Population Variation and Phylogeography of Cherry Blossom (<i>Prunus conradinae</i>) in China

<i>Prunus conradinae</i> (subgenus <i>Cerasus</i>, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of <i>P. conradinae</i> in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of <i>P. conradinae</i> variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of <i>P. conradinae</i> to ensure adequate germplasm resources in the future. We also found support for a new variant, <i>P. conradinae</i> var. <i>rubrum</i>. We observed high genetic diversity within <i>P. conradinae</i> (haplotype diversity [<i>H_d</i>] = 0.830; ribotype diversity [<i>R_d</i>] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. <i>P. conradinae</i> expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12–5.17 Mya) in the Pliocene. The population of <i>P. conradinae</i> spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47–4.54 Mya), suggesting that the population of <i>P. conradinae</i> differentiated first in Central and East China. The population of <i>P. conradinae</i> experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11–2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for <i>P. conradinae</i>. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of <i>P. conradinae</i>.