摘要Objectives This study aimed to elucidate the molecular mechanisms underlying the increased artemisinin content and enhanced density of glandular secretory trichomes(GSTs)in the HAN1(Hainan)haplotype of Artemisia annua.Methods Employing genetic and phylogenetic analyses,we identified AaCOI1 genes genome-wide,compared plant height,artemisinin content,and GST density in HAN1 and LN(Liaoning)haplotypes,elucidated their evolution and structural features,and analyzed expression of AaCOI1 and associated genes.Results Compared to LN,HAN1 exhibited significantly greater plant height,higher artemisinin content,and increased GST density.Orthologous gene analysis identified 17,724 core genes,21,608 dispensable genes,and 1,645 private genes.Functional identification revealed that private genes in HAN1 were enriched in functions related to insect response,whereas those in shandong were associated with cell growth and differentiation.Pronounced divergence between HAN1 and LQ9(Shandong)was observed in AaCOI1 gene sequence homology,exon-intron structure,motif composition,and cis-regulatory elements.Furthermore,HAN1 showed marked upregulation of AaCOI1 genes and key artemisinin biosynthetic regulators,along with downregulation of jasmonic acid(JA)signaling repressors.Conclusions This study shows AaCOI1 genes are multi-copy.Haplotype analysis reveals population variation in artemisinin regulation and links haplotypic divergence to differential JA response.These findings address critical knowledge gaps,offer molecular breeding targets,and promote a shift toward systems biology.The molecular mechanisms for elevated artemisinin and GST density in HAN1 were revealed.Structural variations upregulate AaCOI1 genes,promoting interaction with JA signaling components like jasmonate ZIM-domain repressors(JAZs),similar to glycogen synthase kinase,cullin-1,and cullin-2.This suppresses JA repressors,activates the pathway,and upregulates genes for artemisinin biosynthesis and GST development,enhancing both traits.These results confirm that elevated expression of AaCOI1 genes boosts artemisinin biosynthesis.