Fig. 5
Manhattan plot and QQ plot from genome-wide association studies with local LD block of three selected loci. a Manhattan plot by NDSI. b Quantile–quantile plot for NDSI. c Local LD block of around Os01g0243400. The square lattice panel represents the extent of LD based on r2. d Local LD block surrounding the locus Os01g0293000. e Local LD block surrounding the locus Os02g0560200. Blue horizontal dashed line and red horizontal dashed line indicates two genome-wide significance thresholds. The red dashed line is the negative logarithm of the 0.1/SNP number and the blue dashed line is the negative logarithm of the 0.01/SNP number. LD block heat maps (c–e) were surrounding the peak on chromosome 1, 2 respectively. Navy blue vertical dashed lines indicate the position of SNP loci