Genome-Wide Identification of the PgFLA Gene Family and Association Analysis with Ginsenoside Biosynthesis in Panax ginseng

Panax ginseng is an economically important medicinal plant, and the biosynthetic regulatory network of ginsenosides, its core bioactive constituents, is extremely complex. Fasciclin-like arabinogalactan proteins (FLAs) are a class of glycoproteins widely involved in plant growth and development that modulate secondary cell wall biosynthesis, phytohormone signal transduction, and stress responses in plants. In this study, we performed a genome-wide identification of the FLA gene family in P. ginseng and identified 21 PgFLA family members. Comprehensive analyses were subsequently conducted to characterize their gene structures, chromosomal distributions, collinearity relationships, phylogenetics, expression patterns, and cis-acting regulatory elements. Subsequently, combined with SNP/InDel-ginsenoside association analysis based on 344 ginseng accessions, correlation analysis between gene expression and ginsenoside content, as well as co-expression network analysis linking PgFLA genes with key enzyme genes of the ginsenoside biosynthetic pathway, eight candidate PgFLA genes associated with ginsenoside biosynthesis were identified. Further mediation effect analysis identified six PgFLA members that potentially affect ginsenoside biosynthesis by modulating the expression of key enzymes involved in the ginsenoside biosynthetic pathway. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of these pivotal candidate genes in methyl jasmonate (MeJA)-treated ginseng adventitious roots. The results revealed that the transcript abundances of five genes (PgFLA02, PgFLA05-01, PgFLA05-02, PgFLA06, and PgFLA09-06) were significantly negatively correlated with the levels of protopanaxadiol-type ginsenosides (Rb1, Rb2, Rb3, Rc, and Rd). These findings provide a theoretical foundation for further dissecting the molecular regulatory network underlying ginsenoside biosynthesis and supply valuable candidate genes for marker-assisted breeding and quality improvement of cultivated P. ginseng.