Genetic Relationships, Whole-Fruit Oil Variations, and Quantitative Trait Diversity in Elite Symplocos paniculata Accessions from Hunan Revealed by GBS

Symplocos paniculata is a promising woody oil species, but the genetic diversity and joint variation in whole-fruit, tissue-specific oil, fatty acid, and quantitative traits remain insufficiently characterized. Thirty elite accessions from six geographic origins in Hunan Province were evaluated using genotyping-by-sequencing, whole-fruit and tissue-specific oil measurements, fatty acid profiling, and 12 quantitative traits. A total of 6335 single-nucleotide polymorphisms revealed geographic differentiation together with substantial within-origin heterogeneity. The principal diversity, PCoA, AMOVA, and pairwise FST patterns remained stable after exclusion of a high-missingness accession. Whole-fruit oil content averaged 34.91% and ranged from 18.54% to 51.35%, with oleic acid as the predominant fatty acid. An additional tissue-specific experiment showed higher mean oil contents in non-seed than seed tissues (37.22% vs. 30.32%) and clear differences in fatty acid composition. Dry-mass-weighted reconstruction closely reproduced measured whole-fruit oil content (Pearson r = 0.935), indicating that whole-fruit variation reflects tissue-specific oil accumulation rather than tissue proportion alone. In the original 72-test analysis, pooled morphology–oil associations did not retain Benjamini–Hochberg significance after adjustment for geographic origin or genetic structure. In a separate 15-test tissue-specific reassessment, infructescence width remained positively associated with non-seed oil content in pooled, origin-adjusted, and genetic-adjusted models. These results characterize complementary genetic and oil-related variations among the sampled accessions and identify tissue-specific relationships that warrant independent validation in replicated common-garden and multi-year trials.