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Conservation Genetics Resources

, Volume 5, Issue 2, pp 541–544 | Cite as

Characterization of EST-based SSR loci in the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae)

  • B. M. T. BrunetEmail author
  • D. Doucet
  • B. R. Sturtevant
  • F. A. H. Sperling
Technical Note

Abstract

After identifying 114 microsatellite loci from Choristoneura fumiferana expressed sequence tags, 87 loci were assayed in a panel of 11 wild-caught individuals, giving 29 polymorphic loci. Further analysis of 20 of these loci on 31 individuals collected from a single population in northern Minnesota identified 14 in Hardy–Weinberg equilibrium.

Keywords

Spruce budworm Expressed sequence tag Microsatellite Simple sequence repeat Choristoneura fumiferana Tortricidae 

Notes

Acknowledgments

We thank P. Stothard for assistance in post-processing and analysis of ESTs, and P. Beldade and A. Long for the use of their SSR-mining Perl script. This study was funded by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada to F. Sperling, a Genomics Research and Development Initiative Grant (NRCAN) to D. Doucet, and a United States Department of Agriculture, Cooperative State Research Education and Extension Service, National Research Initiative Grant (WISR-2005-02815) to Brian Sturtevant.

Supplementary material

12686_2012_9847_MOESM1_ESM.xls (146 kb)
Online Resource 1: Characteristics of 87 EST-SSR loci tested on a validation panel of 11 individuals from Alberta. (XLS 146 kb)

References

  1. Anderson DP, Sturtevant BR (2011) Pattern analysis of eastern spruce budworm Choristoneura fumiferana dispersal. Ecography 34:488–497CrossRefGoogle Scholar
  2. de Arruda MP, Goncalves EC, Schneider MPC, da Costa da Silva AL, Morielle-Versute E (2010) An alternative genotyping method using dye labeled universal primer to reduce unspecific amplifications. Mol Biol Rep 37:2031–2036PubMedCrossRefGoogle Scholar
  3. Beldade P, van’t Hoff A, Jeronimo MA, Long AD (2009) Microsatellite markers associated with genes expressed in developing wings of Bicyclus anynana butterflies. Mol Ecol Resour 9:1487–1492PubMedCrossRefGoogle Scholar
  4. Boulanger Y, Arsenault D, Morin H, Jardon Y, Bertrand P, Dagneau C (2012) Dendrochronological reconstruction of spruce budworm (Choristoneura fumiferana) outbreaks in southern Quebec for the last 400 years. Can J Forest Res 42:1264–1276Google Scholar
  5. Ewing B, Hillier L, Wendl M, Green P (2008) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185Google Scholar
  6. Kim KS, Ratcliffe ST, French BW, Liu L, Sappington TW (2008) Utility of EST-derived SSRs as population genetic markers in a beetle. J Hered 99:112–124PubMedCrossRefGoogle Scholar
  7. Lumley LM, Davis CS, Sperling FAH (2009) Isolation and characterization of eight microsatellite loci in the spruce budworm species Choristoneura fumiferana and Choristoneura occidentalis, and cross-species amplification in related tortricid moths. Conserv Genet Resour 1:501–504CrossRefGoogle Scholar
  8. Meglecz E (2007) MicroFamily: a computer program for detecting flanking region similarities among different microsatellite loci. Mol Ecol Notes 7:18–20CrossRefGoogle Scholar
  9. Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. thesis, University of DublinGoogle Scholar
  10. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2002) TIGR Gene Indices Clustering Tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652CrossRefGoogle Scholar
  11. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  12. Rousset F (2008) GENEPOP’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106PubMedCrossRefGoogle Scholar
  13. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  14. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234PubMedCrossRefGoogle Scholar
  15. Sinama M, Dubut V, Costedoat C, Gilles A, Junker M, Malausa T, Martin J-F, Neve G, Pech N, Schmitt T, Zimmermann M, Meglecz E (2011) Challenges of microsatellite development in Lepidoptera: Euphydryas aurinia (Nymphalidae) as a case study. Eur J Entomol 108:261–266Google Scholar
  16. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  17. van’t Hof AE, Brakefield PM, Saccheri IJ, Zwaan BJ (2007) Evolutionary dynamics of multilocus microsatellite arrangements in the genome of the butterfly Bicyclus anynana, with implications for other Lepidoptera. Heredity 98:320–328PubMedCrossRefGoogle Scholar
  18. Volney WJA, Fleming RA (2000) Climate change and impacts of boreal forest insects. Agr Ecosyst Environ 82:283–294Google Scholar
  19. Volney WJA, Fleming RA (2007) Spruce budworm (Choristoneura spp.) biotype reactions to forest and climate characteristics. Glob Change Biol 13:1630–1643CrossRefGoogle Scholar
  20. White JR, Roberts M, Yorke JA, Pop M (2008) Figaro: a novel statistical method for vector sequence removal. Bioinformatics 15:462–467CrossRefGoogle Scholar
  21. Zhang DX (2004) Lepidopteran microsatellite DNA: redundant but promising. Trends Ecol Evol 19:507–509PubMedCrossRefGoogle Scholar

Copyright information

© © Her Majesty the Queen in Right of Canada 2013

Authors and Affiliations

  • B. M. T. Brunet
    • 1
    Email author
  • D. Doucet
    • 2
  • B. R. Sturtevant
    • 3
  • F. A. H. Sperling
    • 1
  1. 1.Department of Biological SciencesUniversity of AlbertaEdmontonCanada
  2. 2.Natural Resources Canada, Great Lakes Forestry CentreSault Ste. MarieCanada
  3. 3.USDA Forest Service, Northcentral Research StationRhinelanderUSA

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