Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

J Exp Bot. 2016 Nov;67(21):6037-6049. doi: 10.1093/jxb/erw361. Epub 2016 Oct 4.


Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.

Keywords: Anther; Argonaute; microRNA; phasiRNA; rice; spikelet..

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Argonaute Proteins / genetics
  • Argonaute Proteins / physiology
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / physiology
  • Genes, Plant
  • In Situ Hybridization
  • MicroRNAs / genetics*
  • MicroRNAs / physiology
  • Mutation
  • Oryza / genetics*
  • Oryza / metabolism
  • Oryza / physiology
  • RNA, Plant / genetics*
  • RNA, Plant / metabolism
  • RNA, Plant / physiology
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / physiology
  • Reproduction / genetics
  • Reproduction / physiology


  • Argonaute Proteins
  • MicroRNAs
  • RNA, Plant
  • RNA, Small Interfering