Global Dissemination of a Single Mutation Conferring White Pericarp in Rice

Abstract

Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa. Understanding the history and origin of genetic mutations that have changed wild plants into crops can help us understand the history of the people who cultivated these plants. Rice is one of the oldest crops grown in Asia and it contains two different subspecies that are believed to have been domesticated in different locations by different people. Surprisingly, some of the genetic mutations responsible for domestication are common in all rice. We here show that a mutation in the Rc gene that changed the red seed of wild rice into the white seeds of modern rice is shared by a large majority of all rice varieties, regardless of subspecies. This transfer of genes requires contact among rice types and implies contact among the people who cultivated the different subspecies. We have traced the origin of the mutation in Rc to the japonica subspecies. As additional domestication genes are cloned and their evolutionary history described, we will see how many times and in how many directions such gene transfers have occurred.