Genetic Background of the Hetian Rose Inferred from SNPs in Single-Copy Nuclear Loci and Plastid Genomes

Background/Objectives: The Hetian Rose (Rosa ‘Hetian’) is a locally important oil-bearing rose cultivar grown in Hetian, Xinjiang, China, but its genetic origin remains unclear. Methods: To clarify its genetic background, we sampled R. ‘Hetian’ together with 35 related Rosa species and cultivars and performed phylogenetic and genetic-structure analyses using 7478 SNPs in 1851 single-copy nuclear loci. We also reconstructed a plastid genome phylogeny to assess its maternal-lineage affinity. Results: In the nuclear SNP phylogeny, R. ‘Hetian’ was associated with European rose lineages rather than Chinese Hybrid Rugosa roses. Genetic-structure analyses indicated that R. ‘Hetian’ showed its strongest nuclear genomic affinity to Gallica roses, with weaker affinities to several other Eurasian lineages. In the plastid phylogeny, R. ‘Hetian’ clustered with Gallica and Alba roses, sect. Caninae, and European sect. Synstylae accessions. Conclusions: Together, these results indicate that the genetic background of R. ‘Hetian’ is closely related to European Old Garden Roses. A Gallica-related lineage may have made a major contribution to its genomic background. Historical genetic exchange with other Eurasian Rosa lineages may also have contributed to its present genomic composition.