Phylogeography and evolutionary history of Prunus tomentosa in China: guiding germplasm conservation and development

BACKGROUND: Prunus tomentosa is a fruit tree native to China, with a broad distribution and high conservation value from ornamental, economic, and ecological perspectives. The germplasm resource is valuable for developing new cherry cultivars due to its high adaptability to almost all soil types and climatic conditions. However, little is known about the genetic diversity, phylogeographic structure and historical events, with its abundant genetic information. Here, we clarified the phylogeography of P. tomentosa based on chloroplast DNA (cpDNA) fragments and nuclear ribosomal internal transcribed spacer (ITS) across 779 individuals from 42 populations. RESULTS: We found 26 unique chloroplast haplotypes and 23 unique ITS haplotypes. Haplotype diversity was high based on cpDNA (Hd = 0.689) and ITS (Hd = 0.877) haplotypes. We observed a significant difference in the genetic differentiation based on Wright’s fixation index (cpDNA: Fst = 0.6077; ITS: Fst = 0.3447). Comparing two genetic differentiation indices, Nst and Gst, it was inferred that the P. tomentosa populations have a phylogeographical structure. Combination of network map, phylogenetic tree, population distribution, and population structure of P. tomentosa haplotype revealed two phylogeographic groups—eastern phylogeographic group (EG) and western phylogeographic group (WG). The divergence time of EG and WG occurred about 12.31 Ma and the common ancestor of P. tomentosa may have emerged during the Miocene period, and a significant correlation was observed between genetic distance and geographical distance of the populations. Signals from cpDNA and ITS data indicate that P. tomentosa has undergone recombination and population expansion. The expansion time was about 5.74 Ka based on the chloroplast data. CONCLUSION: Our findings illuminated the genetic diversity, species divergence and phylogeographical history of P. tomentosa and provided robust genetic evidence to support that Xiaolong Mountains, Hua Mountains, and Qian Mountains might be the glacial refuges of P. tomentosa. Our findings will not only guide conservation and utilization strategies for P. tomentosa but also contribute to the development of germplasm for breeding novel cherry cultivars.