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

Abstract

Switchgrass (<i>Panicum Virgatum</i> 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 <i>U2AF</i> 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, <i>18S rRNA</i> was demonstrated to be the best reference gene. <i>CYP5</i> was determined to be the optimal reference gene in Cd treated root tissues. The least stable reference gene was identified to be <i>CYP2</i> 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 (<i>PvZIP4</i> and <i>PvPDB8</i>) in young leaves and roots of switchgrass. Our results demonstrated that the relative expression of the target genes consistently changed during the treatment when <i>CYP5/UBQ1</i>, <i>U2AF/ACT12</i>, <i>eEF1a/U2AF,</i> or <i>18S rRNA/ACT12</i> were combined as the internal reference genes. However, the time-dependent change pattern of the target genes was significantly altered when <i>CYP2</i> 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.