxin signalling. In conclusion, epigenetic regulation of both auxin and ethylene homeostasis control grain filling of rice spikelet was established, but evidences were more robust for the latter.

Light- and hormone-mediated development in non-flowering plants: An overview.

MAIN CONCLUSION: Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.

Perspective of mitigating atmospheric heavy metal pollution: using mosses as biomonitoring and indicator organism.

Mosses were proved as an ideal and reliable biomonitor as well as an indicator of atmospheric trace metal pollution. They are used as model indicator species of air pollution since long back due to their simple structure, genetic diversity, totipotency, rapid colony-forming ability, and high metal resistance behavior. Bryomonitoring technique is gradually being popularized as an economically viable procedure for estimating the degrees of environmental health and evaluating the toxic pollutants in biosphere. Thus, in the present scenario, many parts of the world use these organisms for monitoring the air pollution. This article describes an overview of the relationship of terrestrial mosses with trace metals with respect to their uptake, accumulation, and toxification as well as detoxification and tolerance mechanisms. The review article explicitly expresses the caliber of the cryptogamic mosses in establishing the pristine environment around the world. It also highlights the underpinning mechanisms and potential for future research directions. We have referred more than 250 articles, which deals with the assessment and impact of different heavy metals on 52 numbers of different moss species belongs to different climatic zones. The present review covers the research work in this area carried out worldwide since 1965.