Fig. 7

Genome-wide association study with the MLM for curved fruit shape index. A1 and A2 are Manhattan plots of the mixed linear model (MLM). The abscissa represents the position of the chromosome, and the ordinate represents the P-value (−log10 P). The negative logarithm of the base 10 and the scattered points (or lines) on the graph represent the −log10 (p) corresponding to each SNP locus. The red dotted line is the negative logarithm of 0.05/all SNPs, and the blue dotted line is the negative logarithm of 0.1/all SNPs. Scattered dots (or lines) above the threshold line are candidate sites. B1 and B2 are QQ-plot plots. The abscissa represents the expected value, and the ordinate represents the observed value. In the initial stage, the actual observed P-value was close to the expected P-value, indicating that the influence of population structure on the association analysis could be effectively controlled under this model, and thus false positives could also be effectively controlled. The same applies below