Selection of suitable inner reference genes for normalisation of microRNA expression response to abiotic stresses by RT-qPCR in leaves, flowers and young stems of peach

Luo, Xiaoyan; Shi, Ting; Sun, Hailong; Song, Juan; Ni, Zhaojun; Gao, Zhihong

doi:10.1016/j.scienta.2013.10.030

Cited by 23 publications

(33 citation statements)

References 30 publications

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“…According to the criterion mentioned above, four genes including miR156, miR396, U6 snRNA , and 25S rRNA were excluded due to unsatisfactory efficiency and specificity. The remaining 13 candidates, with E -values ranging from 0.81 to 1.21 (Luo et al, 2014 ), and the R 2 -values higher than 0.98, were kept for further investigation.…”

Section: Resultsmentioning

confidence: 99%

“…According to previous studies, various reference genes for miRNA RT-qPCR have been used in plants, including the 5S ribosomal RNA ( 5S rRNA ), 5.8S ribosomal RNA ( 5.8S rRNA ), U6 small nuclear RNA ( U6 snRNA ), and glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ; Song et al, 2010 ; Yu et al, 2011 ; Gao et al, 2012 ; Thiebaut et al, 2012 ). To date, only a few reports are related to the selection of reference genes for miRNA RT-qPCR, such as in Amygdalus persica L. (Luo et al, 2014 ), Triticum aestivum L. (Feng et al, 2012 ), Dimocarpus longan Lour. (Lin and Lai, 2013 ), Citrus reticulata Blanco.…”

Section: Introductionmentioning

confidence: 99%

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Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress

et al. 2016

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Sugarcane, accounting for 80% of world's sugar, originates in the tropics but is cultivated mainly in the subtropics. Therefore, chilling injury frequently occurs and results in serious losses. Recent studies in various plant species have established microRNAs as key elements in the post-transcriptional regulation of response to biotic and abiotic stresses including cold stress. Though, its accuracy is largely influenced by the use of reference gene for normalization, quantitative PCR is undoubtedly a popular method used for identification of microRNAs. For identifying the most suitable reference genes for normalizing miRNAs expression in sugarcane under cold stress, 13 candidates among 17 were investigated using four algorithms: geNorm, NormFinder, deltaCt, and Bestkeeper, and four candidates were excluded because of unsatisfactory efficiency and specificity. Verification was carried out using cold-related genes miR319 and miR393 in cold-tolerant and sensitive cultivars. The results suggested that miR171/18S rRNA and miR171/miR5059 were the best reference gene sets for normalization for miRNA RT-qPCR, followed by the single miR171 and 18S rRNA. These results can aid research on miRNA responses during sugarcane stress, and the development of sugarcane tolerant to cold stress. This study is the first report concerning the reference gene selection of miRNA RT-qPCR in sugarcane.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress

et al. 2016

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“…The validation of references as the same principle of mRNA expressions through RT-qPCR, was also suggested before the detection of miRNAs’ expressions3031. To select good candidate reference miRNAs, we selected those with high counts (>100) and low expression variabilities indicated by sequencing data.…”

Section: Methodsmentioning

confidence: 99%

Infections of virulent and avirulent viruses differentially influenced the expression of dicer-1, ago-1, and microRNAs in Bombus terrestris

Niu

Meeus

Coninck

et al. 2017

Sci Rep

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The microRNA (miRNA) pathway is well established to be involved in host-pathogen interactions. As key insect pollinators, bees are suffering from widely spreading viruses, especially honeybees and bumblebees. In order to better understand bee-virus interaction, we comparatively analyzed the involvement of the bumblebee miRNA pathway upon infection by two different viruses. In our setup, an avirulent infection is induced by slow bee paralysis virus (SBPV) and a virulent infection is induced by Israeli acute paralysis virus (IAPV). Our results showed the increased expressions of dicer-1 and ago-1 upon SBPV infection. There were 17 and 12 bumblebee miRNAs differentially expressed upon SBPV and IAPV infections, respectively. These results may indicate the involvement of the host miRNA pathway in bumblebee-virus interaction. However, silencing of dicer-1 did not influence the genome copy number of SBPV. Target prediction for these differentially expressed miRNAs showed their possible involvement in targeting viral genomic RNA and in the regulation of networks in bumblebee. Our study opens a new insight into bee-virus interaction meditated by host miRNAs.

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“…A set of miRNAs was selected for evaluation in plants, such as castor bean, cotton, watermelon, wheat and sugarcane [30][31][32][33]. Luo et al, 2014, found miR5059 and miR5072 were the best reference genes in different peach tissues under different abiotic stress treatments using poly(A)-tailed RT-qPCR approach [34]. In Arabidopsis, stress-induced miRNAs were cloned by sequencing and the computational method [35,36].…”

Section: Introductionmentioning

confidence: 99%

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

Lyu

et al. 2019

Genes

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MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.

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Selection of suitable inner reference genes for normalisation of microRNA expression response to abiotic stresses by RT-qPCR in leaves, flowers and young stems of peach

Cited by 23 publications

References 30 publications

Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress

Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress

Infections of virulent and avirulent viruses differentially influenced the expression of dicer-1, ago-1, and microRNAs in Bombus terrestris

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

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