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Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan

Author

Listed:
  • Niraj Shah

    (Aarhus University)

  • Tomomi Wakabayashi

    (Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsucho)

  • Yasuko Kawamura

    (Tohoku University)

  • Cathrine Kiel Skovbjerg

    (Aarhus University)

  • Ming-Zhuo Wang

    (Tohoku University)

  • Yusdar Mustamin

    (Tohoku University)

  • Yoshiko Isomura

    (Tohoku University)

  • Vikas Gupta

    (Aarhus University)

  • Haojie Jin

    (Aarhus University)

  • Terry Mun

    (Aarhus University)

  • Niels Sandal

    (Aarhus University)

  • Fuyuki Azuma

    (Niigata University)

  • Eigo Fukai

    (Niigata University)

  • Ümit Seren

    (Gregor Mendel Institute, Austrian Academy of Sciences, Vienna B(VBC))

  • Shohei Kusakabe

    (Tohoku University)

  • Yuki Kikuchi

    (Tohoku University)

  • Shogo Nitanda

    (Tohoku University)

  • Takashi Kumaki

    (Tohoku University)

  • Masatsugu Hashiguchi

    (University of Miyazaki)

  • Hidenori Tanaka

    (University of Miyazaki)

  • Atsushi Hayashi

    (Kazusa DNA Research Institute)

  • Mads Sønderkær

    (Section for Biotechnology, Aalborg University)

  • Kaare Lehmann Nielsen

    (Section for Biotechnology, Aalborg University)

  • Korbinian Schneeberger

    (Max Planck Institute for Plant Breeding Research)

  • Bjarni Vilhjalmsson

    (Aarhus University)

  • Ryo Akashi

    (University of Miyazaki)

  • Jens Stougaard

    (Aarhus University)

  • Shusei Sato

    (Tohoku University)

  • Mikkel Heide Schierup

    (Aarhus University)

  • Stig Uggerhøj Andersen

    (Aarhus University)

Abstract

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.

Suggested Citation

  • Niraj Shah & Tomomi Wakabayashi & Yasuko Kawamura & Cathrine Kiel Skovbjerg & Ming-Zhuo Wang & Yusdar Mustamin & Yoshiko Isomura & Vikas Gupta & Haojie Jin & Terry Mun & Niels Sandal & Fuyuki Azuma & , 2020. "Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-14213-y
    DOI: 10.1038/s41467-019-14213-y
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    Cited by:

    1. Moritz Sexauer & Hemal Bhasin & Maria Schön & Elena Roitsch & Caroline Wall & Ulrike Herzog & Katharina Markmann, 2023. "A micro RNA mediates shoot control of root branching," Nature Communications, Nature, vol. 14(1), pages 1-9, December.

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