Reloading DNA History in Rice Domestication

Although crop domestication is a prehistoric event, DNA (or genome) sequences of modern cultivars and the accession lines of wild relatives contain information regarding the history of crop domestication and the breeding process. Accordingly, with plentiful genomic data, many new findings have been obtained concerning the crop domestication process, for which various (some controversial) interpretations exist. Since approximately 20 years ago, dozens of quantitative trait genes (QTGs) related to the domestication process have been cloned from several crops including rice, a global staple food. However, the determination of how and when these QTGs were involved in rice domestication requires a precise understanding of the DNA code. In addition to the identification of domestication-related QTGs, large-scale rice genome analysis based on short-read Illumina data (but with shallow depth) including more than 1,000 rice cultivars and hundreds of wild rice (or Oryza rufipogon) lines, along with extensive genome analysis including more than 3,000 cultivars with sufficient Illumina data, has been reported. From these data, the genome-wide changes during rice domestication have been explained. However, these genome-wide changes were not interpreted based on QTG changes for domestication-related traits during rice domestication. In addition, a substantial gap remains between the archeological hypothesis based on ancient relics and findings from DNA variations among current cultivars. Thus, this review reconsiders the present status of rice domestication research from a biologist’s perspective.