Genetic diversity and population structure of native, naturalized, and cultivated Salix purpurea

Salix purpurea is a woody perennial that is bred as a high-yielding bioenergy crop in North America. To gain an understanding of the genotypic variation associated with phenotypic diversity, this study characterized the population structure and genetic diversity of S. purpurea from its native range of Europe and naturalized range of the Northeastern United States (US). A total of 273 genotypes of S. purpurea were analyzed, which included 95 naturalized accessions and 19 horticultural cultivars from the US and 159 accessions collected from the native range of four European countries. All individuals were evaluated using a filtered set of 2287 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) markers. Using five clustering techniques (PCA, neighbor joining, STRUCTURE, DAPC, and affinity propagation), population structure was resolved into three broadly classified groups. Further analysis revealed seven to eight subpopulations which corresponded to geographical collection sites, where performance of the DAPC and affinity propagation methods was superior to STRUCTURE analysis for the purposes of characterizing population structure and performing population assignment. The native European accessions exhibited greater diversity and subpopulation structure than the US naturalized accessions, where there was a clear geographical delineation between the alpine/subalpine collections and the lowland collections at the Baltic Sea and Oder River. We also show that a subset of the horticultural cultivars had a higher likelihood of similarity to US naturalized populations which display hybrid ancestry, where both naturalized and cultivated genotypes appear to share a common ancestor. Additionally, several accessions collected from different sites were found to be clonal. Ongoing and future conservation and association studies will benefit from these known substructures and diversity assessments.