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Open AccessArticle

Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses

by 1, 2 and 3,*
1
Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China
2
Zonation Fringe Technology Co., Metro Vancouver, BC V5C 2A0, Canada
3
College of Science and Technology, Wenzhou-Kean University, Wenzhou 325060, China
*
Author to whom correspondence should be addressed.
Genes 2020, 11(5), 502; https://doi.org/10.3390/genes11050502
Received: 14 April 2020 / Revised: 30 April 2020 / Accepted: 1 May 2020 / Published: 3 May 2020
(This article belongs to the Section Plant Genetics and Genomics)
Switchgrass (Panicum Virgatum L.) has been recognized as the new energy plant, which makes it ideal for the development of phytoremediation on heavy metal contamination in soils with great potential. This study aimed to screen the best internal reference genes for the real-time quantitative PCR (RT-qPCR) in leaves and roots of switchgrass for investigating its response to various heavy metals, such as cadmium (Cd), lead (Pb), mercury (Hg), chromium (Cr), and arsenic (As). The stability of fourteen candidate reference genes was evaluated by BestKeeper, GeNorm, NormFinder, and RefFinder software. Our results identified U2AF as the best reference gene in Cd, Hg, Cr, and As treated leaves as well as in Hg, Pb, As, and Cr stressed root tissues. In Pb treated leaf tissues, 18S rRNA was demonstrated to be the best reference gene. CYP5 was determined to be the optimal reference gene in Cd treated root tissues. The least stable reference gene was identified to be CYP2 in all tested samples except for root tissues stressed by Pb. To further validate the initial screening results, we used the different sets of combinatory internal reference genes to analyze the expression of two metal transport associated genes (PvZIP4 and PvPDB8) in young leaves and roots of switchgrass. Our results demonstrated that the relative expression of the target genes consistently changed during the treatment when CYP5/UBQ1, U2AF/ACT12, eEF1a/U2AF, or 18S rRNA/ACT12 were combined as the internal reference genes. However, the time-dependent change pattern of the target genes was significantly altered when CYP2 was used as the internal reference gene. Therefore, the selection of the internal reference genes appropriate for specific experimental conditions is critical to ensure the accuracy and reliability of RT-qPCR. Our findings established a solid foundation to further study the gene regulatory network of switchgrass in response to heavy metal stress. View Full-Text
Keywords: reference genes; Panicum Virgatum L.; heavy metal stresses; real-time quantitative PCR reference genes; Panicum Virgatum L.; heavy metal stresses; real-time quantitative PCR
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MDPI and ACS Style

Zhao, J.; Zhou, M.; Meng, Y. Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses. Genes 2020, 11, 502. https://doi.org/10.3390/genes11050502

AMA Style

Zhao J, Zhou M, Meng Y. Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses. Genes. 2020; 11(5):502. https://doi.org/10.3390/genes11050502

Chicago/Turabian Style

Zhao, Junming; Zhou, Man; Meng, Yu. 2020. "Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses" Genes 11, no. 5: 502. https://doi.org/10.3390/genes11050502

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