Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer

Ginseng, Panax ginsengC.A. Meyer, is one of the most important medicinal herbs for human health and medicine in which ginsenosidesare known to play critical roles. The genes from the cytochrome P450 (CYP) gene superfamily have been shown to play important roles in ginsenoside biosynthesis. Here we report genome-wide identification of the candidate PgCYP genes for ginsenoside biosynthesis, development of functional SNP markers for its manipulation and systems analysis of its underlying molecular mechanism. Correlation analysis identified 100 PgCYP genes, including all three published ginsenoside biosynthesisPgCYP genes, whose expressions were significantly correlated with the ginsenosidecontents. Mutation association analysis identified that six of these 100 PgCYP genes contained SNPs/ InDelsthat were significantly associated with ginsenosides biosynthesis(P ≤ 1.0e-04). These six PgCYP genes, along with all ten published ginsenoside biosynthesisgenes from the PgCYP and other gene families, formed a strong co-expression network, even though they varied greatly in spatio-temporal expressions. Therefore, this study has identified six new ginsenoside biosynthesiscandidate genes, provided a genome-wide insight into how they are involved in ginsenoside biosynthesisand developed a set of functional SNP markers useful for enhanced ginsenoside biosynthesisresearch and breeding in ginsengand related species.