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

Abstract

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.

High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness

“…In general, the spatial and temporal regulation of miRNAs varies between different tissues or organs of rice [39][40][41]. Thus far, a few studies have analyzed miRNAs in rice developing grains [42][43][44], while other studies used entire spikelets [45,46]. In this study, we specifically used caryopsis tissue from the R6 stage, which is defined as "the grain depth expansion stage at which milky starch in the developing grain is beginning to become firm but is still soft" [47], for analyzing miRNAs regulated by HDT.…”

“…This is especially notable for Osa-miR1855, which was not detected in LaGrue at all. Osa-miR1846, which has been found to be highly expressed during grain filling in the spikelets [46], has been shown to target a heat shock factor (HSF) [96]. HSFs may induce chalkiness by promoting heat shock protein (HSP) expression [8,97].…”

Effect of Panicle Morphology on Grain Filling and Rice Yield: Genetic Control and Molecular Regulation

“…Such differential expressions influenced the transcript abundance of MYB , MADS -box, GRF , ARF , and the Brassinosteroid insensitive 1 -associated receptor kinase 1 precursor ( BAK1 ), regulating various aspects of grain filling and development ( Zhu et al, 2008 ; Xue et al, 2009 ; Peng et al, 2013 ; Yi et al, 2013 ). Later on, the differential expressions of miRNAs in the spikelets based on their spatial locations have also been studied in order to throw light on the possible influence of miRNAs in differential grain filling in the superior and inferior spikelets of compact and heavy panicles ( Peng et al, 2011 ; Peng et al, 2014 ; Chandra et al, 2021 ; Panigrahi et al, 2021 ; Teng et al, 2021 ). These studies revealed that several miRNAs, including miR164/miR167, miR159, miR1861, and miR396h targeting auxin-responsive factor ARF8 , MYB , beta-amylase, and auxin efflux carrier protein, respectively, were expressed higher in the poorly filled inferior spikelets compared with the well-filled superior spikelets, indicating negative regulatory role of these miRNAs in grain filling.…”

Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway

“…Thus, the role of miRNAs in corm development and starch and sucrose metabolism could be expected. This expectation is based on the earlier report in cassava that miRNAs effect the expression of genes involved in plant development, starch biosynthesis, and responses to the environmental stresses ( Panigrahi et al, 2021 ). Since, CircRNAs act as miRNA sponge to regulate target gene expression by inhibiting miRNA activity.…”