Phylogeography and Population Variation in Prunus discoidea (Prunus subg. Cerasus) in China

<i>Prunus discoidea</i> is a unique cherry blossom germplasm resource native to China. It is widely distributed across the provinces of Anhui, Zhejiang, Jiangxi, Jiangsu, and Henan, with significant variation. We employed phylogeographic analysis to reveal the evolutionary history of <i>P. discoidea</i> to better understand its genetic diversity and structure. This study provides more accurate molecular insights for the effective conservation and utilization of this germplasm resource. We conducted a phylogeographic analysis of 348 individual plants from 13 natural populations using three fragments (<i>rpoB</i>, <i>rps16</i>, and <i>trnD-E</i>) of chloroplast DNA (cpDNA) and one fragment (ITS) of ribosomal DNA. The results revealed that <i>P. discoidea</i> demonstrates a significant level of genetic diversity (<i>H_d</i> = 0.782; <i>R_d</i> = 0.478). Gene flow among populations was limited, and the variation within populations was the main source of genetic diversity in <i>P. discoidea</i> (among populations: 34.26%, within populations: 65.74%). Regarding genetic differences among populations, <i>N_st</i> (0.401) showed greater differences than <i>G_st</i> (0.308; <i>p</i> < 0.05), demonstrating that there was a significant geographical structure of lineage. One lineage was the central region of Anhui and the western region of Hubei. The other lineage was the Jiangsu region and the Zhejiang region. <i>P. discoidea</i> diverged from <i>Prunus campanulata</i> approximately 1.5 million years ago, during the Pleistocene epoch. This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of <i>P. discoidea</i>.