The study performed transcriptome profiling of Cryptomeria japonica individuals from different geographic origins grown in three common gardens across Japan, assembling 77,212 transcripts guided by the species' genome. Using SNP-based genetic clustering and weighted gene co‑expression network analysis, they identified gene modules whose expression correlated with genetic differentiation, revealing that defense‑related genes are up‑regulated in Pacific‑side populations while terpenoid metabolism genes are higher in Sea‑of‑Japan populations, indicating local adaptation via regulatory changes.