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Examining population structure across multiple collections of Cannabis

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Abstract

Population structure of Cannabis sativa L. was explored across nine independent collections that each contained a unique sampling of varieties. Hierarchical Clustering of Principal Components (HCPC) identified a range of three to seven genetic clusters across datasets with inconsistent structure based on use type indicating the importance of sampling particularly when there is limited passport data. There was broader genetic diversity in modern cultivars relative to landraces. Further, in a subset of geo-referenced landrace accessions, population structure was observed based on geography. The inconsistent structure across different collections shows the complexity within Cannabis, and the importance of understanding any particular collection which could then be leveraged in breeding programs for future crop improvement.

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Availability of data and material

Data are available upon reasonable request to the corresponding author.

Code availability

Code and filtered vcfs are available at https://github.com/ahmccormick and high resolution figures at https://figshare.com/authors/Anna_H_McCormick/17741367

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Acknowledgements

We would like to thank Mr. Robert Connell Clarke for his curation of the use-type associations for the Phylos Bioscience (n=1378) dataset as well as for valuable discussions and insights.

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  1. Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mānoa, Honolulu, HI, 96822, USA

    Anna Halpin-McCormick & Michael B. Kantar

  2. LeafWorks Inc., 130 S. High St, Sebastopol, CA, 95472, USA

    Nicholas L. Batora, Rishi R. Masalia, Kerin B. Law & Eleanor J. Kuntz

  3. Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, 06269, USA

    Karolina Heyduk

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Contributions

Conceptualization: AHMC, KH, MBK, NB, RRM, KL, EJK, Formal Analysis: AHMC, RRM, Figure Preparation: AHMC, Manuscript Drafting: AHMC, Writing and Reviewing Manuscript: AHMC, KH, MBK, NB, RRM, KL, EJK.

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Halpin-McCormick, A., Heyduk, K., Kantar, M.B. et al. Examining population structure across multiple collections of Cannabis. Genet Resour Crop Evol (2024). https://doi.org/10.1007/s10722-024-01928-1

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