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.
Highlights
Human efforts to domesticate plant and animal species began thousands of years before recorded history, leaving us to guess at the methods that transformed wild species into agriculturally important crops and livestock
To determine the frequency and distribution of the 14-bp deletion in the Rc gene that has been shown to cause white pericarp in rice [9,10], a set of 440 geographically and genetically diverse rice cultivars were genotyped using the rice indel rice insertion/deletion polymorphism (RID) 12 primers reported in Sweeney et al (2006)
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
Summary
Human efforts to domesticate plant and animal species began thousands of years before recorded history, leaving us to guess at the methods that transformed wild species into agriculturally important crops and livestock. Several estimates have been made for the time of divergence between indica and japonica based on intron sequence and retrotransposon insertions, and all of these calculations place the time to the recent common ancestor at more than 100,000 years ago [4,5,6]. This divergence time is an order of magnitude larger than the oldest estimates for rice domestication. The data strongly support at least two independent domestications of O. sativa from predifferentiated pools of the O. rufipogon wild ancestor [3,4,7,8]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
