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

Abstract

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.

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Acknowledgments

We gratefully thank all of those who provided help and technical assistance with this study, including Juan Lin who collected naturalized S. purpurea material in the US; Jan Gloger who collected native S. purpurea in Europe; Michelle Serapiglia, Jane Lam, and Petra Knauer who assisted with leaf tissue collection and DNA extraction; and Rob Elshire and Sharon Mitchell at Cornell University’s Genomic Diversity Facility for their advice on SNP genotyping and Craig Carlson for his advice on SNP analysis.

Data archiving statement

The data reported here are archived as supplemental material in TGG. SNP genotypes used in this study can be requested from the corresponding author (lbs33@cornell.edu).

Funding

This work was funded by grants from the US Department of Agriculture National Institute of Food and Agriculture for the Northeast Woody/Warm-Season Biomass Consortium (NEWBio, Grant No. 2012-68005-19703) through the Agriculture and Food Research Initiative and from the Northeast Sun Grant Center (NE 11-48).

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Correspondence to Lawrence B. Smart.

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Gouker, F.E., DiFazio, S.P., Bubner, B. et al. Genetic diversity and population structure of native, naturalized, and cultivated Salix purpurea. Tree Genetics & Genomes 15, 47 (2019). https://doi.org/10.1007/s11295-019-1359-0

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Keywords

  • Bioenergy
  • Biomass
  • Clonality
  • Genetics
  • Relatedness
  • Salicaceae