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Table 2 SNP markers associated with sugar contents and chip darkening index in Solanum tuberosum Group Phureja

From: Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja

Gene-SNPa Trait Minor Allele −log10(p-value)b Percent variance
Frequency, % explained and effectc
InvGE-C 2475454 T Chip darkening index 2.0 (T) 2.4** 15.6 ↑
InvGE-G 2475344 A d Fructose 9.4 (A) 2.2** 7.2 ↓
InvGE-C 2475295 A Fructose 9.0 (C) 2.2*** 7.0 ↓
InvGE-G 2475187 A Fructose 9.0 (A) 2.7*** 8.5 ↓
InvGE-G 2475187 A Glucose 9.0 (A) 2.0* 6.6 ↓
InvGE-G 2475187 A Total sugars 9.0 (A) 2.0*** 8.8 ↓
SssI-C 45711901 T Sucrose 35.5 (C) 2.0* 13.5 ↑
  1. aThe SNP reference allele is followed by its position in the chromosome and the nucleotide from the allelic variant
  2. bSNP markers with a − log10 (p-value) higher than two were considered with significant effect on the variables studied with the mixed model approach. The markers were confirmed with an ANOVA considering a level of significance of α = 0.05. p-values: ***, p ≤ 0.001; **, p ≤ 0.01; *, p ≤ 0.05
  3. cThe percent variance explained expresses the effect of the minor allele in the trait. Arrows indicate the direction of the effect on the trait, upwards for a positive effect (low sugar content, therefore light chip color) and downwards for a negative effect (high sugar content, therefore dark chip color)
  4. dBold SNP markers were in strong linkage disequilibrium, showed similar effects in the trait, and presented similar distributions in the population