Integration of structural variation enhances the resolution of population structure and helps delineate conservation...

Rhododendron griersonianum has been classified as Critically Endangered (CR) and listed as a National Key Protected Wild Plant Species in China. Unfortunately, none of its populations were found within nature reserves, leaving them vulnerable to anthropogenic threats. Identifying conservation units is crucial to ensure its survival and recovery.

We employed whole genome resequencing to identify 5 800 675 single nucleotide polymoprhisms (SNPs) and 11 940 structural variants (SVs). Using these genomic markers, we compared genomic diversity, population clustering and differentiation. By integrating gene flow analysis and demographic reconstruction, we delineated conservation units and formulated management recommendations.

Population genomic analysis revealed relatively low genomic diversity in R. griersonianum, with values of 1.61 × 10-3 for SNPs and 1.36 × 10-5 for SVs. Despite the close geographical distances (minimum 5.9 km between populations), we detected limited gene flow (mean D = 0.054) and a high inbreeding level (FROH = 0.16), which was estimated to have begun approximately 3500 years ago. The four populations formed three genetic clusters. Population demographic analysis indicated a declining trend in effective population size from 3000 to 1000 years ago. Based on these results, we delineated two management units (MUs), three evolutionarily significant units (ESUs) and three adaptive (putative) units (AUs). We also made recommendations for the future conservation of R. griersonianum.

The integration of both SNPs and SVs enhanced the resolution of population structure and refined the delineation of conservation units in this narrowly distributed, small-population species. Our results provide important baseline genetic data, improving our understanding of recent human activities shaping contemporary population structure of small-population species.