Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera)

Matthew S. Olson, Amanda L. Robertson, Naoki Takebayashi, Salim Silim, William R. Schroeder, Peter Tiffin

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. We analysed 590 gene fragments (average length 565bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. Nucleotide diversity (Θtotal = 0.0028, π = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750bp, consistent with the low estimates of the scaled recombination parameter, ρ = 0.0092. Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.

Original languageEnglish
Pages (from-to)526-536
Number of pages11
JournalNew Phytologist
Issue number2
StatePublished - Apr 2010


  • Effective population size
  • Genomic diversity
  • Insertion deletion diversity
  • Poplar
  • Purifying selection
  • Single nucleotide polymorphisms (SNPs)


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