Monoclonality and Low Genetic Diversity in Vanilla shenzhenica: Highlighting Urgent Need for Genetic Preservation of China’s Only Endangered Vanilla

Long-term clonality has profound consequences for genetic structure despite offering an alternative means of reproductive assurance under unfavorable conditions for sexual reproduction. <i>Vanilla shenzhenica</i> Z. J. Liu & S. C. Chen (Orchidaceae), the only endangered <i>Vanilla</i> species in China, exhibits a clear tendency towards asexual propagation, as evidenced by its small, fragmented wild populations. To develop effective conservation strategies for this species, it is essential to assess the extent of clonality and evaluate genetic diversity both within and among populations. In this study, we sampled 43 individuals from cultivated and wild populations of <i>V. shenzhenica</i> and analyzed their phylogenetic relationships, genetic structure, and diversity based on single-nucleotide polymorphisms (SNPs). Our results indicate that all the studied wild populations are predominantly sustained by vegetative growth, each forming a monoclonal patch with a single genotype. The overall genetic diversity within <i>V. shenzhenica</i> is low likely due to a combination of factors, including clonality, reduced effective population size, and environmental disturbances. These findings underscore the urgent need for the conservation management of this species. Conservation plans should prioritize ex situ conservation efforts, focusing on promoting assisted sexual reproduction to produce viable seeds and offspring that combine diverse genotypes from different populations. This study provides valuable insights in relation to effective conservation planning for endangered clonal species.