Open AccessDivergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting
Author(s) -
Jessica A. Rodrigues,
Ping-Hung Hsieh,
Deling Ruan,
Toshiro Nishimura,
Manoj K. Sharma,
Rita Sharma,
Xinyi Ye,
Nathalie Nguyen,
S. Nijjar,
Pamela C. Ronald,
Robert L. Fischer,
Daniel Zilberman
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2104445118
Subject(s) - genomic imprinting , biology , imprinting (psychology) , epigenetics , genetics , gene , endosperm , transposable element , allele , dna methylation , gene expression , genome
Significance Plant gene imprinting (allele-specific chromatin modification) results in parent-of-origin–dependent expression in endosperm, a nutritive tissue essential for embryo viability. Imprinted genes function in species reproductive isolation by causing embryo abortion in crosses. We analyzed the evolution of rice gene imprinting using four cultivars spanning domestication and the divergence of two subspecies 9,000 and 300,000 y ago, respectively. Most imprinted genes are imprinted across cultivars and enriched in regulatory functions. However, approximately 10% of imprinted genes have lost or gained imprinting, often associated with stably inherited epigenetic and genetic variation, suggesting a role in rice diversification. Our results highlight the role of transposable elements and epigenetic variation in shaping heritable changes in gene expression during rice evolution.