Asymmetric variation in DNA methylation during domestication and de-domestication of rice

Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture. A pan-DNA methylome of rice uncovers reversal of DNA methylation changes during domestication and de-domestication.

Automated summary

By studying the DNA methylomes of wild rice, cultivated rice, and weedy rice, we found that DNA methylation levels significantly decrease during rice domestication but unexpectedly increase during de-domestication. These methylation changes occur in different genomic regions for the two opposite stages and contribute to morphological changes by affecting chromatin accessibility, histone modifications, transcription factor binding, and chromatin looping. These insights into population epigenomics of rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture.