The sliding window profiles of θ in two 5 Mb regions.

The window size is 100 kb and step size is 10 kb. The horizontal lines are the cutoffs determined for each subspecies by whole-genome random shuffling. A) A typical region on chromosome 11 where no sub-region is lower than the cutoff in all species. B) A region on chromosome 7 that contains PROG1, a locus known to be associated with domestication [24]. Both the indica and japonica genomes are below the cutoff in the neighborhood (300 kb and 780 kb, respectively) of PROG1.