DNA methylation site loss for plasticity-led novel trait genetic fixation
Abstract
Phenotypic plasticity allows organisms to adapt traits in response to environmental changes, yet the molecular basis by which such plastic traits become genetically fixed remains unclear. Here, we investigated gut-length plasticity in medaka fish ( Oryzias latipes ) through genome-wide methylation profiling, CRISPR/Cas9-mediated deletion, and population genomic analyses. We found that seasonal methylation of CpG sites upstream of the Plxnb3 is correlated with gut-length plasticity, and deletion of this region abolishes plasticity. Additionally, standing variation in Ppp3r1 is associated with genetically fixed longer gut length in populations lacking plasticity. These results suggest that loss of epigenetic regulation via CpG site reduction triggers the genetic fixation of novel traits. Our findings provide molecular evidence linking epigenetic plasticity and genetic assimilation, advancing understanding of plasticity-led evolution in natural populations.
Article Details
Journal Info
Proceedings of the National Academy of Sciences
National Academy of Sciences
Authors (17)
Takafumi Katsumura
Department of Anatomy, Kitasato University School of Medicine
Suguru Sato
Department of Biological Sciences, Kitasato University School of Science
Kana Yamashita
Department of Biological Sciences, Kitasato University School of Science
Shoji Oda
Department of Integrated Biosciences, The University of Tokyo
Takashi Gakuhari
Institute of Human and Social Sciences, Kanazawa University
Shodai Tanaka
Department of Biological Sciences, Kitasato University School of Science
Kazuko Fujitani
Molecular Biology Research Center, Kitasato University School of Medicine
Toshiyuki Nishimaki
Department of Anatomy, Kitasato University School of Medicine
Tadashi Imai
Production Engineering Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency
Yasutoshi Yoshiura
Production Engineering Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency
Hirohiko Takeshima
Department of Marine Biology, Tokai University School of Biological Sciences
Yasuyuki Hashiguchi
Department of Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University
Yoichi Sekita
Department of Biosciences, Kitasato University School of Science
Hiroshi Mitani
Department of Integrated Biosciences, The University of Tokyo
Motoyuki Ogawa
Department of Anatomy, Kitasato University School of Medicine
Hideaki Takeuchi
Department of Biological Science, Graduate School of Natural Science and Technology, Okayama University
Hiroki Oota
Department of Anatomy, Kitasato University School of Medicine