Identification and expression analysis of microRNAs during ovule development in rice (Oryza sativa) by deep sequencing
- 479 Downloads
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.
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.
KeywordsRice ovule development High-throughput sequencing MiRNA expression Integrating expression analysis Programmed cell death
Growth responding factor
Minimum free energy
Programmed cell death
Transcripts per million
Web gene ontology annotation plot
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.
- Baucher M, Moussawi J, Vandeputte OM, Monteyne D, Mol A, Pérez-Morga D, EI Jaziri M (2013) A role for the miR396/GRF network in specification of organ type during flower development, as supported by ectopic expression of Populus trichocarpa miR396c in transgenic tobacco. Plant Biol 15:892–898CrossRefPubMedGoogle Scholar
- Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 21:3119–3132CrossRefPubMedPubMedCentralGoogle Scholar
- Pang M, Woodward AW, Agarwal V, Guan X, Ha M, Ramachandran V, Chen XM, Triplett BA, Stelly DM, Chen ZJ (2009) Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol 10:R122CrossRefPubMedPubMedCentralGoogle Scholar
- Tian C, Muto H, Higuchi K, Matamura T, Tatematsu K, Koshiba T, Yamamoto KT (2004) Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyls elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition. Plant J 40:333–343CrossRefPubMedGoogle Scholar