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Identification of COS markers in the Pinaceae

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Abstract

Conserved ortholog set (COS) markers are evolutionary conserved, single-copy genes, identified from large databases of express sequence tags (ESTs). They are of particular use for constructing syntenic genetic maps among species. In this study, we identified a set of 1,813 putative single-copy COS markers between spruce and loblolly pine, then designed primers for 931 of these markers and tested these primers with DNA from spruce, pine, and Douglas fir. Of these 931 primers, 56% (524) amplified a product in both spruce and pine, and 71% (373) of these were single-banded; 224 amplicons were single-banded in all three species. Even though these COS markers were selected from large EST databases, a substantial proportion (20–30%) of amplicons displayed multiple bands or smears, suggesting significant paralogy. Sequencing of three single-banded amplicons showed high nucleotide similarities among 29 conifer species, suggesting orthology of single-banded amplicons. Screening for COS marker polymorphism in two pedigrees of white spruce and two pedigrees of loblolly pine revealed an average informativeness of 36% for spruce and 24% for pine (e.g., at least one parent was heterozygous for a single-nucleotide polymorphism within the entire amplified product). This corresponds to an average nucleotide heterozygosity of 0.05% and 0.03%, respectively, which is considerably lower than that found in other studies of spruce and pine. Thus, the advantages of COS markers for constructing syntenic maps are offset by their lower polymorphism.

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Acknowledgements

This work was funded by the Genome BC/Genome Canada “Conifer Forest Health Genomics” project to J.B. and K.R. We sincerely thank Barry Jaquish from the British Columbia Ministry of Forests for providing the spruce crosses, Craig Echt from USDA Forest Service for contributing the DNA of loblolly pine crosses, and Tristan Gillan from the University of British Columbia for sampling plant materials. We acknowledge the support of the Vancouver Genome Sciences Center for sequencing.

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Authors and Affiliations

  1. Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada

    Cherdsak Liewlaksaneeyanawin, Michelle Tang, Nima Farzaneh, Gillian Lueng, Claire Cullis, Susan Findlay, Carol E. Ritland & Kermit Ritland

  2. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, 20850, USA

    Jun Zhuang

  3. Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada

    Jörg Bohlmann

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  1. Cherdsak Liewlaksaneeyanawin
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  2. Jun Zhuang
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  3. Michelle Tang
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  4. Nima Farzaneh
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  5. Gillian Lueng
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  6. Claire Cullis
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  8. Carol E. Ritland
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  9. Jörg Bohlmann
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  10. Kermit Ritland
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Correspondence to Kermit Ritland.

Additional information

Communicated by D. Grattapaglia

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Table S1

Total of 1,815 putative single-copy COS between spruce and loblolly pine (XLS 672 KB)

Table S2

Test of COS primers in loblolly pine (Lp), white spruce (Ws), and Douglas fir (Df). A = approximately size to the nearest 50 bp of the product size including forward (19 bp) and reverse (20) primer tails. 0 = no product, 1 = single product, 2 = multiple products with clear band, 3 = multiple products with smear band (XLS 468 KB)

Supplementary Fig. 1

Sequence alignment of COS marker at locus C20992 amplified from 29 conifer species. Loblolly pine and spruce EST sequences are indicated by EST. The remaining sequences are genomic sequences. The dots indicate conserved nucleotides and dashed lines indicate indels (relative to P. menziesii) (GIF 256 KB)

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Liewlaksaneeyanawin, C., Zhuang, J., Tang, M. et al. Identification of COS markers in the Pinaceae. Tree Genetics & Genomes 5, 247–255 (2009). https://doi.org/10.1007/s11295-008-0189-2

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  • DOI: https://doi.org/10.1007/s11295-008-0189-2

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