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

Abstract

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.

A comparative study of microRNAs in different stages of Eimeria tenella

“…Through the first base bias analysis, we found that the first base of the remaining miRNAs was not U, except for miRNAs with a length of 24 nt. Whereas, in other eukaryotes, such as Drosophila, Penicillium marneffei, Swarnaprabha rice and Rat, there is a high proportion of miRNAs whose first base is U (35)(36)(37)(45)(46)(47). Considering the cutting point preference of Dicer on the first base of miRNA, this different characteristics may result in significant differences in miRNAs of E. tenella compared to other organisms (48).…”

Light-Dependent Regulatory Interactions between the Redox System and miRNAs and Their Biochemical and Physiological Effects in Plants

“…Based on the many-fold and small increase in the level of pri-miR163 and pri-miR840, respectively, their response to high light was controlled at different steps of their biogenesis. In hyl1 mutant having disturbed pre-miRNA pro- Similarly to high light, low light intensity also modifies the expression of miRNAs, as observed in rice [140]. Shade during the reproductive stage increased the expression of miRNAs related to the cell wall, membrane, cytoskeleton, and cellulose synthesis, and it decreased the transcription of those involved in the control of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism.…”