*3.6. LD and Candidate Genes Analysis*

Pairwise comparisons were performed between all SNPs for the estimation of LD decay. At a cutoff value of r2 = 0.1, the averaged LD decay distance of the 384 peanuts was approximately 150 kb (Supplementary Figure S3). The pattern of LD across the entire genome presented a number of haplotype blocks containing SNPs that can be used to determine the range of the candidate gene. The genomic locations harboring significant SNPs from the GWAS were investigated to identify putative candidate genes based on the peanut reference genome (*A. hypogaea* Tifrunner 1.0). Strong and extensive pairwise LD was observed among highly significant SNPs around AX-177640219 (*p*-value = 0.000015) on chromosome Araip.B08 from the 12,629,161 to 13,029,161 bp region (*D'* > 0.80) in which *D'* varied from 0.036 to 1 (Figure 5d and Supplementary Table S5).

Fifteen annotated genes at the association regions flanked by SNP AX-177640219 on chromosome Araip.B08 were identified within the estimated ±150 kb window based on the reference genome (Figure 5c and Supplementary Table S6).
