Diversity within agronomically important genes.

a) Average diversity (average number of pairwise differences per kilobasepair) for genes grouped following the minor categories defined in the OGRO database. Red and blue dashed lines indicate average diversity values across the whole genome (including non-genic regions) within indica and within japonica respectively. The green dashed line, showing the average pairwise Fst between indica and japonica, is scaled in the secondary Y axis. b) SNPs identified within the gene LOC_Os02g40860 in the 104 varieties analyzed in this study. Characteristic alleles of the temperate japonica haplotype are painted blue. Vertical dashed rectangles show the locations of the two missense SNPs with high minor allele frequency within indica. The horizontal rectangle shows the haplotype of the variety Camponi. Colors in the left panel differentiate the following groups: O. rufipogon (RUF), aromatic (ARO), temperate japonica (TEJ), tropical japonica (TRJ), indica (IND), aus (AUS), O. nivara (NIV), and admixed (ADM).