Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune

Renjun Qu,Fangquan Wang,Yiwen Cao,Jie Yang,Yingjing Cui,Ying Zhou,Xiaoqing Tang,Yujing Miao

doi:10.1186/s12867-019-0126-y

Abstract

BackgroundIsatis indigotica, a traditional Chinese medicine, produces a variety of active ingredients. However, little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathways of these ingredients. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful, commonly-used method for gene expression analysis, but the accuracy of the quantitative data produced depends on the appropriate selection of reference genes.ResultsIn this study, the systematic analysis of the reference genes was performed for quantitative real-Time PCR normalization in I. indigotica. We selected nine candidate reference genes, including six traditional housekeeping genes (ACT, α-TUB, β-TUB, UBC, CYP, and EF1-α), and three newly stable internal control genes (MUB, TIP41, and RPL) from a transcriptome dataset of I. indigotica, and evaluated their expression stabilities in different tissues (root, stem, leaf, and petiole) and leaves exposed to three abiotic treatments (low-nitrogen, ABA, and MeJA) using geNorm, NormFinder, BestKeeper, and comprehensive RefFind algorithms. The results demonstrated that MUB and EF1-α were the two most stable reference genes for all samples. TIP41 as the optimal reference gene for low-nitrogen stress and MeJA treatment, while ACT had the highest ranking for ABA treatment and CYP was the most suitable for different tissues.ConclusionsThe results revealed that the selection and validation of appropriate reference genes for normalizing data is mandatory to acquire accurate quantification results. The necessity of specific internal control for specific conditions was also emphasized. Furthermore, this work will provide valuable information to enhance further research in gene function and molecular biology on I. indigotica and other related species.

Highlights

Isatis indigotica, a traditional Chinese medicine, produces a variety of active ingredients
Selecting reference genes based on transcriptome data and the performance of amplification primers Based on previous reports in Arabidopsis [25], cucumber [26] and wheat [27], we selected nine genes as candidate genes by mining the Isatis indigotica transcriptome data [14]
We will be able to establish a better understanding of gene functions [40]. Quantitative real-time polymerase chain reaction (qRT-PCR) has emerged as a broadly accepted method for gene expression analysis due to its accuracy, highthroughput, and sensitivity [18]

Summary

Introduction

A traditional Chinese medicine, produces a variety of active ingredients. Little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathways of these ingredients. Most of them have a low abundance in plants, for example, indican, isatin, indirubin, and indigotin account for 1.16–43.6 μg/g DW (dry weight), 0.30–3.45 μg/g DW, 1.01–34.4 μg/g DW, and 1.45–18.7 μg/g DW, respectively [12]. These active compounds are secondary metabolites that accumulate during normal plant growth or exposure to environmental stresses [13]. An understanding of functional gene expression profiling will provide us with better insight into the metabolic pathway and the regulatory mechanism operating under stresses in this medical herb

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