Genetic diversity, phylogenetic relationships, and marker development between Hydrangea serrata and H. macrophylla based on plastome and 45S nrDNA

Ornamental hydrangeas (genus Hydrangea ) are cultivated worldwide for their diverse flower colors and attractive morphology. Here, we assembled the complete plastid genome (plastome) and 45S nuclear ribosomal DNA (45S nrDNA) sequences of 22 individuals representing H. serrata , H. macrophylla , and related species ( H. arborescens , H. paniculata , H. petiolaris , and H. hydrangeoides ). The plastomes contained up to 2,344 single-nucleotide polymorphisms (SNPs) and 367 insertions/deletions (InDels) within the genus, whereas the assembled 45S nrDNA sequences showed 119 SNPs and 10 InDels. Phylogenetic analyses based on plastome and 45S nrDNA sequences clearly separated H. serrata and H. macrophylla from the other Hydrangea species. In the plastome-based tree, H. petiolaris was placed in the same clade as H. arborescens , whereas in the 45S nrDNA-based tree it showed a close relationship to H. hydrangeoides . The H. serrata and H. macrophylla samples were not always separated according to their species boundaries, as observed in samples Hse8–Hse12. Notably, one H. serrata sample (Hse8), collected from a wild mountainous region of Japan, exhibited a closer genetic relationship to H. macrophylla samples, indicating that cultivated hydrangeas may have originated from a specific wild lineage of H. serrata adapted to mountainous habitats. Using plastome-derived molecular markers, 66 Hydrangea samples were further classified into five groups, with Group II comprising both cultivated H. macrophylla and a subset of wild H. serrata samples, suggesting a close genetic affinity between this group and the ancestral gene pool of cultivated H. macrophylla . Based on these genomic resources, eight plastome-derived molecular markers were developed to differentiate cultivated hydrangeas from wild genotypes and to assess genetic diversity within H. serrata and H. macrophylla , providing practical tools for germplasm identification, breeding, and genetic resource management of Hydrangea species.

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