Objective To identify the key genes of secondary xylem development response to planting density for a well understanding of molecular mechanism of planting density affecting radial growth of eucalypts.

Method By a combination of PacBio Iso-Seq and RNA-Seq analysis, the differentially expressed transcriptomes of xylem cells in Eucalyptus urophylla × E. grandis were identified under high and low planting densities. The tissues expression profiles of these key genes were analyzed via qRT-PCR.

Result A total of 45 490 non-redundant full-length transcripts and 443 transcripts differentially expressed in xylem cells were obtained under high and low planting densities, and 60 transcripts encoding regulatory factors were obtained. Under low planting density, the diameters of trees increased significantly. The PXL2 and its interactional genes CUL1, T15D22.7 related to cell division, the MYB46, C3H14 with their downstream genes CesAs and LACs related to secondary wall regulation were preferentially expressed in the xylem cells. These genes might play key roles in the regulation of diameter growth under different densities. In addition, the NAC86 homologous genes involved in sieve element development and the inhibitor PTL homologous genes with dual functions in cambial cell proliferation and xylem differentiation were also up-regulated. They could promote the xylem development, which were different from the functions in herbaceous plants. The results of tissue expression analysis showed that PXL2, CUL1, T15D22.7, NAC86 and PTL were predominantly expressed in phloem and xylem, whereas MYB46, C3H14, CesA and LAC17 were predominantly expressed in xylem.

Conclusion In this study, the candidate genes of xylem development related to planting density are identified and a model of molecular regulatory network that how the planting density affects radial growth of E. urophylla × E. grandis is proposed, which will benefit the intensive study of the molecular mechanism under different planting densities affecting radial growth for trees.