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

Mingzhu Zhao,Yanping Lin,Meiping Zhang,Yi Wang,Yilai Han,Chunyu Sun,Xiangyu Li,Yanfang Wang,Kangyu Wang

doi:10.1038/s41598-018-36349-5

Mingzhu Zhao, Yanping Lin + Show 7 more

Open Access

https://doi.org/10.1038/s41598-018-36349-5

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Abstract

Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal herbs for human health and medicine in which ginsenosides are 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 biosynthesis PgCYP genes, whose expressions were significantly correlated with the ginsenoside contents. Mutation association analysis identified that six of these 100 PgCYP genes contained SNPs/InDels that were significantly associated with ginsenosides biosynthesis (P ≤ 1.0e-04). These six PgCYP genes, along with all ten published ginsenoside biosynthesis genes 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 biosynthesis candidate genes, provided a genome-wide insight into how they are involved in ginsenoside biosynthesis and developed a set of functional SNP markers useful for enhanced ginsenoside biosynthesis research and breeding in ginseng and related species.

Highlights

This study has identified six new candidate PgCYP genes involved in ginsenoside biosynthesis and developed functional SNP/InDel markers for these genes, which are important for advanced ginsenoside biosynthesis research and enhanced breeding in ginseng and related species
Identification of the candidate PgCYP genes involved in ginsenoside biosynthesis
These results indicated that the PgCYP gene superfamily plays important roles in ginsenoside biosynthesis

Summary

Introduction

Farnesyl phosphate synthase (FPS)[15], UDP-glycosyltransferase (UGT)[16], and cytochrome P450 (CYP716A53v2, CYP716A52v2 and CYP716A47)[17,18,19] These studies indicate that it is likely that additional genes, including those of the CYP gene superfamily encoding cytochrome P450, are involved in ginsenoside biosynthesis. We analyzed these 100 PgCYP genes by association study and identified five SNPs and three InDels from 6 of them that were significantly associated with the ginsenoside contents in the four-year-old roots of 42 genotypes We characterized these six PgCYP genes in several aspects and examined their relationships with those published ginsenoside biosynthesis genes that were previously cloned from the PgCYP gene superfamily, CYP716A53v2, CYP716A52v2 and CYP716A4717–19, and from other gene families, including SS9, CAS10, SE11, DS12,13, β-AS14, FPS15 and UGT16. This study has identified six new candidate PgCYP genes involved in ginsenoside biosynthesis and developed functional SNP/InDel markers for these genes, which are important for advanced ginsenoside biosynthesis research and enhanced breeding in ginseng and related species

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