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Identification and characterization of microRNAs from wheat (Triticum aestivum L.) under phosphorus deprivation

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Abstract

Plant microRNAs (miRNAs) are non-coding RNAs (19–24 nucleotides long) that play a critical role in the sequence-specific regulation of target gene transcripts. In this study, 32 miRNAs from wheat (Triticum aestivum L.) (TaMIRs) currently released in the miRBase database were subjected to expression pattern analysis under conditions of normal inorganic phosphate (Pi) supply and Pi deprivation stress. Semi-quantitative and quantitative reverse transcriptase polymerase chain reaction analysis revealed that 9 TaMIRs responded to Pi starvation: TaMIR159b, TaMIR167, TaMIR399, TaMIR408, TaMIR1122, TaMIR1125, TaMIR1135, TaMIR1136, and TaMIR1136 were up-regulated, whereas TaMIR408 was down-regulated. Small RNA blot analysis confirmed these results. Target prediction analysis indicated that the low Pi-responsive TaMIRs possessed variable target genes, ranging from none in TaMIR399 and TaMIR1122 to more than 20 in TaMIR1136. The target genes randomly selected from each low Pi-responsive TaMIR (except TaMIR399 and TaMIR1122) demonstrated an opposite expression pattern to the TaMIR, suggesting that the target genes were transcriptionally regulated by miRNA-mediated pathways. The target genes that interacted with the low Pi-responsive TaMIRs could be classified into diverse gene families, such as those involving transcription regulation, cell cycling, chromosome establishment, signal transduction, primary metabolism, phytohormone response, trafficking, defense response, and protein degradation. This study helps elucidate the plant regulatory mechanisms in response to low Pi signaling via the miRNA-mediated pathways in wheat.

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Abbreviations

miRNA:

microRNA

TaMIR:

wheat microRNA

RT-PCR:

Reverse transcription polymerase chain reaction

qRT-PCR:

Quantitative reverse transcripttion polymerase chain reaction

RNAi:

RNA interference

RISC:

RNA-induced silencing complex

PSR:

Phosphorus-starvation responsive

CS:

Chinese spring

DNase:

Deoxyribonuclease

CK:

Non-stress control

TC:

Tentative consensus

BLAST:

Basic local alignment search tool

AGO:

argonaute

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Acknowledgments

This work was supported by the China’s Major Projects for Transgenic Breeding (Grant number 2009ZX08009-011B) and the Key Crop Growth Regulation Laboratory of Hebei Province.

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Authors and Affiliations

  1. College of Agronomy, Agricultural University of Hebei, Baoding, Hebei Province, 071001, People’s Republic of China

    Xiaolei Zhao, Xiaoman Liu, Chengjin Guo & Kai Xiao

  2. College of Life Sciences, Agricultural University of Hebei, Baoding, China, 071001

    Juntao Gu

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  1. Xiaolei Zhao
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  2. Xiaoman Liu
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  3. Chengjin Guo
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  4. Juntao Gu
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  5. Kai Xiao
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Correspondence to Kai Xiao.

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Xiaolei Zhao and Xiaoman Liu contributed equally to this work

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Zhao, X., Liu, X., Guo, C. et al. Identification and characterization of microRNAs from wheat (Triticum aestivum L.) under phosphorus deprivation. J. Plant Biochem. Biotechnol. 22, 113–123 (2013). https://doi.org/10.1007/s13562-012-0117-2

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