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

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, Eigo Fukai, Ümit Seren, Shohei Kusakabe, Yuki Kikuchi, Shogo Nitanda, Takashi Kumaki, Masatsugu Hashiguchi, Hidenori Tanaka, Atsushi Hayashi, Mads Sønderkær, Kaare Lehmann Nielsen, Korbinian Schneeberger, Bjarni Vilhjalmsson, Ryo Akashi, Jens Stougaard, Shusei Sato (), Mikkel Heide Schierup () and Stig Uggerhøj Andersen ()
Additional contact information
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

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: 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.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-14213-y

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DOI: 10.1038/s41467-019-14213-y

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