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

http://ir.library.oregonstate.edu/concern/defaults/vh53ww184

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at:  http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • •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 (N[subscript 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.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Slavov, G. T., DiFazio, S. P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M. F., Pennacchio, C. P., Hellsten, U., Pennacchio, L. A., Gunter, L. E., Ranjan, P., Vining, K., Pomraning, K. R., Wilhelm, L. J., Pellegrini, M., Mockler, T. C., Freitag, M., Geraldes, A., El-Kassaby, Y. A., Mansfield, S. D., Cronk, Q. C. B., Douglas, C. J., Strauss, S. H., Rokhsar, D. and Tuskan, G. A. (2012), Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist, 196: 713–725. doi: 10.1111/j.1469-8137.2012.04258.x
Academic Affiliation
Series
Keyword
Rights Statement
Funding Statement (additional comments about funding)
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Submitted by Deanne Bruner (deanne.bruner@oregonstate.edu) on 2012-11-28T01:01:42Z No. of bitstreams: 1 StraussStevenForestryGenomeResequencingReveals.pdf: 1076011 bytes, checksum: 252be7f62da75ee1bb2c694cd48463ef (MD5)
  • description.provenance : Approved for entry into archive by Deanne Bruner(deanne.bruner@oregonstate.edu) on 2012-11-28T01:23:39Z (GMT) No. of bitstreams: 1 StraussStevenForestryGenomeResequencingReveals.pdf: 1076011 bytes, checksum: 252be7f62da75ee1bb2c694cd48463ef (MD5)
  • description.provenance : Made available in DSpace on 2012-11-28T01:23:39Z (GMT). No. of bitstreams: 1 StraussStevenForestryGenomeResequencingReveals.pdf: 1076011 bytes, checksum: 252be7f62da75ee1bb2c694cd48463ef (MD5) Previous issue date: 2012-11

Relationships

In Administrative Set:
Last modified: 07/06/2017

Downloadable Content

Download PDF
Citations:

EndNote | Zotero | Mendeley

Items