The origins of rice have been cast in a new light by research published in PLoS Genetics. By reconciling two theories, the authors show that the domestication of rice occurred at least twice independently but with extensive “borrowing” between two subspecies, Oryza sativa indica and Oryza sativa japonica, the southern and northern varieties of rice and they are major staple crops in Asia. Whether they share a single origin of domestication or were domesticated independently twice interests both historians and biologists, and the two views had seemed mutually exclusive. However, researchers are now suggesting that these two views may both be correct, depending on the traits or genes being discussed.
The research teams studied the kinship of rice by examining the 50,000 or so genes in the rice genome. For most of the genes, indica and japonica are indeed no closer to each other in kinship than each is to wild rice, supporting the more popular view that the two cultivars were independently domesticated. However, when the gene regions for traits influenced by artificial selection were examined, indica and japonica appear to share a surprisingly strong kinship.
In light of this new data, the story of rice domestication may need to be revisited. Early northern and southern farmers may have cultivated rice independently but it seems that they also borrowed desired traits extensively from rice farmed by others, resulting in the opposing kinships reported. This begs the question as to whether intellectual piracy has been with us since humans first became engaged in agricultural production.
He Z, Zhai W, Wen H, Tang T, Wang Y, et al. (2011) Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genet 7(6): e1002100. doi:10.1371/journal.pgen.1002100
Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been ‘‘rediscovered’’ by this approach. In summary, we identified 13 additional candidate genes of domestication.