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Plant Cell Reports

, Volume 36, Issue 11, pp 1815–1827 | Cite as

Identification and expression analysis of microRNAs during ovule development in rice (Oryza sativa) by deep sequencing

  • Ya Wu
  • Liyu Yang
  • Meiling Yu
  • Jianbo Wang
Original Article

Abstract

Key message

MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death.

Abstract

MiRNAs are 20–24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage. Based on the sequencing data, 486 known and 204 novel miRNAs were identified during rice ovule development. Moreover, 56, 65 and 11 differentially expressed miRNAs between adjacent developmental stages were identified. By analyzing transcriptome and degradome data, we identified 41, 65 and 12 coherent target genes for the differentially expressed miRNAs in ovule development. We found that changes in the expression of plant hormone-related miRNAs may play important roles in embryo sac development, providing evidence for cross-talk communication between sporophytic tissue and the female gametophyte. Additionally, we revealed that miRNAs may be involved in programmed cell death after fertilization. Finally, we constructed miRNA-mediated regulatory networks that are active during rice ovule development.

Keywords

Rice ovule development High-throughput sequencing MiRNA expression Integrating expression analysis Programmed cell death 

Abbreviations

GA

Gibberellic acid

GRF

Growth responding factor

MFE

Minimum free energy

PCD

Programmed cell death

TPM

Transcripts per million

WEGO

Web gene ontology annotation plot

Notes

Acknowledgements

This work was supported by the State Key Basic Research and Development Plan of China (2013CB126900).

Compliance with ethical standards

Conflict of interest

The authors declared that they have no conflicts of interest with this work.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina

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