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Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species

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Abstract

Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same features, however, make oak communities suited for the study of speciation, hybridization, and genetic adaptation. Efforts to develop new and to adapt existing genomic resources to less-studied members of this genus should not only improve oak conservation and management but also aid the study of fundamental evolutionary processes. Here, we present a suite of 27 highly polymorphic simple sequence repeat (SSR) markers tested in four North American red oak (Quercus section Lobatae) species: Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina. Five markers are genomic SSRs (gSSRs) — four novel and one previously transferred from Q. petraea — and 22 are gene-based SSRs derived from Q. robur and Q. petraea expressed sequence tags (EST-SSRs). Overall, levels of polymorphism detected with these primer pairs were high, with gene diversity (H e) averaging 0.66 across all loci in natural populations. In addition, we show that EST-SSR markers may have the potential to detect divergent selection at stress-resistance candidate genes among closely related oak species.

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Notes

  1. Sequence data have been deposited in the GenBank, DDBJ Nucleotide Sequence Database and EMBL databases under the accession numbers JQ929659 (locus 1P10), JQ929660 (2P24), JQ929661 (3A05), and JQ929662 (3D15).

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Acknowledgements

We thank James Schmierer for his help in sample collection in the Ford Forestry Center and Dr. Andrew Hipp for providing Q. ellipsoidalis, Q. coccinea and Q. velutina samples. Additionally, we thank John Lampereur and Linda Parker for kindly guiding us to Q. rubra stands in the Nicolet-Chequamegon National Forest. We are also grateful to Erin Hickey who assisted in sample collection and marker analyses. Two anonymous referees provided helpful comments on an earlier draft. Funding for the study came from Michigan Technological University start-up funds to Oliver Gailing, the Michigan Technological University Research Excellence fund, the USDA McIntire Stennis fund, the Huron Mountain Wildlife Foundation, the Hanes Trust and the NSF Plant Genome Research program (NSF 1025974). We are also grateful to the Northern Institute of Applied Climate Science for their support.

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  1. School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA

    Alexis R. Sullivan, Jennifer F. Lind & Oliver Gailing

  2. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

    Tim S. McCleary & Jeanne Romero-Severson

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  1. Alexis R. Sullivan
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  2. Jennifer F. Lind
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Correspondence to Oliver Gailing.

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Sullivan, A.R., Lind, J.F., McCleary, T.S. et al. Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species. Plant Mol Biol Rep 31, 231–239 (2013). https://doi.org/10.1007/s11105-012-0495-6

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