Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

Gancho Trifonu Slavov, Stephen P. Difazio, Joel Martin, Wendy Schackwitz, Wellington Muchero, Eli Rodgers-Melnick, Mindie F. Lipphardt, Christa P. Pennacchio, Uffe Hellsten, Len A. Pennacchio, Lee E. Gunter, Priya Ranjan, Kelly Vining, Kyle R. Pomraning, Larry J. Wilhelm, Matteo Pellegrini, Todd C. Mockler, Michael Freitag, Armando Geraldes, Yousry A. El-KassabyShawn D. Mansfield, Quentin C. B. Cronk, Carl J. Douglas, Steven H. Strauss, Dan Rokhsar, Gerald A. Tuskan

Research output: Contribution to journalArticlepeer-review

138 Citations (SciVal)


Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.

We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.

Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r2 dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (Ne ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.

Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
Original languageEnglish
Pages (from-to)713-725
Number of pages13
JournalNew Phytologist
Issue number3
Early online date03 Aug 2012
Publication statusPublished - Nov 2012


  • allele frequency gradients
  • black cottonwood (Populus trichocarpa)
  • genome resequencing
  • linkage disequilibrium (LD)
  • population structure
  • recombination


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