Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication

Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica japonica five subgroups (aus, (sensu stricto), tropical japonica, aromatic) are broadly accepted, how they phylogenetically related not transparent. To clarify their relationships, sample 121 diverse genes was chosen here from 12 Oryza genomes (two parental ten O. (Os)) parallel to allow genealogy-based mutation (GGM) analysis. From sample, 361 Os mutations were shared by two or more (referred as trans mutations) 549 identified at 51 loci. The GGM analysis tests indicates that aus diverged time significantly earlier than when split japonica. results also indicate aromatic selected hybrid progeny all share significant number early previously. suggest aus, emerged sequentially within most 4–5 millennia after