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A species-diagnostic SNP panel for discriminating lodgepole pine, jack pine, and their interspecific hybrids

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Abstract

Accurate stock identification is important for forest management, yet this can be a challenge for tree species that hybridize naturally. Species discriminating molecular markers provide a means to identify stock with high accuracy. In Canada, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a large hybrid zone in Alberta and Northwest Territories; within this hybrid zone, the identification of parentals and hybrids is difficult due to an overlap in morphological characteristics. Pure and hybrid ancestry can be resolved using microsatellite markers, but these are difficult and costly to type. We have developed a panel of SNP markers using 454 transcriptome sequence data that are more cost-effective, easier to score, and have greater discriminating power for differentiating species than microsatellites. Our SNP panel provides accurate and cost-efficient forest seed stock identification and will thereby facilitate reforestation and our pipeline can be applied to other hybrid systems globally.

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Acknowledgments

The authors would like to thank Leonard Barnhardt and Deogratias Rweyongeza (Environment and Sustainable Resource Development, Government of Alberta) for their expertise and access to samples; Stephanie Boychuck, Joël Fillon, Dominik Royko (University of Alberta) and staff members at the McGill University and Genome Quebec Innovation Centre for laboratory and bioinformatic support; and Matt Bryman (University of Alberta) for logistics. We would also like to thank comments from Sally Aitken and two anonymous reviewers for improving the manuscript. We acknowledge funding for this research from the Government of Alberta (AAET/AFRI-859-G07), as well as grants from Genome Canada, the Government of Alberta through Genome Alberta, and Genome British Columbia in support of the Tria I and Tria II projects (http://www.thetriaproject.ca) of which J.E.K.C and D.W.C. are principle investigators.

Data archiving statement

All 454 read data for lodgepole and jack pine have been archived on the NCBI Short Read Archive (SRP004517) and this is cross-referenced on the European Bioinformatics Institute, European Nucleotide Archive (http://www.ebi.ac.uk/ena/data/view/SRP004517), and the DNA Databank of Japan (http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP004517). Contig sequences for species discriminating SNPs are archived on NCBI (accessions, KC411636–KC411658). Microsatellite genotyping data are available from Dryad, DOI: 10.5061/dryad.456q26k3.

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Authors and Affiliations

  1. Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

    C. I. Cullingham, J. E. K. Cooke, S. Dang & D. W. Coltman

Authors
  1. C. I. Cullingham
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  2. J. E. K. Cooke
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  3. S. Dang
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  4. D. W. Coltman
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Corresponding author

Correspondence to C. I. Cullingham.

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Communicated by S. Aitken

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Cullingham, C.I., Cooke, J.E.K., Dang, S. et al. A species-diagnostic SNP panel for discriminating lodgepole pine, jack pine, and their interspecific hybrids. Tree Genetics & Genomes 9, 1119–1127 (2013). https://doi.org/10.1007/s11295-013-0608-x

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  • DOI: https://doi.org/10.1007/s11295-013-0608-x

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