Skip to main content

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


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.

This is a preview of subscription content, access via your institution.


  • Anderson DP, Sturtevant BR (2011) Pattern analysis of eastern spruce budworm Choristoneura fumiferana dispersal. Ecography 34:488–497

    Article  Google Scholar 

  • 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 37:2031–2036

    Article  PubMed  CAS  Google Scholar 

  • 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 9:1487–1492

    Article  PubMed  CAS  Google Scholar 

  • 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 42:1264–1276

    Google Scholar 

  • Ewing B, Hillier L, Wendl M, Green P (2008) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185

    Google Scholar 

  • 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 99:112–124

    Article  PubMed  CAS  Google Scholar 

  • 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 1:501–504

    Article  Google Scholar 

  • Meglecz E (2007) MicroFamily: a computer program for detecting flanking region similarities among different microsatellite loci. Mol Ecol Notes 7:18–20

    Article  CAS  Google Scholar 

  • Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. thesis, University of Dublin

  • 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 19:651–652

    Article  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Rousset F (2008) GENEPOP’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • 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 365–386

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  • 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 108:261–266

    Google Scholar 

  • 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 4:535–538

    Article  Google Scholar 

  • 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 98:320–328

    Article  PubMed  Google Scholar 

  • Volney WJA, Fleming RA (2000) Climate change and impacts of boreal forest insects. Agr Ecosyst Environ 82:283–294

    Google Scholar 

  • Volney WJA, Fleming RA (2007) Spruce budworm (Choristoneura spp.) biotype reactions to forest and climate characteristics. Glob Change Biol 13:1630–1643

    Article  Google Scholar 

  • White JR, Roberts M, Yorke JA, Pop M (2008) Figaro: a novel statistical method for vector sequence removal. Bioinformatics 15:462–467

    Article  Google Scholar 

  • Zhang DX (2004) Lepidopteran microsatellite DNA: redundant but promising. Trends Ecol Evol 19:507–509

    Article  PubMed  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to B. M. T. Brunet.

Electronic supplementary material

Below is the link to the electronic supplementary material.


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

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Brunet, B.M.T., Doucet, D., Sturtevant, B.R. et al. Characterization of EST-based SSR loci in the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae). Conservation Genet Resour 5, 541–544 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


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