Phytohormone and transcriptome analyses reveal the mechanisms underlying branch inclination angle formation in narrow-crowned Chamaecyparis hodginsii

Chamaecyparis hodginsii with a naturally narrow-crowned form combines ornamental value, landscape greening functions, and timber production potential, making it a promising species for forestry applications. Therefore, we aimed to identify superior narrow-crowned provenances and to elucidate the physiological and molecular mechanisms underlying branch inclination angle (BIA) variation. Among the 14 provenances, provenance 4 had the lowest BIA; provenance 2 showed the highest proportion of narrow-crowned individuals and the highest ZT levels, while IAA was the lowest in provenance 14. Comprehensive evaluation identified provenances 3 and 4 as the most promising narrow-crowned sources. BIA was significantly negatively correlated with both ZT and IAA, with path analysis revealing a strong negative direct effect of IAA on BIA. Transcriptome analysis identified 2272 differentially expressed genes, including 27 involved in phytohormone signaling pathways. Six up-regulated and three down-regulated SAUR family members exhibited unique expression patterns in the narrow-crowned provenance, suggesting their involvement in auxin signaling output during BIA development. Cytokinin regulators A-ARR and B-ARR showed opposite expression patterns. The gibberellin receptor GID1 was down-regulated, while the growth repressor DELLA was up-regulated, indicating suppression of cell division and elongation. Genes in salicylic acid and jasmonic acid signaling were suppressed, whereas the ABA regulator PP2C decreased and the ethylene component EIN2 increased, suggesting reprogramming of defense-related phytohormone signaling. These findings highlight the importance of auxin and downstream SAUR genes in regulating BIA and confirm provenances 3 and 4 as superior narrow-crowned sources. Our findings provides new insights and genetic resources for early selection and molecular design breeding of narrow-crowned C. hodginsii .