A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions

Li He, Wenwu Wu, Gaurav Zinta, Lan Yang, Dong Wang, Renyi Liu, Huiming Zhang, Zhimin Zheng, Huan Huang, Qingzhu Zhang () and Jian-Kang Zhu ()
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Li He: Chinese Academy of Sciences
Wenwu Wu: Chinese Academy of Sciences
Gaurav Zinta: Chinese Academy of Sciences
Lan Yang: Chinese Academy of Sciences
Dong Wang: Chinese Academy of Sciences
Renyi Liu: Chinese Academy of Sciences
Huiming Zhang: Chinese Academy of Sciences
Zhimin Zheng: Chinese Academy of Sciences
Huan Huang: Chinese Academy of Sciences
Qingzhu Zhang: Chinese Academy of Sciences
Jian-Kang Zhu: Chinese Academy of Sciences

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named “NMR19” (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH). We find that the DNA methylation status of NMR19-4 is stably inherited and independent of genetic variation. In addition, further analysis indicates that DNA methylation of NMR19-4 correlates with local climates, implying that NMR19-4 is an environmentally associated epiallele. In summary, we discover a novel epiallele, and provide mechanistic insights into its origin and potential function in local climate adaptation.

Date: 2018
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DOI: 10.1038/s41467-018-02839-3

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