Table 2. Significant QTL associated with seed colour and fiber traits in the GH06 x P174 F9 RIL population (n = 172) after phenotyping in 4 different field environments.
| Trait | Environment | QTL | Chromosome | Marker interval | LOD score | Additive effect | R2 (%) |
| ADL content (% DW) | 2008 Cq | qADLA09 | A09 | SNP21195A09-SNP21172A09 | 14.31 | −0.66 | 32.8 |
| qADLC05 | C05 | SNP37372-SNP37409 | 4.52 | −0.32 | 9.1 | ||
| 2008 Gi | qADLA09 | A09 | SNP21195A09-SNP21172A09 | 15.39 | −0.45 | 33.3 | |
| qADLC05 | C05 | SNP37372-SNP37409 | 9.54 | −0.28 | 14.1 | ||
| 2008 Ho | qADLA09 | A09 | SNP21195A09-SNP21172A09 | 20.72 | −0.75 | 42.8 | |
| qADLC05 | C05 | SNP37372-SNP37409 | 5.33 | −0.31 | 8.1 | ||
| 2009 Gi | qADLA09 | A09 | SNP21195A09-SNP21172A09 | 15.2 | −0.53 | 31.6 | |
| qADLC05 | C05 | SNP37372-SNP37409 | 6.95 | −0.28 | 13.1 | ||
| Seed colour | 2008 Gi | qColA09 | A09 | SNP21195A09-SNP21172A09 | 17.8 | −0.44 | 36.9 |
| 2008 Ho | qColA09 | A09 | SNP21195A09-SNP21172A09 | 23.6 | −0.62 | 47.2 | |
| 2009 Gi | qColA09 | A09 | SNP21195A09-SNP21172A09 | 18.56 | −0.53 | 39.1 | |
| Cellulose content (% DW) | 2008 Cq | qCelA08 | A08 | SNP17683A08-SNP17656A08 | 6.51 | −0.18 | 13.5 |
| qCelA09 | A09 | SNP20823A09-SNP20748A09 | 11.33 | 0.23 | 21.9 | ||
| 2008 Gi | qCelA08 | A08 | SNP17683A08-SNP17656A08 | 6.27 | −0.32 | 12.1 | |
| qCelA09 | A09 | SNP19925A09-SNP20492A09 | 5.38 | 0.55 | 4.7 | ||
| 2008 Ho | qCelA08 | A08 | SNP17683A08-SNP17656A08 | 8.86 | −0.31 | 15.1 | |
| qCelC02 | C02 | SNP37983C02-SNP35881C02 | 4.41 | −0.20 | 6.4 | ||
| qCelC03 | C03 | SNP34516C03-SNP34515C03 | 5.85 | −0.25 | 7.9 | ||
| 2009 Gi | qCelA08 | A08 | SNP17683A08-SNP17656A08 | 6.91 | −0.31 | 14.0 | |
| qCelC03 | C03 | SNP34516C03-SNP34515C03 | 5.95 | −0.25 | 7.5 | ||
| Hemi-cellulose (% DW) | 2008 Gi | qHemA03 | A03 | SNP7833A03-SNP5891A03 | 6.29 | −0.22 | 8.3 |
| 2008 Ho | qHemA03 | A03 | SNP7833A03-SNP5891A03 | 4.23 | −0.15 | 7.3 | |
| 2009 Gi | qHemA03 | A03 | SNP7833A03-SNP5891A03 | 5.18 | −0.18 | 8.3 | |
| qHemA06 | A06 | SNP12895A06-SNP13359A06 | 5.51 | 0.19 | 10.2 | ||
| qHemA09 | A09 | SNP20527A09-SNP20457A09 | 4.68 | −0.24 | 16.9 |
QTL were localized on high-density SNP map to allow navigation directly from QTL confidence intervals to genomic sequence regions of interest. Negative additive effect values indicate a decrease in the trait value caused by QTL alleles from parent GH06, while positive additive values indicate increasing trait values with QTL alleles from parent GH06. R 2 is the percentage of variation explained by each QTL. Cq: Chongqing, China; Ho, Hohenlieth, Germany; Gi: Giessen Germany. QTL consistent over different environments are shown in bold font.