Table 2 Associations of SNP alleles with CQA and CQS, TSC, TY, and/or TSY in the CHIPS-ALL population
SNPaMinor Allele Frequency, %CQA Percent Variance ExplainedbCQS Percent Variance ExplainedbTSC Percent Variance ExplainedbTY Percent Variance ExplainedbTSY Percent Variance Explainedb
GWD-A3259G (A3072T, C3400G)6.6 (G)nsns3.6* ↑cns4.6** ↑
GWD-A3452G2.6 (G)nsns5.9** ↑2.6* ↓4.4** ↑
PWD-T10547C (C10911T)49.0 (C)nsns7.2** ↑ns4.4* ↑
PWD-G11140A (G11112A)2.2 (A)3.4** ↑7.3*** ↑ns2.2* ↓ns
PWD-G10758A3.8 (A)5.6*** ↓ns2.1* ↓nsns
PWD-T11148A1.0 (A)ns2.3* ↑3.9** ↑ns2.4* ↑
BMY1-G2533A30.1 (A)nsns4.6** ↓ns3.0* ↓
BMY1-G2565A1.5 (A)2.8** ↑3.5** ↑7.9*** ↑ns4.5** ↑
BMY1-C2649A (A2694G, C2811T)6.9 (A)4.5** ↓6.5** ↓7.2** ↓ns4.4* ↓
BMY1-G2657A (G2767A)10.0 (A)3.4* ↑7.1** ↑7.5** ↑ns6.7** ↑
BMY1-G2751A5.1 (A)ns5.6** ↓4.3** ↓ns4.2** ↓
PHO1b-A3931G (C4206G)1.5 (G)3.3** ↓nsnsnsns
PHO1b-A3982C27.6 (C)3.1* ↑9.9*** ↑8.9*** ↑ns3.8* ↑
PHO1b-C3990T (G4049A)8.8 (T)2.8* ↑7.0** ↑ns4.7* ↓ns
PHO1b-G4181A19.7 (A)3.4* ↑7.2** ↑6.2* ↑nsns
PHO1b-G4106A (G4109C)23.1 (A)3.4* ↑5.6** ↑nsnsns
PHO1b-A4207GT18.0 (GT)ns8.8** ↑4.8* ↑5.2* ↓ns
PHO1b-AT4207G16.0 (G)ns7.0** ↑ns5.4* ↓ns
PHO1b-T4404C (A4365G)11.8 (C)ns5.7** ↓9.3*** ↓ns4.9* ↓
SssI-A5858G26.1 (G)nsns5.9** ↑nsns
PGM-A408T13.7 (T)nsns6.8** ↑ns4.8* ↑
PGM-T441AC8.0 (AC)nsnsns8.2** ↓↑cns
PGM-T468C38.0 (C)nsns10.5*** ↑ns6.3* ↑
AGPaseS-T1259C (T1612C)8.5 (C)7.4*** ↓10.1*** ↓19.9*** ↓ns10.3*** ↓
AGPaseS-G1592C (A1348G)20.6 (C)ns5.4*↓15.0*** ↓ns7.8**↓
AGPaseS-T1284C (C1411T, G1457C)5.0 (C)1.6* ↑8.3*** ↑6.9*** ↑ns2.3* ↑
AGPaseS-A1286G31.6 (G)5.1** ↓5.8** ↓7.9** ↓5.5* ↑ns
AGPaseS-T1392C34.2 (C)nsns9.0** ↑ns5.1* ↑
INV-8/2-T2076C (A2065G, T2272A)37.6 (C)7.8*** ↓7.7** ↓9.2*** ↓ns8.0** ↓
INV-8/2-T2134G (G2116A)41.7 (G)5.3** ↑5.8* ↑4.4* ↑4.8* ↓5.3* ↑
INV-8/2-T2320C (G2255A)13.0 (C)2.1* ↑3.0* ↑7.2*** ↑2.8* ↓ns
INV-8/2-G2182A16.2 (A)4.6** ↑4.3* ↑9.2*** ↑3.9* ↓ns
  • SNP, single-nucleotide polymorphism; CQA, chip color after harvest in autumn; CQS, chip color after 3 months storage at 4°; TSC, tuber starch content; TY, tuber yield; TSY, tuber starch yield; ns, not significant, MFA, minor frequency allele.

  • a SNPs in parentheses were in strong LD, showed similar associations and the same direction of effect as the SNP, for which the data are shown.

  • b Significance is indicated by “ns” (P > 0.05), *0.05 > P ≥ 0.01, **0.01 > P ≥ 0.001 and ***P < 0.001.

  • c Arrows indicate the direction of the effect of the MFA on the trait, upwards for a positive (lighter chip color corresponding to lower sugar content, greater starch content, yield, starch yield) and downward for a negative effect (darker chip color corresponding to greater sugar content, lower starch content, yield, starch yield). ↑↓: direction of effect was inconsistent between genotypic groups.