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A set of 204 SNP and INDEL markers for Bigleaf maple (Acer macrophyllum Pursch)

Conservation Genetics Resources volume 7, pages 797–801 (2015)Cite this article

Abstract

Novel single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) were identified for the Bigleaf maple (Acer macrophyllum Pursch) using a combined next generation sequencing approach on the Ion Torrent PGM system with genotyping on the MassARRAY® iPLEX™ platform. Five hundred and ninety-eight putative loci were identified through sequencing of DNA fragments following a double restriction enzyme digest method. Two hundred and four polymorphic loci (199 SNPs and five INDELs) were successfully amplified across 65 individuals from seven populations across the native range of the species. Twenty-nine loci showed evidence of deviation from Hardy–Weinberg Equilibrium, and 85 were significantly linked. Expected heterozygosity ranged from 0.015 to 0.472 and F ST from 0.011 to 0.359. These genetic resources will prove useful for future studies into the population genetics and phylogeography of this important and iconic timber species.

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Acknowledgments

This work was supported by the World Resources Institute through Double Helix Tracking Technologies. We would like to thank Anne Minden and Jason O’Brien for their collection efforts, and gratefully acknowledge the help of United State Forest Services staff Shelley Gardner, Valerie Hipkins, Ron Malamphy, Phil Huff and Mark Camisa.

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    Authors and Affiliations

    1. School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia

      D. I. Jardine, E. E. Dormontt, K.-J. van Dijk, R. R. M. Dixon, B. Dunker & A. J. Lowe

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    1. D. I. Jardine
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    2. E. E. Dormontt
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    3. K.-J. van Dijk
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    4. R. R. M. Dixon
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    5. B. Dunker
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    6. A. J. Lowe
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    Correspondence to A. J. Lowe.

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    D. I. Jardine and E. E. Dormontt have contributed equally.

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    Jardine, D.I., Dormontt, E.E., van Dijk, KJ. et al. A set of 204 SNP and INDEL markers for Bigleaf maple (Acer macrophyllum Pursch). Conservation Genet Resour 7, 797–801 (2015). https://doi.org/10.1007/s12686-015-0486-7

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    • DOI: https://doi.org/10.1007/s12686-015-0486-7

    Keywords

    • Single nucleotide polymorphism
    • Insertion/deletion
    • MassARRAY