Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa)

Verstraeten, Bruno; Smet, Lien De; Kyndt, Tina; Meyer, Tim De

doi:10.1007/s00425-019-03289-x

Cited by 10 publications

(11 citation statements)

References 36 publications

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“…Over recent years, several novel reference genes have been identified for quantitative gene expression studies in plants [26,18,16]. However, this research has primarily been focused on annual crop plants, as opposed to perennial plants [7].…”

Section: Discussionmentioning

confidence: 99%

“…miR167c and miR167f can be used as internal standards for gene expression studies in both squash roots and watermelon leaves under nutrient starvation [32]. miR1849, miR390-5p, miR1868, and miR7694-3p have been used as reference genes in rice during infection with the root-knot nematode Meloidogyne graminicola or treatment with BABA [18]. In this work, we found that miR390a expression levels decreased 0.78-fold, and were ranked as the fourth most stable according to the geNorm and NormFinder programs, suggesting that miR390a is not the optimal reference gene in poplar under biotic stress.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, in cotton miR169, miR171/170, and miR172 were found to be stably expressed under various abiotic stresses [17]. miR390-5p, miR7694-3p, miR1868, and miR1849 were found to be suitable miRNA reference genes in rice throughout infection with the root-knot nematode Meloidogyne graminicola or treatment with beta-aminobutyric acid (BABA) [18]. miR156b and miR1520d also exhibited stable expression in soybean under abiotic stress [15].…”

Section: Introductionmentioning

confidence: 99%

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Identification and validation of miRNA reference genes in poplar under pathogen stress

et al. 2021

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Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression.However, few universal genes especially miRNAs have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using three reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g and miR156a were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a was used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different lenth between detected miRNAs and traditional referece genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification and validation of miRNA reference genes in poplar under pathogen stress

et al. 2021

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification and validation of miRNA reference genes in poplar under pathogen stress

Zhang

Yang

Yin

et al. 2021

Preprint

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Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression. However, few universal genes especially miRNAs have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using three reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g and miR156a were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a was used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different lenth between detected miRNAs and traditional referece genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

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Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato

Liu

Zhang

et al. 2020

Plant Physiology and Biochemistry

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Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa)

Cited by 10 publications

References 36 publications

Identification and validation of miRNA reference genes in poplar under pathogen stress

Identification and validation of miRNA reference genes in poplar under pathogen stress

Identification and validation of miRNA reference genes in poplar under pathogen stress

Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato

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