Rice domestication: histories and mysteries

Domesticated rice (Oryza sativa) is one of the worlds most important food crops, culturally, nutritionally and economically (Khush 1997). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long-held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology (Huang 2012) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O.similar to rufipogon and O.similar to sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O.similar to rufipogon, it stands in contrast to previous findings that the two major varieties of O.similar to sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.