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Theoretical and Applied Genetics

, Volume 109, Issue 2, pp 361–369 | Cite as

Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs

  • Cherdsak LiewlaksaneeyanawinEmail author
  • Carol E. Ritland
  • Yousry A. El-Kassaby
  • Kermit Ritland
Original Paper

Abstract

Microsatellites, or simple sequence repeats (SSRs), are usually regarded as the “markers of choice” in population genetics research because they exhibit high variability. The development cost of these markers is usually high. In addition, microsatellite primers developed for one species often do not cross-amplify in related species, requiring separate development for each species. However, microsatellites found in expressed sequence tags (ESTs) might better cross-amplify as they reside in or near conserved coding DNA. In this study, we identified 14 Pinus taeda (loblolly pine) EST-SSRs from public EST databases and tested for their cross-species transferability to P. contorta ssp. latifolia, P. ponderosa, and P. sylvestris. As part of our development of a P. contorta microsatellite set, we also compared their transferability to that of 99 traditional microsatellite markers developed in P. taeda and tested on P. contorta ssp. latifolia. Compared to traditional microsatellites, EST-SSRs had higher transfer rates across pine species; however, the level of polymorphism of microsatellites derived from ESTs was lower. Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST-SSRs are more conserved than traditional SSRs. Our results also provide a battery of 23 polymorphic, robust microsatellite primer pairs for lodgepole pine.

Keywords

Microsatellite Locus Flank Region Base Substitution Trinucleotide Repeat Genomic SSRs 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was funded through NSERC grants to K.R. We sincerely thank D.B. Neale for providing loblolly pine EST sequences, and C.H. Newton for contributing the DNA of 24 individual lodgepole pines. We also would like to thank two anonymous reviewers and O. Savolainen for helpful comments on the manuscript.

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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Cherdsak Liewlaksaneeyanawin
    • 1
    Email author
  • Carol E. Ritland
    • 1
  • Yousry A. El-Kassaby
    • 1
  • Kermit Ritland
    • 1
  1. 1.Department of Forest SciencesUniversity of British ColumbiaVancouverCanada

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