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).
| Markera | Minor Allele Frequency, % | T0 Percent Variance Explainedb | T1 Percent Variance Explainedb | T2 Percent Variance Explainedb | T4 Percent Variance Explainedb | T12 Percent Variance Explainedb |
|---|---|---|---|---|---|---|
| PWD-G11140A | 7.5 (A) ↑c | ns | 9.6** | 11.3** | 19.2*** | 19.0*** |
| BMY1-G2533A | 29.4 (A) ↑ | 6.1* | 7.0* | ns | 5.2* | ns |
| BMY1-G2657A | 7.0 (A) ↑ | 8.1** | 5.4* | 4.6* | 4.7* | ns |
| BMY1-G2751A | 6.4 (A) ↓ | 3.7* | 5.3* | 4.2* | 3.7* | 3.6* |
| StpL(PHO1b)-3e_G1305T1311d | 13.1 (1) ↑ | 18.0*** | 19.5*** | 16.9*** | 13.3*** | 15.6*** |
| StpL(PHO1b)-3b_A158C159 A1250d | 9.4 (1) ↓ | 16.3*** | 25.4*** | 18.5*** | 21.1*** | 17.1*** |
| PHO1b-A3931G | 2.6 (G) ↓ | 12.6*** | 13.9*** | 13.4*** | 11.7*** | 13.0*** |
| PHO1b-A3982C | 25.6 (C) ↑↓ | 9.1* | 9.8** | 9.3* | 10.3** | 7.9* |
| PHO1b-C3990T | 7.0 (T) ↑ | 6.2* | 6.5* | 11.2** | 5.7* | ns |
| PHO1b-G4181A | 16.7 (A) ↑↓ | 15.1*** | 14.2*** | 12.4** | 11.6** | 8.7** |
| PHO1b-G4106A | 30.1 (A) ↑ | 18.9*** | 23.0*** | 25.7*** | 32.0*** | 25.9*** |
| PHO1b-A4207G | 16.0 (G) ↑ | 11.3* | 14.6** | 13.5** | ns | 10.0* |
| PHO1b-T4404C | 8.1 (C) ↑ | 8.9** | 14.1*** | 16.3*** | 15.6*** | 8.8** |
| Stp23-8b_PHO1a-HAd | 6.2 (1) ↑ | 4.1* | 5.8** | 11.0*** | 9.3** | 10.9*** |
| AGPaseS-T1284C | 5.6 (C) ↑ | 6.3** | 4.1* | 3.4* | 7.2** | 10.8*** |
| AGPaseS-A1286G | 35.2 (G) ↓ | 16.8*** | 18.7*** | 16.0** | 16.2** | 16.6** |
| INV-8/2-T2076C | 36.2 (C) ↓ | 37.1*** | 42.6*** | 34.5*** | 34.0*** | 28.7*** |
| INV-8/2-T2134G | 35.0 (G) ↑ | 37.3*** | 40.0*** | 31.1*** | 33.8*** | 34.6*** |
| INV-8/2-T2320C | 11.2 (C) ↑↓ | 11.6** | 8.4** | 8.2** | 7.4* | 10.6** |
| INV-8/2-G2182A | 16.2 (A) ↑ | 7.5* | 5.6* | ns | ns | ns |
| Pain1-8c_C552 A718d | 5.0 (1) ↑ | 5.0* | 3.9* | 7.5** | 10.9*** | 11.4*** |
| InvGE-6f_A1103d | 6.2 (1) ↑ | 9.6** | 7.8** | 7.6** | 12.1*** | 9.3** |
| InvCD141-C339T (G280A, C288T, C543T, G630Ae | 13.7 (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.
Markers, for which box plots are shown in Figure 3 are in bold letters.
Significance is indicated by “ns” not significant (P > 0.05), *0.05 > P ≥ 0.01, **0.01 > P ≥ 0.001 and ***P < 0.001.
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.
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.
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.