2023/06/05 by Shuai Cao, Kai Chen, Kening Lu +11 · 1 citation
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #GABA and Rice Research #Genetic Mapping and Diversity in Plants and Animals #Rice Cultivation and Yield Improvement
paper · doi:10.1093/plcell/koad160
openalex publication_date 2023/06/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.