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Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

Abstract

A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions1,2,3,4,5. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions6,7. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

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Figure 1: The decay of average FST around the 200 most strongly soil-associated polymorphisms.

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Acknowledgements

We are grateful to M. Nordborg, R. Pakeman and R. Brooker for their advice and support, and to M. Woodhead, J. Russell and C. Booth for assistance with microsatellite analysis. This work was supported by the US National Science Foundation (NSF) grant DEB-0548991 and US National Institutes of Health (NIH) grant RGM-076643 (S.V.N.), NSF DEB-0723935 (to M. Nordborg), the University of Southern California (S.V.N., T.L.T. and T.T.H.), an NSF predoctoral fellowship (T.L.T.), the Macaulay Development Fund (E.C.B.), the Gregor Mendel Institute (T.L.T.) and an NIH NRSA fellowship (E.J.V.W.).

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T.L.T. and S.V.N. designed experiments; T.L.T., E.C.B. and T.T.H. performed analyses; E.C.B. and E.J.V.W. designed and performed all field collections; T.L.T., E.J.V.W. and S.V.N. wrote the paper.

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Correspondence to Thomas L Turner.

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The authors declare no competing financial interests.

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Supplementary Text and Figures

Supplementary Tables 1–3 and Supplementary Figures 1–9 (PDF 820 kb)

Supplementary Table 2

Number of mismatches per aligned read (XLS 36 kb)

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Turner, T., Bourne, E., Von Wettberg, E. et al. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 42, 260–263 (2010). https://doi.org/10.1038/ng.515

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