Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains

PLoS One. 2015 Oct 1;10(10):e0139658. doi: 10.1371/journal.pone.0139658. eCollection 2015.

Abstract

Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computational Biology
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks
  • Genes, Plant / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism*
  • Molecular Sequence Data
  • RNA, Plant / genetics*
  • Real-Time Polymerase Chain Reaction
  • Sequence Analysis, RNA / methods*
  • Sequence Homology, Nucleic Acid
  • Triticum / genetics*
  • Triticum / growth & development
  • Triticum / metabolism

Substances

  • MicroRNAs
  • RNA, Plant

Grants and funding

This work was supported by the National Natural Science Foundation of China (31301313), Hi-Tech Research and Development Program of China (2012AA10A308) and CAAS-Innovation Team Project.