Genome-wide analysis of LBD genes in the medicinal plant Panax ginseng reveals the roles and molecular mechanisms of PgLBD18 and PgLBD49 in regulating lateral root development

Panax ginseng C. A. Meyer ( P. ginseng ) is a valuable medicinal plant with significant therapeutic and economic importance. The development of its lateral roots (LRs) is closely associated with the accumulation of bioactive compounds, particularly ginsenosides. To elucidate the genetic basis of lateral root development in P. ginseng and uncover the regulatory mechanisms of the LBD gene family in this process, this study conducted the first genome-wide identification of the LBD transcription factor family in P. ginseng . A total of 73 PgLBD genes were identified, and phylogenetic analysis classified these genes into two major categories: Class I (84 %) and Class II (16 %). Evolutionary analysis revealed that segmental duplication served as the primary mechanism for family expansion, with most genes undergoing purifying selection during evolution. Through expression profiling and functional validation, we identified PgLBD18 (IAA-inducible) and PgLBD49 (LR-specific) as key regulators of LR development. Overexpression of PgLBD18 in Arabidopsis thaliana ( A. thaliana ) significantly increased both LR number and length in an IAA-dependent manner. PgLBD18 mediates LR development via an auxin-dependent pathway, with its expression being directly activated by PgARF through binding to the AuxRE element (754–933 bp promoter region). In contrast, PgLBD49 promotes LR development through an auxin-independent mechanism by forming heterodimers with PgARF to stabilize transcriptional complexes and enhance downstream gene expression. These two genes coordinately optimize root system plasticity through dual regulatory pathways of “transcriptional regulation-protein interaction”, demonstrating their crucial roles in LR development. This study elucidates the molecular mechanism by which the “PgARF-PgLBD module” mediates auxin signaling to regulate LR development in P. ginseng . It proposes a novel strategy for targeted modulation of LBD genes to optimize root architecture in medicinal plants, offering practical significance for improving ginsenoside accumulation in medicinal tissues. • A total of 73 PgLBD genes were systematically identified from the Panax ginseng genome. • Revealing the auxin-dependent molecular mechanism by which PgLBD18 regulates lateral root development. • Elucidating the auxin-independent molecular mechanism by which PgLBD49 regulates lateral root development. • PgARF-PgLBD module dually regulates roots via transcription-protein interaction synergy.