Evolutionary histories of functional mutations during the domestication and spread of japonica rice in Asia

Abstract

Studying the history of rice dispersal allows us to examine the relationships between crop movement, climatic changes, and human cultural interactions. Our analysis suggests that plant–pathogen interactions may be a key component of local adaptation to crop landraces in new environments. Ancestral recombination graph analyses also reveal that most rice functional mutations have their origins in the Pleistocene, preceding the domestication of rice, and suggest that crop domestication and diversification may be driven by standing genetic variation rather than de novo mutations. Reconstructing the evolutionary trajectories of functional mutations over the last 20,000 y reveals how specific genes were selected during the history of rice. Keywords: domestication, crop evolution, domestication genes, species dispersal, local adaptation