Figure 2 | Scientific Reports

Figure 2

From: Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice

Figure 2

SNP-based GWAS for grain length (GL) that confirmed GS3. Manhattan plots of the genome-wide association studies on GL for japonica (A,D), indica (B,E) and combined (C,F) panel in raw and cooked grain, respectively. The topmost significant SNP (snp_03_16733441) in both raw and cooked grains was detected within the genic region of GS3. The boxplot (mentioned in B,C,E and F) visualized phenotypic variations in raw grain length (B,C) in indica and cooked grain length (E,F) in the combined indica and japonica panel for each haplotype formed by two of the most significant SNPs. The haplotype with the A allele of the most significant SNP (C to A) had the highest contribution to the grain length variation in both raw and cooked grains. Horizontal red and blue line represents the genome-wide significant threshold −log10(P) value of 7 and 5, respectively.

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