Tree Genetics & Genomes

, Volume 5, Issue 1, pp 247–255 | Cite as

Identification of COS markers in the Pinaceae

  • Cherdsak Liewlaksaneeyanawin
  • Jun Zhuang
  • Michelle Tang
  • Nima Farzaneh
  • Gillian Lueng
  • Claire Cullis
  • Susan Findlay
  • Carol E. Ritland
  • Jörg Bohlmann
  • Kermit Ritland
Original Paper

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.

Keywords

COS markers Conifers 

Supplementary material

11295_2008_189_MOESM1_ESM.xls (669 kb)
Table S1Total of 1,815 putative single-copy COS between spruce and loblolly pine (XLS 672 KB)
11295_2008_189_MOESM2_ESM.xls (468 kb)
Table S2Test 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)
11295_2008_189_Fig1_ESM.gif (254 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)

11295_2008_189_Fig1_ESM.tif (2.2 mb)
High-resolution image (TIF 2.16 MB)

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Cherdsak Liewlaksaneeyanawin
    • 1
  • Jun Zhuang
    • 2
  • Michelle Tang
    • 1
  • Nima Farzaneh
    • 1
  • Gillian Lueng
    • 1
  • Claire Cullis
    • 1
  • Susan Findlay
    • 1
  • Carol E. Ritland
    • 1
  • Jörg Bohlmann
    • 3
  • Kermit Ritland
    • 1
  1. 1.Department of Forest SciencesUniversity of British ColumbiaVancouverCanada
  2. 2.The Institute for Genomic ResearchRockvilleUSA
  3. 3.Michael Smith LaboratoriesUniversity of British ColumbiaVancouverCanada

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