*3.1. SNP Genotyping*

Of the 58K informative SNPs, a total of 47,837 polymorphic SNPs were selected (Supplementary Table S3). Of the 47,837 SNPs, 19,554 and 21,876 SNPs were derived from the subgenomes A and B, respectively, and 6407 SNPs were derived from scaffolds (Supplementary Table S3 and Figure 1a). A total of 14,030 SNPs were selected for association analysis after eliminating SNPs with high levels of missing data (>20%), heterozygosity (>20%), or low a minor allele frequency (MAF) (<0.01). Of the 14030 SNPs, 6623 and 7407 SNPs were derived from A and B subgenomes, respectively. The majority of SNPs were evenly distributed across the chromosomes; however, there were some large gaps between SNPs on the chromosomes Aradu.A09, Aradu.A10, Araip.B05, Araip.B06, Araip.B07, Araip.B09, and Araip.B10 (Figure 1b). The peanut genome had an overall SNP density of 5.91 SNPs/Mb, with the Aradu.A09 (3.45 SNPs/Mb) and Aradu.A08 (9.35 SNPs/Mb) chromosomal densities being the lowest and highest, respectively (Supplementary Table S4).

**Figure 1.** Single nucleotide polymorphisms (SNP) distribution in the 20 chromosomes of the cultivated peanut. The horizontal axis shows chromosome length (Mb), the shades of red represent SNP density. The vertical axis shows the 20 chromosomes. (**a**) Polymorphic SNPs except for scaffold markers; (**b**) Polymorphic SNPs (except for scaffold markers) after filter by GAPIT coding.
