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Fig. 2 | BMC Genetics

Fig. 2

From: Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)

Fig. 2

Genome wide association mapping of GP in the freshly-harvested seeds of rice populations using LMM method. Identified significant loci are shown in red dots. Known genes identified within 100 kb near association peaks are indicated in red. The Manhattan plots for GP shows –log10 P-values from genome-wide scan plotted against the position on each of the 12 chromosomes. The dashed line indicates the genome-wide significance thresholds, P = 6.6 × 10−8 (whole population), 2.1 × 10−7 (Aus), 8.7 × 10−8 (indica) and 2.0 × 10−7 (japonica). The horizontal axis in quantile-quantile plots shows –log10 transformed expected-values and the vertical axis indicates –log10 transformed observed P-values. (a) and (b) are Manhattan plot and quantile-quantile plot for GP, respectively in whole population. (c) and (d) are Manhattan plot and quantile-quantile plot for GP respectively, in Aus. (e) and (f) are Manhattan plot and quantile-quantile plot for GP respectively, in indica. g and (h) are Manhattan plot and quantile-quantile plot for GP respectively, in japonica

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