Accelerating Dalbergia odorifera Plantation Breeding: SSR-Based Genetic Diversity and Trait Associations for Enhanced Heartwood Yield

<i>Dalbergia odorifera</i> T. Chen possesses significant aromatic, medicinal, and timber value, yet its wild populations are critically endangered due to habitat degradation. Breeding programs are urgently needed to address resource shortages, but the suitability of large-scale plantations as alternative genetic resources remains unverified. This study systematically evaluated the genetic diversity of 380 individuals from five populations using 24 polymorphic SSR markers, identifying 278 alleles. The results demonstrated a moderate level of genetic diversity in plantation populations, comparable to wild resources. Additionally, nine phenotypic traits were measured in 70 individuals. Correlation analysis revealed that the heartwood ratio (HWR) was significantly positively correlated with diameter at breast height (DBH) and ground diameter (GD) (<i>p</i> ≤ 0.05). Our association analysis, based on general linear (GLM) and mixed linear models (MLM), revealed two key findings: one locus (96c-345) was significantly associated with diameter traits, and four loci (34a-241, S03-265, JXHT097-252, JXHT136-270) were strongly linked to the HWR (<i>p</i> ≤ 0.01). This research provides initial evidence that plantations are viable substitutes for wild germplasm and establishes a foundation for marker-assisted breeding in this valuable species.