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

Bibliographische Detailangaben
Veröffentlicht in:	The New phytologist. - 1979. - 196(2012), 3 vom: 23. Nov., Seite 713-725
1. Verfasser:	Slavov, Gancho T (VerfasserIn)
Weitere Verfasser:	DiFazio, Stephen P, Martin, Joel, Schackwitz, Wendy, Muchero, Wellington, Rodgers-Melnick, Eli, Lipphardt, Mindie F, Pennacchio, Christa P, Hellsten, Uffe, Pennacchio, Len A, Gunter, Lee E, Ranjan, Priya, Vining, Kelly, Pomraning, Kyle R, Wilhelm, Larry J, Pellegrini, Matteo, Mockler, Todd C, Freitag, Michael, Geraldes, Armando, El-Kassaby, Yousry A, Mansfield, Shawn D, Cronk, Quentin C B, Douglas, Carl J, Strauss, Steven H, Rokhsar, Dan, Tuskan, Gerald A
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2012
Zugriff auf das übergeordnete Werk:	The New phytologist
Schlagworte:	Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. DNA, Plant

Beschreibung
Zusammenfassung:	© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust. • 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
Beschreibung:	Date Completed 08.03.2013 Date Revised 30.03.2022 published: Print-Electronic CommentIn: New Phytol. 2012 Nov;196(3):652-654. doi: 10.1111/j.1469-8137.2012.04362.x. - PMID 23043586 Citation Status MEDLINE
ISSN:	1469-8137
DOI:	10.1111/j.1469-8137.2012.04258.x