Identification of reference genes for quantitative expression analysis of microRNAs and mRNAs in barley under various stress conditions

PloS One
Jannatul FerdousPenny J Tricker

Abstract

For accurate and reliable gene expression analysis using quantitative real-time reverse transcription PCR (qPCR), the selection of appropriate reference genes as an internal control for normalization is crucial. We hypothesized that non-coding, small nucleolar RNAs (snoRNAs)would be stably expressed in different barley varieties and under different experimental treatments,in different tissues and at different developmental stages of plant growth and therefore might prove to be suitable reference genes for expression analysis of both microRNAs (miRNAs)and mRNAs. In this study, we examined the expression stability of ten candidate reference genes in six barley genotypes under five experimental stresses, drought, fungal infection,boron toxicity, nutrient deficiency and salinity. We compared four commonly used housekeeping genes; Actin (ACT), alpha-Tubulin (α-TUB), Glycolytic glyceraldehyde-3-phosphate dehydrogenase(GAPDH), ADP-ribosylation factor 1-like protein (ADP), four snoRNAs; (U18,U61, snoR14 and snoR23) and two microRNAs (miR168, miR159) as candidate reference genes. We found that ADP, snoR14 and snoR23 were ranked as the best of these candidates across diverse samples. Additionally, we found that miR168 was a suitable refe...Continue Reading

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Citations

Dec 4, 2016·Functional & Integrative Genomics·Yawei TangTashi Nyima
Apr 24, 2018·The Plant Journal : for Cell and Molecular Biology·Hui ZhouBujun Shi
May 8, 2016·Plant, Cell & Environment·Jannatul FerdousPenny J Tricker
Jul 22, 2019·Nature Communications·Bastien ChristJing-Ke Weng
Oct 13, 2016·Functional & Integrative Genomics·Jannatul FerdousPenny J Tricker
Apr 18, 2017·PloS One·Anna Karoline Silva FaustoMaite F S Vaslin
Dec 12, 2019·Frontiers in Molecular Neuroscience·Theodora KalpachidouMichaela Kress
Jul 13, 2018·Frontiers in Plant Science·Ganesh ThapaFiona M Doohan
Apr 23, 2019·The Plant Journal : for Cell and Molecular Biology·Margaret A PallottaRyan Whitford
Nov 9, 2019·International Journal of Molecular Sciences·Naoki UbeAtsushi Ishihara
Feb 2, 2021·Frontiers in Genetics·Prabin TamangRobert S Brueggeman
May 11, 2021·PLoS Genetics·Ken-Ichiro HibaraJun-Ichi Itoh

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Datasets Mentioned

BETA
MIMAT0018216
MIMAT0018210

Methods Mentioned

BETA
electrophoresis
PCR
salt treatment

Software Mentioned

geNorm
Normfinder
Norm Finder
BestKeeper
AlleleID

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