The genomics of rice: Evolutionary, ecological and practical implications
Michael D. Purugganan, Center for Genomics and Systems Biology, New York University

Asian rice, Oryza sativa, is one of world’s oldest and most important crop species. Rice has two main subspecies, indica and japonica, which are believed to have been domesticated ~9000 years ago domesticated from O. rufipogon. Genomic approaches allow us to examine the evolutionary history of rice, the genes/genomic regions that contribute to adaptation. Using patterns of single nucleotide polymorphisms (SNPs) from genomic data, we date the origin of domestication at ~8,200-13,500 years ago, which is consistent with known archeological data that suggests rice first originated at around this time in the Yangtze Valley of China. We also identify 26 genomic regions that appear to have undergone selective sweeps in cultivated rice. Finally, we are in the process of developing computational and experimental methods that can use large scale genome-wide expression data to determine molecular networks associated with rice response to environmental conditions. This new direction will allow us to study how gene networks facilitate plant adaptation and how they evolve within and between species.

Background Review Article:
The nature of selection during plant domestication. Purugganan MD, Fuller DQ.
Nature. 2009 Feb 12;457(7231):843-8.

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