Genetic Diversity Evaluation and Population Structure Analysis of the Genus Paphiopedilum in Guangxi: Promoting the Selection and Breeding of New Species

The genus <i>Paphiopedilum</i> (Orchidaceae) has high ornamental value due to its long flowering period, brilliant flower color, and peculiar floral morphology. Guangxi is the center of ecological diversity of <i>Paphiopedilum</i>, and therefore it is urgent to conduct rescue studies on the genetic resources and genetic structure of this genus in Guangxi. In this study, the genetic diversity of 39 populations from eight <i>Paphiopedilum</i> species in Guangxi was analyzed using ten selected EST-SSR primer pairs and fluorescent PCR amplification. The results show that genetic diversity varied among species, with large differences in expected heterozygosity (<i>He</i>). The highest genetic diversity was observed in <i>P. barbigerum</i> (<i>I</i> = 0.923; <i>He</i> = 0.480), while <i>P. dianthum</i> (<i>I</i> = 0.179; <i>He</i> = 0.098) showed the lowest diversity. From the genus perspective, molecular variance analysis (AMOVA) revealed that 57% of the genetic variation occurred among populations and 43% within populations, with inter-population variation being the main source of genetic variation. From a species perspective, genetic differentiation varied, with inter-individual differentiation ranging from 79% to 95%. The percentage of molecular variance indicated that genetic variation mainly occurred among individuals, which was the main source of total variation. According to the principle of maximum likelihood, the optimal K value was determined to be 6, and 760 <i>Paphiopedilum</i> samples were divided into six subgroups. The results of this study not only identify priority populations for conservation and establish a germplasm repository to preserve existing resources, but also provide references for research on asexual reproduction, seed propagation, and hybrid breeding of <i>Paphiopedilum</i>, thereby promoting the conservation and sustainable utilization of <i>Paphiopedilum</i> germplasm resources.