Table 5 Effects of markers associated with chip quality in the CHIPS-ALL population on reducing sugar content in the SUGAR40 panel after 0 (T0), 1 (T1), 2 (T2), 4 (T4), and 12 wk (T12) storage at 4° (log10 transformation, ANOVA)
MarkeraMinor Allele Frequency, %T0 Percent Variance ExplainedbT1 Percent Variance ExplainedbT2 Percent Variance ExplainedbT4 Percent Variance ExplainedbT12 Percent Variance Explainedb
PWD-G11140A7.5 (A) ↑cns9.6**11.3**19.2***19.0***
BMY1-G2533A29.4 (A) ↑6.1*7.0*ns5.2*ns
BMY1-G2657A7.0 (A) ↑8.1**5.4*4.6*4.7*ns
BMY1-G2751A6.4 (A) ↓3.7*5.3*4.2*3.7*3.6*
StpL(PHO1b)-3e_G1305T1311d13.1 (1) ↑18.0***19.5***16.9***13.3***15.6***
StpL(PHO1b)-3b_A158C159 A1250d9.4 (1) ↓16.3***25.4***18.5***21.1***17.1***
PHO1b-A3931G2.6 (G) ↓12.6***13.9***13.4***11.7***13.0***
PHO1b-A3982C25.6 (C) ↑↓9.1*9.8**9.3*10.3**7.9*
PHO1b-C3990T7.0 (T) ↑6.2*6.5*11.2**5.7*ns
PHO1b-G4181A16.7 (A) ↑↓15.1***14.2***12.4**11.6**8.7**
PHO1b-G4106A30.1 (A) ↑18.9***23.0***25.7***32.0***25.9***
PHO1b-A4207G16.0 (G) ↑11.3*14.6**13.5**ns10.0*
PHO1b-T4404C8.1 (C) ↑8.9**14.1***16.3***15.6***8.8**
Stp23-8b_PHO1a-HAd6.2 (1) ↑4.1*5.8**11.0***9.3**10.9***
AGPaseS-T1284C5.6 (C) ↑6.3**4.1*3.4*7.2**10.8***
AGPaseS-A1286G35.2 (G) 16.8***18.7***16.0**16.2**16.6**
INV-8/2-T2076C36.2 (C) 37.1***42.6***34.5***34.0***28.7***
INV-8/2-T2134G35.0 (G) ↑37.3***40.0***31.1***33.8***34.6***
INV-8/2-T2320C11.2 (C) ↑11.6**8.4**8.2**7.4*10.6**
INV-8/2-G2182A16.2 (A) ↑7.5*5.6*nsnsns
Pain1-8c_C552 A718d5.0 (1) ↑5.0*3.9*7.5**10.9***11.4***
InvGE-6f_A1103d6.2 (1) ↑9.6**7.8**7.6**12.1***9.3**
InvCD141-C339T (G280A, C288T, C543T, G630Ae13.7 (T) ↓30.0***30.6***32.4***37.1***32.3***
  • ANOVA, analysis of variance; ns, not significant; SNP, single-nucleotide polymorphism; LD, linkage disequilibrium.

  • a Markers, for which box plots are shown in Figure 3 are in bold letters.

  • b Significance is indicated by “ns” not significant (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, upwards for a positive (lower sugar content) and downward for a negative effect (higher sugar content); ↑↓: direction of effect was inconsistent between genotypic groups.

  • d Marker was scored by allele specific PCR assay, presence and absence of the MFA was scored as 1 and 0, respectively, without considering allele dosage.

  • e 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.