Genome-Wide Analysis of 24-nt siRNAs Dynamic Variations during Rice Superior and Inferior Grain Filling

24 nt-siRNAs are the most abundant small interfering RNAs in rice grains aside from microRNAs. To investigate the roles that 24 nt-siRNAs played in the poor grain filling of rice inferior grains, dynamic variations of 24 nt-siRNAs in inferior grains were compared with those of superior grains by using small RNA deep sequencing technology. The results showed that 24 nt-siRNAs derived from multiple regions of rice genome, and the maintenance of the two strands of 24 nt-siRNA duplex was a non-random process. The amounts of 24 nt-siRNAs declined with the process of grain filling in both superior and inferior grains, but 24 nt-siRNAs in inferior grains was much higher than that of superior grains in each period we sampled. Bioinformatics prediction indicated that 24 nt-siRNAs targeted on more genes involved in most of the known KEGG rice pathways, such as the starch and sucrose biosynthesis pathway. Combined with digital gene expression profiling of target genes, 24 nt-siRNAs mapped on the antisense strands of exons were specifically investigated, but the abundance of 24 nt-siRNAs did not show negative correlations with their corresponding target genes. The results indicated that 24 nt-siRNAs were not involved in down-regulation of target genes. The potential biological meanings for this inconsistency were probably the results of methylation directed gene expression activation, or competition for small RNA stability methylation.

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-04-12

• Fields of study

  Agricultural and Food Sciences, Medicine, Biology

• Identifiers
  DOI 10.1371/journal.pone.0061029PMID 23593380PMCID 3625182
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Reconstruction

  2022cited by this paper
• SHORT VEGETATIVE PHASE (SVP) protein negatively regulates miR172 transcription via direct binding to the pri‐miR172a promoter in Arabidopsis

  2012cited by this paper
• Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.

  2012cited by this paper
• Characterization of grapevine microR164 and its target genes

  2012cited by this paper
• Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants.

  2012cited by this paper
• Role of SEPALLATA3 (SEP3) as a downstream gene of miR156-SPL3-FT circuitry in ambient temperature-responsive flowering

  2012cited by this paper
• psRNATarget: a plant small RNA target analysis server

  2011cited by this paper
• Regulation of flowering time and floral patterning by miR172.

  2011cited by this paper
• Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa).

  2011influential reference
• LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers

  2011cited by this paper
• Regulation of expression of starch synthesis genes by ethylene and ABA in relation to the development of rice inferior and superior spikelets

  2011cited by this paper
• miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions

  2011cited by this paper
• siRNAs: the hidden face of the small RNA world.

  2010cited by this paper
• Grain-filling problem in 'super' rice.

  2010cited by this paper
• Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq.

  2010cited by this paper
• Biogenesis and function of endogenous and exogenous siRNAs

  2010cited by this paper
• siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis

  2010cited by this paper
• On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development

  2010cited by this paper
• Roles of plant small RNAs in biotic stress responses.

  2009cited by this paper
• Hormones in the grains and roots in relation to post-anthesis development of inferior and superior spikelets in japonica/indica hybrid rice.

  2009cited by this paper
• The effect of sucrose and abscisic acid interaction on sucrose synthase and its relationship to grain filling of rice (Oryza sativa L.).

  2009cited by this paper
• Origin, biogenesis, and activity of plant microRNAs.

  2009cited by this paper
• Control of rice grain-filling and yield by a gene with a potential signature of domestication

  2008cited by this paper
• Characterization and expression profiles of miRNAs in rice seeds

  2008cited by this paper
• A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.

  2008cited by this paper
• KAAS: an automatic genome annotation and pathway reconstruction server

  2007cited by this paper
• Oryza sativa Dicer-like4 Reveals a Key Role for Small Interfering RNA Silencing in Plant Development[W][OA]

  2007cited by this paper
• Activating gene expression in mammalian cells with promoter-targeted duplex RNAs.

  2007cited by this paper
• Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

  2007cited by this paper
• Functions of microRNAs and related small RNAs in plants

  2006cited by this paper
• The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.

  2006cited by this paper
• Erratum: Functions of microRNAs and related small RNAs in plants

  2006cited by this paper
• [Small RNA world in plants].

  2006cited by this paper
• Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice.

  2006cited by this paper
• The small RNA world of plants.

  2006cited by this paper
• Expression patterns of genes encoding carbohydrate-metabolizing enzymes and their relationship to grain filling in rice (Oryza sativa L.): comparison of caryopses located at different positions in a panicle.

  2005cited by this paper
• Real-time quantification of microRNAs by stem–loop RT–PCR

  2005cited by this paper
• Journal of Experimental Botany Advance Access published December 5, 2005 Journal of Experimental Botany, Page 1 of 12

  2005cited by this paper
• Small RNAs: classification, biogenesis, and function.

  2005cited by this paper
• Methylation as a Crucial Step in Plant microRNA Biogenesis

  2005cited by this paper
• Genetic and Functional Diversification of Small RNA Pathways in Plants

  2004influential reference
• MicroRNAs: small RNAs with a big role in gene regulation

  2004cited by this paper
• siRNAs can function as miRNAs.

  2003cited by this paper
• Role of MicroRNAs in Plant and Animal Development

  2003cited by this paper
• siRNAs can function as miRNAs

  2003cited by this paper
• Reviving China's ruined rivers.

  2002cited by this paper
• MicroRNAs in plants.

  2002cited by this paper
• Basic local alignment search tool.

  1990influential reference

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  2020cites this paper
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  2020cites this paper
• Favorable alleles can improve the grain-filling rate in hybrid japonica rice by enhancing both

  2019cites this paper
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  2019cites this paper
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  2019cites this paper
• Small RNAs in Rice: Molecular Species and Their Functions

  2018cites this paper
• Germination vigour difference of superior and inferior rice grains revealed by physiological and gene expression studies

  2018cites this paper
• SMARTER De-Stressed Cereal Breeding.

  2016cites this paper
• Small RNA changes in synthetic Brassica napus

  2016cites this paper
• Small RNAs and Gene Network in a Durable Disease Resistance Gene—Mediated Defense Responses in Rice

  2015influential citation
• Epigenetic regulation of rice flowering and reproduction

  2015cites this paper
• MicroRNA‐Based Biotechnology for Plant Improvement

  2015cites this paper
• Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice

  2014cites this paper