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

Bruno Verstraeten (UGent) , Lien De Smet (UGent) , Tina Kyndt (UGent) and Tim De Meyer (UGent)
(2019) PLANTA. 250(6). p.2101-2110
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Abstract
RT-qPCR is a widely used method to investigate the expression levels of genes under certain conditions. A key step, however, to have reliable results is the normalization of expression. For every experimental condition, suitable reference genes must be chosen. These reference genes must not be affected by differences in experimental conditions. MicroRNAs are regulatory RNA molecules, able to direct the expression levels of protein coding genes. In plants, their attributed functions range from roles in development to immunity. In this work, microRNAs (miRNAs) are evaluated for their suitability as reference genes in rice after infection with root-knot nematode Meloidogyne graminicola or after priming with beta-amino butyric acid. The evaluation was based on their amplification efficiency and their stability estimates according to geNorm, NormFinder and BestKeeper. All tested miRNAs, excluding one, were considered acceptable for normalization. Furthermore, miRNAs were validated using miRNA sequencing data. The set of microRNAs miR390-5p and miR7694-3p was found to be the most stable combination under the tested conditions. Another miRNA set consisting of miR7694-3p, miR1868 and miR1849 also shows potential to be used for miRNA expression normalization under experimental conditions beyond the scope of this study. This work is the first report on reference miRNAs in rice for the purpose of plant defence studies.
Keywords
REAL-TIME, NEMATODES, VALIDATION, RESISTANCE, RT-qPCR, BABA, Rice, Meloidogyne graminicola, Plant defence

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MLA
Verstraeten, Bruno, et al. “Selection of MiRNA Reference Genes for Plant Defence Studies in Rice (Oryza Sativa).” PLANTA, vol. 250, no. 6, 2019, pp. 2101–10, doi:10.1007/s00425-019-03289-x.
APA
Verstraeten, B., De Smet, L., Kyndt, T., & De Meyer, T. (2019). Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa). PLANTA, 250(6), 2101–2110. https://doi.org/10.1007/s00425-019-03289-x
Chicago author-date
Verstraeten, Bruno, Lien De Smet, Tina Kyndt, and Tim De Meyer. 2019. “Selection of MiRNA Reference Genes for Plant Defence Studies in Rice (Oryza Sativa).” PLANTA 250 (6): 2101–10. https://doi.org/10.1007/s00425-019-03289-x.
Chicago author-date (all authors)
Verstraeten, Bruno, Lien De Smet, Tina Kyndt, and Tim De Meyer. 2019. “Selection of MiRNA Reference Genes for Plant Defence Studies in Rice (Oryza Sativa).” PLANTA 250 (6): 2101–2110. doi:10.1007/s00425-019-03289-x.
Vancouver
1.
Verstraeten B, De Smet L, Kyndt T, De Meyer T. Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa). PLANTA. 2019;250(6):2101–10.
IEEE
[1]
B. Verstraeten, L. De Smet, T. Kyndt, and T. De Meyer, “Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa),” PLANTA, vol. 250, no. 6, pp. 2101–2110, 2019.
@article{8647086,
  abstract     = {{RT-qPCR is a widely used method to investigate the expression levels of genes under certain conditions. A key step, however, to have reliable results is the normalization of expression. For every experimental condition, suitable reference genes must be chosen. These reference genes must not be affected by differences in experimental conditions. MicroRNAs are regulatory RNA molecules, able to direct the expression levels of protein coding genes. In plants, their attributed functions range from roles in development to immunity. In this work, microRNAs (miRNAs) are evaluated for their suitability as reference genes in rice after infection with root-knot nematode Meloidogyne graminicola or after priming with beta-amino butyric acid. The evaluation was based on their amplification efficiency and their stability estimates according to geNorm, NormFinder and BestKeeper. All tested miRNAs, excluding one, were considered acceptable for normalization. Furthermore, miRNAs were validated using miRNA sequencing data. The set of microRNAs miR390-5p and miR7694-3p was found to be the most stable combination under the tested conditions. Another miRNA set consisting of miR7694-3p, miR1868 and miR1849 also shows potential to be used for miRNA expression normalization under experimental conditions beyond the scope of this study. This work is the first report on reference miRNAs in rice for the purpose of plant defence studies.}},
  author       = {{Verstraeten, Bruno and De Smet, Lien and Kyndt, Tina and De Meyer, Tim}},
  issn         = {{0032-0935}},
  journal      = {{PLANTA}},
  keywords     = {{REAL-TIME,NEMATODES,VALIDATION,RESISTANCE,RT-qPCR,BABA,Rice,Meloidogyne graminicola,Plant defence}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{2101--2110}},
  title        = {{Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa)}},
  url          = {{http://doi.org/10.1007/s00425-019-03289-x}},
  volume       = {{250}},
  year         = {{2019}},
}

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