Resource Article

A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

  1. A. Geraldes1,*,
  2. S. P. DiFazio2,
  3. G. T. Slavov2,3,
  4. P. Ranjan4,
  5. W. Muchero5,
  6. J. Hannemann6,
  7. L. E. Gunter5,
  8. A. M. Wymore5,
  9. C. J. Grassa1,
  10. N. Farzaneh1,
  11. I. Porth7,
  12. A. D. McKown8,
  13. O. Skyba7,
  14. E. Li1,
  15. M. Fujita1,
  16. J. Klápště8,
  17. J. Martin9,
  18. W. Schackwitz9,
  19. C. Pennacchio9,
  20. D. Rokhsar9,
  21. M. C. Friedmann1,
  22. G. O. Wasteneys1,
  23. R. D. Guy8,
  24. Y. A. El-Kassaby8,
  25. S. D. Mansfield7,
  26. Q. C. B. Cronk1,
  27. J. Ehlting6,
  28. C. J. Douglas1,
  29. G. A. Tuskan5,9

Article first published online: 11 JAN 2013

DOI: 10.1111/1755-0998.12056

Issue

Molecular Ecology Resources

Molecular Ecology Resources

Volume 13, Issue 2, pages 306–323, March 2013

Additional Information

How to Cite

Geraldes, A., DiFazio, S. P., Slavov, G. T., Ranjan, P., Muchero, W., Hannemann, J., Gunter, L. E., Wymore, A. M., Grassa, C. J., Farzaneh, N., Porth, I., McKown, A. D., Skyba, O., Li, E., Fujita, M., Klápště, J., Martin, J., Schackwitz, W., Pennacchio, C., Rokhsar, D., Friedmann, M. C., Wasteneys, G. O., Guy, R. D., El-Kassaby, Y. A., Mansfield, S. D., Cronk, Q. C. B., Ehlting, J., Douglas, C. J. and Tuskan, G. A. (2013), A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources, 13: 306–323. doi: 10.1111/1755-0998.12056

Author Information

  1. 1

    Department of Botany, University of British Columbia, Vancouver, BC, Canada

  2. 2

    Department of Biology, West Virginia University, Morgantown, WV, USA

  3. 3

    Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK

  4. 4

    Food Sciences Department, University of Tennessee, Knoxville, TN, USA

  5. 5

    Plant Systems Biology Group, BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

  6. 6

    Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada

  7. 7

    Department of Wood Science, University of British Columbia, Vancouver, BC, Canada

  8. 8

    Department of Forest Science, University of British Columbia, Vancouver, BC, Canada

  9. 9

    The Joint Genome Institute, Walnut Creek, CA, US

*Correspondence: Armando Geraldes, Fax: 604-822-6089; E-mail: geraldes@mail.ubc.ca

Publication History

  1. Issue published online: 14 FEB 2013
  2. Article first published online: 11 JAN 2013
  3. Manuscript Accepted: 3 DEC 2012
  4. Manuscript Revised: 30 NOV 2012
  5. Manuscript Received: 20 JUL 2012

Funded by

  • Genome British Columbia Applied Genomics Innovation Program. Grant Number: 103BIO

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Keywords:

  • genotype accuracy;
  • high-throughput SNP genotyping;
  • hybridization;
  • Populus balsamifera ;
  • Populus trichocarpa

Abstract

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

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