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Massive haplotypes underlie ecotypic differentiation in sunflowers

View ORCID ProfileMarco Todesco, View ORCID ProfileGregory L. Owens, Natalia Bercovich, View ORCID ProfileJean-Sébastien Légaré, View ORCID ProfileShaghayegh Soudi, Dylan O. Burge, Kaichi Huang, View ORCID ProfileKatherine L. Ostevik, Emily B. M. Drummond, View ORCID ProfileIvana Imerovski, Kathryn Lande, Mariana A. Pascual, Winnie Cheung, S. Evan Staton, Stéphane Muños, View ORCID ProfileRasmus Nielsen, Lisa A. Donovan, View ORCID ProfileJohn M. Burke, Sam Yeaman, View ORCID ProfileLoren H. Rieseberg
doi: https://doi.org/10.1101/790279
Marco Todesco
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Gregory L. Owens
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
2Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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Natalia Bercovich
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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  • For correspondence: lriesebe@mail.ubc.ca nataliab@biodiversity.ubc.ca
Jean-Sébastien Légaré
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Shaghayegh Soudi
3Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Dylan O. Burge
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Kaichi Huang
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Katherine L. Ostevik
4Department of Biology, Duke University, Durham, North Carolina, USA
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  • ORCID record for Katherine L. Ostevik
Emily B. M. Drummond
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Ivana Imerovski
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Kathryn Lande
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Mariana A. Pascual
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Winnie Cheung
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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S. Evan Staton
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Stéphane Muños
5LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Rasmus Nielsen
2Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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Lisa A. Donovan
6Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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John M. Burke
6Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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Sam Yeaman
3Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Loren H. Rieseberg
1Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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  • ORCID record for Loren H. Rieseberg
  • For correspondence: lriesebe@mail.ubc.ca nataliab@biodiversity.ubc.ca
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Abstract

Species often include multiple ecotypes that are adapted to different environments. But how do ecotypes arise, and how are their distinctive combinations of adaptive alleles maintained despite hybridization with non-adapted populations? Re-sequencing of 1506 wild sunflowers from three species identified 37 large (1-100 Mbp), non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics. Limited recombination in these regions keeps adaptive alleles together, and we find that they differentiate several sunflower ecotypes; for example, they control a 77 day difference in flowering between ecotypes of silverleaf sunflower (likely through deletion of a FLOWERING LOCUS T homolog), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, associated with polymorphic structural variants, and often appear to represent introgressions from other, possibly extinct, congeners. This work highlights a pervasive role of structural variation in maintaining complex ecotypic adaptation.

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Posted October 02, 2019.
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Massive haplotypes underlie ecotypic differentiation in sunflowers
Marco Todesco, Gregory L. Owens, Natalia Bercovich, Jean-Sébastien Légaré, Shaghayegh Soudi, Dylan O. Burge, Kaichi Huang, Katherine L. Ostevik, Emily B. M. Drummond, Ivana Imerovski, Kathryn Lande, Mariana A. Pascual, Winnie Cheung, S. Evan Staton, Stéphane Muños, Rasmus Nielsen, Lisa A. Donovan, John M. Burke, Sam Yeaman, Loren H. Rieseberg
bioRxiv 790279; doi: https://doi.org/10.1101/790279
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Massive haplotypes underlie ecotypic differentiation in sunflowers
Marco Todesco, Gregory L. Owens, Natalia Bercovich, Jean-Sébastien Légaré, Shaghayegh Soudi, Dylan O. Burge, Kaichi Huang, Katherine L. Ostevik, Emily B. M. Drummond, Ivana Imerovski, Kathryn Lande, Mariana A. Pascual, Winnie Cheung, S. Evan Staton, Stéphane Muños, Rasmus Nielsen, Lisa A. Donovan, John M. Burke, Sam Yeaman, Loren H. Rieseberg
bioRxiv 790279; doi: https://doi.org/10.1101/790279

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