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Originally published as Genetics Published Articles Ahead of Print on December 22, 2008.
Genetics, Vol. 181, 1021-1033, March 2009, Copyright © 2009
doi:10.1534/genetics.108.095364
Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis
Bao-Hua Song*,
Aaron J. Windsor*,
,
Karl J. Schmid
,
Sebastian Ramos-Onsins
,
M. Eric Schranz*,**,
Andrew J. Heidel and
Thomas Mitchell-Olds*,1
* Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina 27708, Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden, Centre for Research in Agricultural Genomics, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain, ** Instituut voor Biodiversiteit en Ecosysteem Dynamica, University of Amsterdam, Amsterdam 1090 GB, The Netherlands, Bayer BioScience N.V., 9052 Gent, Belgium and Leibnitz Institute for Age Research, 07745 Jena, Germany
1 Corresponding author: Box 90338, Duke University, Durham, NC 27708.
E-mail: tmo1{at}duke.edu
Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in 
10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have 45% higher recombination per kilobase than outcrossing A. lyrata.
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