Genetic characterization is vital for tree germplasm utilization and conservation. Nanmu (Phoebe zhennan S. Lee. et F. N. Wei) is an extremely valuable tree species that can provide logs for many industrial products. This study aimed to assess the genetic diversity of a Nanmu breeding population using nine nSSR, five newly-developed cpSSR markers, and nine phenotypic traits, and extract a core collection. In general, the Na, Ne, and PIC for each nSSR/cpSSR were 2–37/2–3, 1.160–11.276/1.020–1.940, and 0.306–0.934/0.109–0.384, respectively. Fifteen chlorotype haplotypes were detected in 102 germplasms. The breeding population exhibited a relatively high level of genetic diversity for both nSSR (I = 1.768), cpSSR (I = 0.440, h = 0.286), and phenotypic traits (H′ = 1.98). Bayesian and cluster analysis clustered these germplasms into three groups. The germplasms revealed a high level of admixture between clusters, which indicated a relatively high level of gene exchange between germplasms. The F value (0.124) also showed a moderate genetic differentiation in the breeding population. A core collection consisting of 64 germplasms (62.7% of the whole germplasm) was extracted from phenotypic and molecular data, and the diversity parameters were not significantly different from those of the whole germplasm. Thereafter, a molecular identity was made up for each core germplasm. These results may contribute to germplasm management and conservation in the Nanmu breeding program, as well as genetics estimation and core collection extraction in other wood production rare species.

Nanmu (Phoebe zhennan) is an extremely valuable tree plant that is the main source of famous “golden-thread nanmu” wood. The potential metabolites and gene regulation mechanisms involved in golden thread formation are poorly understood, even though the color change from sapwood to heartwood has been investigated in several tree plants. Here, five radial tissues from sapwood to heartwood were compared via integrative metabolomic and transcriptomic analysis to reveal the secondary metabolites and molecular mechanisms involved in golden thread formation. During heartwood formation, gradual starch grain loss is accompanied by the cell lumen deposition of lipids and color-related extractives. Extractives of 20 phenylpropanoids accumulated in heartwood, including cinnamic acids and derivatives, coumarin acid derivatives, and flavonoids, which were identified as being closely related to the golden thread. Phenylpropanoids co-occurring with abundant accumulated metabolites of prenol lipids, fatty acyls, steroids, and steroid derivatives may greatly contribute to the characteristics of golden thread formation. Additionally, the expression of nine genes whose products catalyze phenylpropanoid and flavonoids biosynthesis was upregulated in the transition zone, then accumulated and used to color the heartwood. The expression levels of transcription factors (e.g., MYB, bHLH, and WRKY) that act as the major regulatory factors in the synthesis and deposition of phenylpropanoid and flavonoids responsible for golden thread formation were also higher than in sapwood. Our results not only explain golden thread formation in nanmu, but also broaden current knowledge of special wood color formation mechanisms. This work provides a framework for future research focused on improving wood color.

Phoebe hui is an extremely valuable tree that is the main source of the fragrant golden-thread nanmu wood. Although the fragrance of wood has been investigated in several trees, the potential substances and gene regulation mechanisms that are involved in fragrance formation are poorly understood. Here, three radial tissues, sapwood (SW), heartwood (HW), and the transition zone (TZ) in between them, were compared via integrative physiological, volatile-metabolomic, and transcriptomic analyses to identify the key metabolites and regulatory mechanisms involved in fragrance formation. During heartwood formation, gradual starch grain loss was accompanied by the deposition of lipids and extractives in the cell lumen. Extracts of terpenoids were synthesized and accumulated in the heartwood, including monoterpenoids (limonene and p-cymene) and sesquiterpenes (cubebene and guaiadiene); these were identified as being closely related to the special fragrance of the wood. Additionally, the expression of transcripts showed that the genes related to primary metabolism were specifically upregulated in the SW, whereas genes annotated in terpenoid biosynthesis were specifically upregulated in the HW. Therefore, we speculated that terpenoid biosynthesis occurs in situ in the HW via the HW formation model of Type-III (Santalum) using the precursors that were produced by primary metabolism in the SW. The expression levels of transcription factors (e.g., MYB, WRKY, and C2H2) acted as the major regulatory factors in the synthesis of terpenoids. Our results explain the special fragrance in P. hui and broaden the current knowledge of the regulatory mechanisms of fragrance formation. This work provides a framework for future research that is focused on improving wood quality and value.