*3.5. Genome-Wide Association Study (GWAS)*

The genotype data of 14,030 filtered polymorphic SNPs and the phenotypic data of the seed aspect ratios were analyzed for GWAS by GAPIT. A total of five candidate SNPs showing significant associations (*p* < 0.0001) with the seed aspect ratio were identified on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09 (Table 1 and Figure 5a). The distribution of the observed −log10(p) for each SNP was compared with the expected distribution in the QQ plot representing that the population structure and kinship relationship were well controlled in the GWAS (Figure 5b). The significance of the marker– trait associations were determined using the FDR with adjusted *p*-value (*p* = 0.05). AX-177640219 on chromosome Araip.B08 was significantly associated with the seed trait at the significant threshold (Table 1).

**Figure 5.** (**a**) Manhattan plot of a genome-wide association analysis by GAPIT; (**b**) Q-Q (quantile-quantile) plot; (**c**) Genes located at the association regions based on the *Arachis hypogaea* Tifrunner 1.0 reference genome; (**d**) Linkage disequilibrium (LD) plot generated using Haploview, D' values that correspond to SNP pairs are shown within the respective squares. Higher D' values are indicated with a brighter red color.


**Table 1.** Significant markers associated with seed aspect ratio of peanut identified using GAPIT analysis.

a FDR\_adjusted\_*p*-value is not significant at the level of 0.05.
