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In silico search and biological validation of microRNAs related to drought response in peach and almond

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Abstract

Plant responses to drought stress are regulated at the transcriptional and post-transcriptional levels through noncoding endogenous microRNAs. These microRNAs play key roles in gene expression, mainly by down-regulating target mRNAs. In this work, an in silico search and validation for microRNAs related to drought response in peach (‘G.H. Hill’), almond (‘Sefied’) and an interspecific peach-almond hybrid (‘GN 15’) has been performed. We used qPCR to analyse the gene expression of several miRNAs described as being related to drought response in peach, including miR156, miR159, miR160, miR167, miR171, miR172, miR398, miR403, miR408, miR842 and miR2275 under mild and severe water deficit. These miRNAs were in silico selected on the basis of previous works, their conservation in plants and their drought response. qPCR analysis confirmed the implication of these miRNAs in the dehydration stress response in the three assayed genotypes. Comparison of miRNA expression patterns in the three evaluated genotypes indicated that the hybrid GN 15 showed higher expression levels of specific miRNAs which should be related to the observed drought tolerance. mRNA target transcripts of the miRNAs studied were predicted using the Rose database, which includes transcription factors that regulate plant growth and development. In addition, results showed that the promoter region contains responsive elements to hormone-mediated regulatory elements. Network analysis not only unravelled the interaction between miRNAs and their predicted gene targets but also highlighted the roles of miRNAs in response to drought stress.

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Abbreviations

ABA:

Abscisic acid

ABREs:

ABA response elements

AREs:

Anaerobic induction elements

BLAST:

Basic Local Alignment Search Tool

CSD:

Copper superoxide dismutase

DW:

Dry weight

EST:

Expressed sequence tags

FW:

Fresh weight

HSEs:

Heat stress-responsive elements

LTRs:

Low temperature-responsive elements

MBS:

MYB binding site

mRNA:

Messenger RNA

miRNA:

MicroRNA

NCBI:

National Center for Biotechnology Information

P. persica :

Prunus persica

RNAPs:

RNA polymerases

ROS:

Reactive oxygen species

RT:

Retro transcription

RWC:

Relative water content

SPL:

Squamosa promoter binding protein-like

TW:

Turgid weight

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Acknowledgments

The authors are grateful to Shahrekord University and the Centre of Excellence for the Biotechnology of Pome Fruits and Almond Diseases in the Central Region of Iran for providing partial financial support to the MSc students (FE). The authors would also like to thank Dr. Esmaeil Ebrahimie of the School of Biological Sciences at the University of Adelaide, Australia, for his help in the construction of a gene network by Pathway Studio software 9. This study has been supported in part by the project AGL2013-43550-R from the Spanish Ministry of Economy and Competiveness.

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Authors and Affiliations

  1. Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Box 115, Shahrekord, Iran

    Fazileh Esmaeili, Behrouz Shiran & Neda Mirakhorli

  2. Institute of Biotechnology, Shahrekord University, Box 115, Shahrekord, Iran

    Behrouz Shiran

  3. Department of Biology, School of Sciences, Razi University, Kermanshah, Iran

    Hossein Fallahi

  4. Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, USA

    Hikmet Budak

  5. Department of Plant Breeding, CEBAS-CSIC, Espinardo, Box 164, Murcia, 30100, Spain

    Pedro Martínez-Gómez

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  1. Fazileh Esmaeili
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  2. Behrouz Shiran
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  3. Hossein Fallahi
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  4. Neda Mirakhorli
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  5. Hikmet Budak
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  6. Pedro Martínez-Gómez
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Correspondence to Behrouz Shiran or Pedro Martínez-Gómez.

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This article forms part of a special issue of Functional & Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang)

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Fig. S1

Predicted miRNA targets and their complementary sites within defined mRNAs. Each bottom strand shows the miRNA sequence, and each top strand shows the corresponding complementary site within specific mRNA targets (GIF 35 kb)

High Resolution Image (TIF 570 kb)

Table S1

List of newly identified computer-based miRNAs and their characteristics in P. dulcis by EST analysis. NM: number of mismatches; LM: length of the mature miRNA; LP: length of the miRNA precursor sequence; MFEI: Minimal folding free energy index (DOCX 15 kb)

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Esmaeili, F., Shiran, B., Fallahi, H. et al. In silico search and biological validation of microRNAs related to drought response in peach and almond. Funct Integr Genomics 17, 189–201 (2017). https://doi.org/10.1007/s10142-016-0488-x

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