Suppression of microRNA159 impacts multiple agronomic traits in rice (Oryza sativa L.)

Abstract

BackgroundmicroRNAs (miRNAs) are important regulators in plant growth and development. miR159 is a conserved miRNA among different plant species and has various functions in plants. Studies on miR159 are mostly done on model plant, Arabidopsis thaliana. In rice, studies on miR159 were either based upon genome-wide expression analyses focused upon responses to different nitrogen forms and abiotic stress or upon phenotypic studies of transgenic plants overexpressing its precursor. STTM (Short Tandem Target Mimic) is an effective tool to block the activity of endogenous mature miRNA activity in plant. Therefore, specific roles of miR159 in rice could be explored by down regulating miR159 through STTM.ResultsIn this study, expression of mature miR159 was successfully suppressed by STTM which resulted in the increased expressions of its two targets genes, OsGAMYB and OsGAMYBL1 (GAMYB-LIKE 1). Overall, STTM159 plants exhibited short stature along with smaller organ size and reduction in stem diameter, length of flag leaf, main panicle, spikelet hulls and grain size. Histological analysis of stem, leaf and mature spikelet hull showed the reduced number of small vascular bundles (SVB), less number of small veins (SV) between two big veins (LV) and less cell number in outer parenchyma. Gene Ontology (GO) enrichment analysis of differentially expressed genes between wild type plants and STTM159 transgenic plants showed that genes involved in cell division, auxin, cytokinin (CK) and brassinosteroids (BRs) biosynthesis and signaling are significantly down-regulated in STTM159 plants.ConclusionOur data suggests that in rice, miR159 positively regulates organ size, including stem, leaf, and grain size due to the promotion of cell division. Further analysis from the RNA-seq data showed that the decreased cell divisions in STTM159 transgenic plants may result, at least partly from the lower expression of the genes involved in cell cycle and hormone homeostasis, which provides new insights of rice miR159-specific functions.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1171-7) contains supplementary material, which is available to authorized users.

Recent hybridization and allopolyploidy reprogrammed Spartina microRNA expression under xenobiotic induced stress

“…The repression of miR156 by miR159 is predominantly mediated by MYB33/62, MYB33 simultaneously impacts the transcription of MIR156 genes, as well as their target SPL9 by directly binding to the promoters of these genes. Interestingly, the STTM159 transgenic resulted in the increased expression of target gene MYBs, and exhibited short stature along with smaller organ size, highlighting the importance of MIR159 genes in promoting cell division and organs development (Zhao et al 2017). In the present work, functional analysis of knock-out mutant harboring a T-DNA insertion in the exon of miR156 homolog showed sensitive phenotype.…”

Microtranscriptome of contrasting sugarcane cultivars in response to aluminum stress

“…In our study, spp-miRNA156 was down-regulated in both cultivars (Table 3) it contains complementary sequences to SQUAMOSA ( SQUA ) promoter - binding - like ( SPL ) target gene which encode plant-specific transcription factors (Table 4). miR156 was induced in soybean, wheat [40] and repressed in rice [41] under drought, it was also identified in sugarcane under drought but it was not differently expressed. In Arabidopsis miR156 and its target SPL3 were associated to the temporal regulation of shoot development [42].…”

“…It targets a MYB domain protein , a transcriptional regulatory region (Table 4). miR159 has been associated with the control of multiple agronomic traits in rice [41], where it suppress cell division regulating negatively organ size. A transcriptome of a mutant suppressing miRNA159 revealed 7899 differentially expressed genes involved in several different pathways.…”

“…A transcriptome of a mutant suppressing miRNA159 revealed 7899 differentially expressed genes involved in several different pathways. Down-regulated genes were involved in pathways related to cell cycle, growth, signal transduction and hormone biosynthesis and signaling [41]. Although miR159 had been associated to aluminum stress in rice [41] and Medicago [23] it was not found in sugarcane before.…”

MicroRNA MIMIC binding sites: Minor flanking nucleotide alterations can strongly impact MIMIC silencing efficacy in Arabidopsis

“…Not only does the same binding site within different backbones result in variable efficacies, but also different binding sites within the same backbone, such as the contrasting strong efficacy of MIM159 to the weak efficacy of MIM165 (Reichel et al., ). Given the current broad use of different miRNA decoy approaches to modulate and understand the miRNA function (Zhang et al., ; Zhao et al., , ), understanding the underlying mechanism(s) responsible for decoy efficacy will be important for their optimal use. Here, we focus on the widely used MIM s, and find their efficacy of miRNA inhibition can be strongly impacted by subtle changes to flanking nucleotide composition.…”