title: Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.
abstract: • 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 r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 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.
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.|Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Gancho T
authors.initials: GT
authors.lastname: Slavov
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: DiFazio
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Martin
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Wendy
authors.initials: W
authors.lastname: Schackwitz
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Wellington
authors.initials: W
authors.lastname: Muchero
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.
authors.forename: Eli
authors.initials: E
authors.lastname: Rodgers-Melnick
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.
authors.forename: Mindie F
authors.initials: MF
authors.lastname: Lipphardt
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Christa P
authors.initials: CP
authors.lastname: Pennacchio
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Lee E
authors.initials: LE
authors.lastname: Gunter
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Priya
authors.initials: P
authors.lastname: Ranjan
authors.affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA.
authors.forename: Kelly
authors.initials: K
authors.lastname: Vining
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA.
authors.forename: Kyle R
authors.initials: KR
authors.lastname: Pomraning
authors.affiliation: Oregon Health Sciences University, Beaverton, OR 97006, USA.
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Wilhelm
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-1606, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Armando
authors.initials: A
authors.lastname: Geraldes
authors.affiliation: Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Yousry A
authors.initials: YA
authors.lastname: El-Kassaby
authors.affiliation: Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Quentin C B
authors.initials: QCB
authors.lastname: Cronk
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA.
authors.forename: Steven H
authors.initials: SH
authors.lastname: Strauss
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Rokhsar
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
mesh_terms: D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D056726:Genetic Association Studies / Q000379:methods; D040961:Genetic Drift; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D005843:Geography; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics*; D025341:Principal Component Analysis; D011995:Recombination, Genetic; D012641:Selection, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D018744:DNA, Plant