Abstract
Rice, as one of the most important crops in the world, is facing an ever-accelerating challenge from climate change. Epigenetic modification with its substantially high epimutation rate and the possibility for some epigenetic variation to act as a heritable contributor to crop environmental adaptability may hold great potentials for rapid crop breeding. Epigenetic modification is controlled by epigenetic pathways, and mutations disturbing the epigenetic pathways may lead to significant epigenetic and/or genetic changes. This is especially true for rice, whose genome is rich in epigenetic modifications and transposable elements (TEs) that are generally epigenetically silenced. Here, in this paper, we first reviewed the pathways that establish, maintain and remove rice DNA methylation, which is the most well studied epigenetic marker, as well as the genes that are involved. We then discussed how TEs amplify the phenotypic impact of epigenetic changes that could be a result of epigenetic pathway disturbances. At last, we presented the enormous amount of rice genome data that are publically available, within which great genetic variation in the genes that are involved within the epigenetic pathways is embedded. This genetic variation awaits to be exploited for their potentials in generating a heritable source of variation for rapid environmental adaptation, which may hold tremendous importance for rice breeding in the face of climate change.
Highlights
As one of the most important food crops in the world [1,2], rice (Oryza) is, rather sensitive to climate change, for its yield may be significantly reduced by increasing temperature, by rising sea levels, as well as by flooding and droughts [3]
Many spontaneous or stress-induced epigenetic changes can be heritable across generations [7,19,20,21,22] and some of these heritable epigenetic changes occur in or near genes that are involved in stress-responsive pathways and may help crop handle adverse environmental conditions by assisting the regulation of these stress-responsive genes’ expression [7,8,22]
DNA methylation is established, maintained and removed by a series of pathways [14], and most of the proteins that are involved in these pathways have already been identified for rice [5], which provides a good starting point for exploiting the breeding potential of rice’s epigenetic pathways
Summary
As one of the most important food crops in the world [1,2], rice (Oryza) is, rather sensitive to climate change, for its yield may be significantly reduced by increasing temperature, by rising sea levels (and the associated salinity intrusion), as well as by flooding and droughts [3]. DNA Methylation Pathways in Rice with many involved Genes having been Identified
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