Rice Genome Sequences Explain the Evolution and Domestication of japonica and indica Rice

The wild A genome species represent an effective gene pool for rice. Sequencing of A genome species has allowed analysis of the relationships with this group. A whole chloroplast genome based phylogeny has now been compared with one based upon nuclear genome sequences.  Wild taxa from Northern Australia have been included in these analyses for the first time.  Compared with domesticated rice, some South American and African taxa had the most divergent chloroplast genomes and some Australian taxa the most divergent nuclear genomes. The domesticated rice (O. sativa  japonica ) nuclear genome shows close relationship with that of O. rufipogonconfirming this as the progenitor of domesticated japonica.   A wild rice from northern Australia was the closest perennial  to indica. This supports domestication of indica from a separate gene pool found in Northern Australia that may still be present in Asia.