The evolving story of rice evolution

Abstract

Recent research related to evolution in the primary gene pool of rice, which consists of Oryza species with the A-genome, provides new perspectives related to current and past eco-genetic setting of rice and its wild relatives and fresh insights into rice domestication. In Asia the traits of the rice domestication syndrome are many but due to the remarkable diversification of rice and introgression with wild rice, few traits are consistently different between wild and domesticated rice. Reduced shattering and reduced dormancy are the principal traits of domestication in rice. Using the principal criteria for distinguishing single and multiple origins of crops, recent key research results do not support a polyphyletic origin of domesticated rice in distinctly different geographic regions. While domestication is a long-term process and continues today, a single event during domestication, the selection of the non-shattering sh4 allele, resulted in rice becoming a species dependent on humans for survival - domesticated. Here the apparent contradictions between a single origin of Asian rice and deep genetic divisions seen in rice germplasm are resolved based on a hypothesis of cycles of introgression, selection and diversification from non-shattering domesticated rice, importantly in the initial stages in its center of origin in the region of the Yangtze river valley, and subsequently beyond, as domesticated rice spread. The evolution of African rice differs from Asian rice mainly in the more restricted gene pool of wild rice from which it was domesticated, ecological diversification rather than eco-geographic diversification, and historic introgression from the Asian rice gene pool. The genetics of post-domestication evolution in Asian rice is well illustrated by changes at the waxy locus. For both Asian and African rice becoming domesticated was a single event, it was the subsequent evolution that led to their genetic complexity.