Fig. 6

GWAS of potato tuber aspect ratio (A), small-sized tuber weight (B) and tuber thickness (C). 1. Manhattan plot of GWAS (left). The middle horizontal dashed line indicates the genome-wide threshold of GWAS signals with a significance level of 0.05 after Bonferroni correction [0.05/ 25,591,215 = 1.95 × 10^− 9 (−log₁₀P = 8.71)] for multiple tests. The upper and lower horizontal dashed lines mark a significance level of 0.01 and 1, respectively. The corresponding QQ plot (right) showed the distribution of observed P values versus those expected under the null for the GWAS. 2. Candidate gene loci by enlarging the region at specific chromosome. The horizontal dashed lines indicate the genome-wide threshold of GWAS signals with a significance level of 0.05. 3. Comparison by the log₁₀ ratio of nucleotide diversity (Π) revealed the nucleotide polymorphisms between Wild and CIP populations. 4. SNPs at 3’UTR and its distribution of 108 CIP accessions showed that three examined traits increased significantly with the increase of alternate allele. Numbers of various genotypes were indicated. There are five genotypes in autotetraploid (0, AAAA; 4, aaaa; 1, 2, 3, heterozygotic allele) and three genotypes in diploid (0, AA; 1, Aa; 2, aa). Genotype of reference allele is 0 and alternate allele is 4 (autotetraploid) or 2 (diploid). 5. Genotype distribution of key SNPs in 170 accessions revealed that Wild was dominated by Ref alleles, and Landrace and Cultivar were dominated by Het and Alt genotypes in tuber aspect ratio (A); Wild, Landrace and Cultivar was dominated by Ref alleles in small-sized tuber weight (B); Wild was dominated by Ref alleles, and Landrace and Cultivar were dominated by Ref and Het genotypes in tuber thickness (C). The four pie charts represent the proportion of different genotypes. Genotypes are indicated above (see 4) and reference allele (Ref) is 0, alternate allele (Alt) is 4 (autotetraploid) or 2 (diploid), and heterozygotic allele (Het, 1–3 in autotetraploid or 1 in diploid)