Journal Article

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

Kumaki, Takashi, Seren, Ümit, Kikuchi, Yuki, Hashiguchi, Masatsugu, Nielsen, Kaare Lehmann, Nitanda, Shogo, Fukai, Eigo, Hayashi, Atsushi, Sønderkær, Mads, Kusakabe, Shohei, Azuma, Fuyuki, Tanaka, Hidenori, Sato, Shusei, Vilhjalmsson, Bjarni, Sandal, Niels, Gupta, Vikas, Shah, Niraj, Skovbjerg, Cathrine Kiel, Akashi, Ryo, Stougaard, Jens, Wakabayashi, Tomomi, Kawamura, Yasuko, Isomura, Yoshiko, Wang, Ming-Zhuo, Andersen, Stig Uggerhøj, Mustamin, Yusdar, Mun, Terry, Schneeberger, Korbinian, Jin, Haojie, Schierup, Mikkel Heide

2020

Overview

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. Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45 / 45/23 / 45/43 / 631/181/2474 / 631/208/182 / 631/208/205/2138 / 631/449/2491 / 631/449/2669 / Acclimatization - genetics / Adaptation / Biological Evolution / Colonization / Demographics / Differentiation / Environmental gradient / Flowering / Gardens & gardening / Gene mapping / Gene sequencing / Genes, Plant - genetics / Genetic Variation / Genome, Plant - genetics / Genome-Wide Association Study / Genomes / Genotype / Geography / Humanities and Social Sciences / Japan / Lotus - genetics / Lotus - growth & development / Lotus - physiology / Lotus japonicus / Mapping / multidisciplinary / Overwintering / Phenotype / Phenotypes / Population structure / Science / Science (multidisciplinary) / Selection, Genetic / Signatures / Subpopulations / Whole genome sequencing