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; Stig Uggerhøj Andersen

doi:10.1038/s41467-019-14213-y

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 TanakaAtsushi Hayashi, Mads Sønderkær, Kaare Lehmann Nielsen, Korbinian Schneeberger, Bjarni Vilhjalmsson, Ryo Akashi, Jens Stougaard, Shusei Sato, Mikkel Heide Schierup, Stig Uggerhøj Andersen

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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.

Original language	English
Article number	253
Journal	Nature Communications
Volume	11
Issue	1
Number of pages	15
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-019-14213-y
Publication status	Published - 2020

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Shah, N., Wakabayashi, T., Kawamura, Y., Skovbjerg, C. K., Wang, M.-Z., Mustamin, Y., Isomura, Y., Gupta, V., Jin, H., Mun, T., Sandal, N., Azuma, F., Fukai, E., Seren, Ü., Kusakabe, S., Kikuchi, Y., Nitanda, S., Kumaki, T., Hashiguchi, M., ... Andersen, S. U. (2020). Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan. Nature Communications, 11(1), Article 253. https://doi.org/10.1038/s41467-019-14213-y

@article{139c52a1d9a549be93b80545356a02bf,

title = "Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan",

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.",

author = "Niraj Shah and Tomomi Wakabayashi and Yasuko Kawamura and Skovbjerg, {Cathrine Kiel} and Ming-Zhuo Wang and Yusdar Mustamin and Yoshiko Isomura and Vikas Gupta and Haojie Jin and Terry Mun and Niels Sandal and Fuyuki Azuma and Eigo Fukai and {\"U}mit Seren and Shohei Kusakabe and Yuki Kikuchi and Shogo Nitanda and Takashi Kumaki and Masatsugu Hashiguchi and Hidenori Tanaka and Atsushi Hayashi and Mads S{\o}nderk{\ae}r and Nielsen, {Kaare Lehmann} and Korbinian Schneeberger and Bjarni Vilhjalmsson and Ryo Akashi and Jens Stougaard and Shusei Sato and Schierup, {Mikkel Heide} and Andersen, {Stig Uggerh{\o}j}",

year = "2020",

doi = "10.1038/s41467-019-14213-y",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Springer Nature",

number = "1",

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Shah, N, Wakabayashi, T, Kawamura, Y, Skovbjerg, CK, Wang, M-Z, Mustamin, Y, Isomura, Y, Gupta, V, Jin, H, Mun, T, Sandal, N, Azuma, F, Fukai, E, Seren, Ü, Kusakabe, S, Kikuchi, Y, Nitanda, S, Kumaki, T, Hashiguchi, M, Tanaka, H, Hayashi, A, Sønderkær, M, Nielsen, KL, Schneeberger, K, Vilhjalmsson, B, Akashi, R, Stougaard, J, Sato, S, Schierup, MH & Andersen, SU 2020, 'Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan', Nature Communications, vol. 11, no. 1, 253. https://doi.org/10.1038/s41467-019-14213-y

TY - JOUR

T1 - Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan

AU - Shah, Niraj

AU - Wakabayashi, Tomomi

AU - Kawamura, Yasuko

AU - Skovbjerg, Cathrine Kiel

AU - Wang, Ming-Zhuo

AU - Mustamin, Yusdar

AU - Isomura, Yoshiko

AU - Gupta, Vikas

AU - Jin, Haojie

AU - Mun, Terry

AU - Sandal, Niels

AU - Azuma, Fuyuki

AU - Fukai, Eigo

AU - Seren, Ümit

AU - Kusakabe, Shohei

AU - Kikuchi, Yuki

AU - Nitanda, Shogo

AU - Kumaki, Takashi

AU - Hashiguchi, Masatsugu

AU - Tanaka, Hidenori

AU - Hayashi, Atsushi

AU - Sønderkær, Mads

AU - Nielsen, Kaare Lehmann

AU - Schneeberger, Korbinian

AU - Vilhjalmsson, Bjarni

AU - Akashi, Ryo

AU - Stougaard, Jens

AU - Sato, Shusei

AU - Schierup, Mikkel Heide

AU - Andersen, Stig Uggerhøj

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-019-14213-y

DO - 10.1038/s41467-019-14213-y

M3 - Journal article

C2 - 31937774

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 253

ER -

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

Abstract

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