A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

  1. Qian-Hao Zhu1,
  2. Andrew Spriggs1,
  3. Louisa Matthew1,
  4. Longjiang Fan2,
  5. Gavin Kennedy1,
  6. Frank Gubler1, and
  7. Chris Helliwell1,3
  1. 1 CSIRO Plant Industry, Canberra, ACT 2601, Australia;
  2. 2 Institute of Crop Science, Zhejiang University, Hangzhou 310029, China

Abstract

Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of ∼5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.

Footnotes

  • 3 Corresponding author.

    3 E-mail chris.helliwell{at}csiro.au; fax 61-2-6246-5000.

  • [Supplemental material is available online at www.genome.org. All small RNA sequences have been submitted to Gene Expression Omnibus in GenBank under the series identifier GSE11014. Transcripts of TAS3a1, TAS3b1, and TAS3b2 have been submitted to GenBank under the accession nos. EU293143, EU293144, and EU293145, respectively. Primary transcripts of miR1850, miR1428e_3p, and their alternative splicing forms have been submitted to GenBank under accession nos. EU563913–EU563918. Novel miRNA sequences have been submitted to miRBase under accession nos. miR1846–miR1884.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.075572.107.

    • Received December 13, 2007.
    • Accepted May 12, 2008.
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