Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

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Abstract

Arabidopsis thaliana is native to Eurasia and is naturalized across the world. Its ability to be easily propagated and its high phenotypic variability make it an ideal model system for functional, ecological and evolutionary genetics. To date, analyses of the natural genetic variation of A. thaliana have involved small numbers of individual plants or genetic markers. Here we genotype 1,307 worldwide accessions, including several regional samples, using a 250K SNP chip. This allowed us to produce a high-resolution description of the global pattern of genetic variation. We applied three complementary selection tests and identified new targets of selection. Further, we characterized the pattern of historical recombination in A. thaliana and observed an enrichment of hotspots in its intergenic regions and repetitive DNA, which is consistent with the pattern that is observed for humans but which is strikingly different from that observed in other plant species. We have made the seeds we used to produce this Regional Mapping (RegMap) panel publicly available. This panel comprises one of the largest genomic mapping resources currently available for global natural isolates of a non-human species.

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Figure 1: PCA of the study samples.
Figure 2: Recombination rate variation for chromosome 1.
Figure 3: The proportion of DNA within and outside of inferred hotspots.
Figure 4: Overlap of selection scans with results from GWAS on chromosome 2.
Figure 5: Enrichment of GWAS results with signals of selection.

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Acknowledgements

We thank M. Hubisz for the code for the CLR statistic and for help in using the software. We also thank E. Leffler for helpful discussions regarding recombination hotspots. M.W.H. was supported by a National Science Foundation Predoctoral Fellowship, a Graduate Assistance in Areas of National Need (GAANN) training grant and an Achievement Rewards for College Scientists (ARCS) Foundation Scholarship. This research was supported by US National Institutes of Health grant GM057994 (J.B.), US National Institutes of Health grant GM083068 (J.B. and M.N.), National Science Foundation 2010 grants (M.N. and J.B.) and a Dropkin Foundation Fellowship (A.M.H.). This is contribution number 11-363-J from the Kansas Agricultural Experiment Station (C.T.).

Author information

M.W.H., M.N., J.O.B. and J.B. conceived of and designed the experiments. M.W.H., A.M.H. and C.T. carried out all population genetic analyses. A.A. developed the method used to identify hotspots of recombination. S.A., N.W.M. and A.P. were responsible for the experimental aspects of choosing and genotyping the selected lines. Y.S.H. and B.J.V. analyzed the raw array data. F.G.S. designed the maps shown in the manuscript and on the project website. M.W.H. and J.B. wrote the paper. All other authors commented on the manuscript.

Correspondence to Joy Bergelson.

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Supplementary Figures 1–5, Supplementary Tables 1 and 2 and Supplementary Note. (PDF 455 kb)

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