Gene Genealogy-Based Mutation Analysis Reveals Emergence of , , and of during the Later Stage of Rice Domestication.

Asian rice ( 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 and and five subgroups (, (), (), , and ) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 genomes (two parental and ten ()) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 mutations were shared by two or more subgroups (referred to here as mutations) from 549 mutations identified at 51 loci. The GGM analysis and related tests indicates that diverged from at a time significantly earlier than when split from . The results also indicate that was selected from hybrid progeny of and and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that , , and emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of and .