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Background: In plants, time information is recorded in strictly ordered sequences of development events, resulting in age-associated physiological and morphological differentiation, including clear spatial gradients from the base to the crown within a single tree. However, the molecular mechanisms driving such ontogeny-related differentiation remain largely unknown.

Results: Based on our newly generated Larix kaempferi (Lamb.) Carr. genome annotation, we identified 307 age-related genes, which were grouped into two expression clusters reflecting opposite temporal trends. Spatial expression analysis further revealed 13 differentially expressed genes along the vertical axis of the tree, suggesting their roles in regulating spatially distinct physiological traits. Yeast one-hybrid and dual-luciferase reporter assays demonstrated that LaAGL2-3b directly binds to the promoters of six genes, including LaAGL2-3a, LaAGL2-3b (self-regulation), and L. kaempferi cycloartenol synthase (LkCAS1). Over-expression of LaAGL2-3 in Arabidopsis thaliana (L.) Heynh. significantly accelerated life cycle progression, supporting its functional involvement in aging-related developmental processes.

Conclusions: Our results indicate that LaAGL2-3 shows coordinated temporal and spatial expression dynamics with other age-related genes in L. kaempferi. This coordinated pattern offers hypotheses about its potential role within age-associated regulatory processes. The genomic and transcriptomic resources generated here offer a foundation for future functional investigations and for improving our understanding of conifer development and ontogeny.