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

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  • Niraj Shah
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  • Tomomi Wakabayashi, Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsucho, Sakyo-ku, Kyoto, 606-8501, Japan.
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  • Yasuko Kawamura, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
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  • Cathrine Kiel Skovbjerg
  • Ming-Zhuo Wang, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
  • ,
  • Yusdar Mustamin, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
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  • Yoshiko Isomura, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
  • ,
  • Vikas Gupta
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  • Haojie Jin
  • ,
  • Terry Mun
  • ,
  • Niels Sandal
  • Fuyuki Azuma, Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata, 950-2181, Japan.
  • ,
  • Eigo Fukai, Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata, 950-2181, Japan.
  • ,
  • Ümit Seren, Gregor Mendel Institute, Austrian Academy of Sciences, Vienna B(VBC), 1030, Vienna, Austria.
  • ,
  • Shohei Kusakabe, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
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  • Yuki Kikuchi, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
  • ,
  • Shogo Nitanda, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
  • ,
  • Takashi Kumaki, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
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  • Masatsugu Hashiguchi, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadainishi 1-1, Miyazaki, 889-2192, Japan.
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  • Hidenori Tanaka, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadainishi 1-1, Miyazaki, 889-2192, Japan.
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  • Atsushi Hayashi, Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan
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  • Mads Sønderkær, Department of Chemistry and Bioscience, Section for Biotechnology, Aalborg University, 9220, Aalborg, Denmark.
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  • Kaare Lehmann Nielsen, Department of Chemistry and Bioscience, Section for Biotechnology, Aalborg University, 9220, Aalborg, Denmark.
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  • Korbinian Schneeberger, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
  • ,
  • Bjarni Vilhjalmsson
  • Ryo Akashi, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadainishi 1-1, Miyazaki, 889-2192, Japan.
  • ,
  • Jens Stougaard
  • Shusei Sato, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. shuseis@ige.tohoku.ac.jp.
  • ,
  • Mikkel Heide Schierup
  • Stig Uggerhøj Andersen

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.

Original languageEnglish
Article number253
JournalNature Communications
Volume11
Issue1
Number of pages15
ISSN2041-1723
DOIs
Publication statusPublished - 2020

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