Identification of biosynthetic pathways involved in flavonoid production in licorice by RNA-seq based transcriptome analysis

Abstract

Liquiritin, a flavonoid, is a key medicinal ingredient in licorice (Glycyrrhiza uralensis), a commonly used herb in traditional Chinese medicine. Biosynthesis of flavonoids is a complex process that involves not only the phenylpropanoid biosynthetic pathway but also many other secondary metabolic pathways. In this study, we tried to identify the key enzymes and pathways for the biosynthesis of flavonoids in G. uralensis by analyzing the gene expression patterns in samples containing different levels of flavonoid. G. uralensis seeds were mutagenized by X-ray irradiation and samples were selected based on HPLC analysis. RNA-seq was used to examine the gene expression in two samples with high flavonoid content (H1 and H2) and one control sample (L1) with low flavonoid content. 61.37 million, 54.21 million, and 54.22 million clean reads were obtained in sample H1, H2, and L1, respectively. A total of 1875 core differentially expressed genes (DEGs) were identified. The expression patterns of core DEGs were similar in samples H1 and H2 but not in sample L1. Flavonoid metabolic pathway, terpenoid biosynthetic pathway, plant hormone signal transduction pathway, plant circadian rhythm pathway, and starch and sucrose metabolic pathway were found to play significant roles for flavonoid biosynthesis in licorice. Ten co-expressed DEGs on the five metabolic pathways were further verified by qRT-PCR, which confirmed that the RNA-Seq results were accurate and reliable. This study provides a basis for future functional genes mining and molecular regulatory mechanism elucidation of flavonoid biosynthesis in licorice.