Identification and adaptive evolution analysis of FAR1/FHY3 in <i>Eleutherococcus senticosus</i> and prediction of target genes regulating saponin synthesis

Light plays a significant role in affecting secondary metabolic processes in the medicinal plant <italic>Eleutherococcus senticosus</italic>. The FAR1/FHY3 gene family responds to variations in light quality and play diverse roles in plant growth and development. However, few studies have explored and functionally analyzed the <italic>Es</italic>FAR1/FHY3 gene family. In this study, 21 <italic>EsFAR1/FHY3</italic> genes, exhibiting uneven distribution across 14 chromosomes, were identified in <italic>E. senticosus</italic> using bioinformatic tools. <italic>Es</italic>FAR1/FHY3 genes were divided into five subfamilies. The gene structure and conserved domains within each subfamily were similar. There were many collinear relationships between FAR1/FHY3 in <italic>E. senticosus</italic> and FAR1/FHY3 in related species. Evolutionary analysis indicated that <italic>EsFAR1/FHY3</italic> underwent predominantly negative selection and was highly conserved. There were 5−15 light response elements in the <italic>EsFAR1/FHY3</italic> promoter. The results of RNA sequencing and real-time fluorescence quantitative PCR showed that 15 <italic>EsFAR1/FHY3</italic> genes were differentially expressed after irradiation with different light qualities. Molecular docking showed that four <italic>Es</italic>FAR1/FHY3 genes stably bind to the promoter of the <italic>farnesyl diphosphate synthase</italic> (FPS) gene involved in saponin synthesis. These findings suggest that <italic>Es</italic>FAR1/FHY3 responds to changes in light quality and interacts with the promoter of the saponin synthase gene in <italic>E. senticosus</italic>, offering insights into the molecular mechanism underlying the impact of light quality on the secondary metabolism of <italic>E. senticosus</italic>.