Fig. 6
The peak regions on rice chromosomes containing significant SNPs from GWAS of PN.day6 (a), PAN (b and c), FG (d) and UFG (e and f). The pair-wise LD for the SNP of the lowest p-value (red letters) is indicated as r2 values, where the markers were divided into bins of 5 kb and the r2 values were averaged and shown as blue bars; the darkest blue represents a value of 1 and the lightest represents a value of 0. The dotted lines denote the regions containing LD blocks that the significant SNPs reside. Examples of other significant SNPs are shown in green letters. Note that the diagram of r2 values represents all neighboring SNPs present in that region, while it is not proportional to the physical distance of the chromosome. PN: net photosynthetic rate; PAN: number of panicles per plant; FG: number of filled grains per plant and UFG: number of unfilled grains per plant