3E-04 Identification of domesticated genomic regions in rice based on population genomic analysis

Cultivated rice (Oryza sativa) are believed to be domesticated from the wild progenitor, O.rufipogon. During domestication, artificial selection might have acted on genetic variation in agricultural traits, such as yields, qualities of grains and morphologies. We aimed to identify the genomic regions involved in these domestication traits. It is expected that such regions should show reduced genetic variation in cultivated populations by selective sweeps. We resequenced the entire genome sequences of 32 strains, including 10 wild rice, 12 indica, and 10 japonica cultivars, and investigated the patterns of genetic variation on a genomic scale. The strains were grouped into three clusters by phylogenetic and STRUCTURE analyses. The levels of LD decayed within 100kb. We found about 10 genomic regions showing remarkable reductions of genetic variation in cultivated populations. These included known domestication related genes, Prog1 and sh4. Some of them corresponded to the locations of QTLs for domestication traits, such as awn length and seed shattering. It is indicated that genome-wide polymorphism analysis is a promising means to explore the footprint of selection.