Table 4. Summary of QTL detected from all analyses.
| Chr | Trait | QTL | Groupa | Peak Marker or Interval | LOD Peak / Threshold | R2 |
|---|---|---|---|---|---|---|
| Chr5 | 09FD_120 Loc1 LEAF | 09FD_120_L1_Lf5 | LFRes5-2 | At2g31970-At4g12590 | 4.27/1.75 | 0.29 |
| 09FD_120 Loc2 LEAF | 09FD_120_L2_Lf5 | LFRes5-2 | At5g49510 | 2.93/1.71 | 0.18 | |
| 09FD_120 Loc1&2 STEM | 09FD_120_L12_St5 | STRes5-5 | T1541-TG69 | 1.89/1.72 | 0.18 | |
| 10FD-early_83 Loc1&2 LEAF | 10FDe_83_L12_Lf5-1 | LFRes5-1 | TG358 | 4.76/1.72 | 0.21 | |
| 10FDe_83_L12_Lf5-2 | LFRes5-2 | At2g31970-At4g12590 | 7.77/1.72 | 0.47 | ||
| 10FD-early_83 Loc1 STEM | 10FDe_83_L1_St5 | STRes5-4 | T1541 | 2.74/1.70 | 0.21 | |
| 10FD-early_83 Loc2 STEM | 10FDe_83_L2_St5 | STRes5-4 | T1541-TG69 | 3.63/1.72 | 0.21 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St5 | STRes5-1 | TG358 | 5.43/1.77 | 0.41 | |
| GC_120 p10353 STEM | GC_120_p10_St5-1 | STRes5-2 | TG23 | 3.01/1.71 | 0.19 | |
| GC_120_p10_St5-2 | STRes5-3 | At2g31970-At4g12590 | 2.34/1.71 | 0.18 | ||
| Chr11 | 09FD_120 Loc1&2 LEAF | 09FD_120_L12_Lf11-1 | LFRes11-3 | At4g22260 | 1.89/1.63 | 0.07 |
| 09FD_120_L12_Lf11-2 | LFRes11-5 | At5g04590 | 3.70/1.63 | 0.17 | ||
| 10FD-early_83 Loc1&2 LEAF | 10FDe_83_L12_Lf11-1 | LFRes11-1 | TG194 | 3.28/1.68 | 0.21 | |
| 10FDe_83_L12_Lf11-2 | LFRes11-5 | At5g04590 | 5.82/1.68 | 0.38 | ||
| 10FD-early_83 Loc1 STEM | 10FDe_83_L1_St11-1 | STRes11-1 | TG194 | 3.39/1.59 | 0.23 | |
| 10FDe_83_L1_St11-2 | STRes11-2 | U340899 | 4.27/1.59 | 0.31 | ||
| 10FD-early_83 Loc2 STEM | 10FDe_83_L2_St11-1 | STRes11-1 | TG194 | 2.44/1.64 | 0.18 | |
| 10FDe_83_L2_St11-2 | STRes11-2 | U340899 | 4.47/1.64 | 0.33 | ||
| 10FD-late_83 Loc1 LEAF | 10FDl_83_L1_Lf11-1 | LFRes11-4 | cLEX4G10 | 3.03/1.76 | 0.24 | |
| 10FDl_83_L1_Lf11-2 | LFRes11-5 | At5g04590 | 2.30/1.76 | 0.15 | ||
| 10FD-late_83 Loc2 LEAF | 10FDl_83_L2_Lf11-1 | LFRes11-3 | At1g21690 | 3.50/1.74 | 0.22 | |
| 10FDl_83_L2_Lf11-2 | LFRes11-4 | cLEB7L1 | 2.97/1.74 | 0.24 | ||
| 10FDl_83_L2_Lf11-3 | LFRes11-5 | At5g04590 | 3.16/1.74 | 0.19 | ||
| 10FD-late_83 Loc1 STEM | 10FDl_83_L1_St11 | STRes11-6 | At5g04590 | 4.56/1.78 | 0.28 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St11-1 | STRes11-2 | At5g16710 | 1.88/1.74 | 0.13 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St11-2 | STRes11-6 | At5g04590 | 3.23/1.74 | 0.23 | |
| GC_120 p7629 LEAF | GC_120_p76_Lf11 | LFRes11-4 | cLEX4G10 | 3.80/1.69 | 0.22 | |
| GC_120 Sal10 LEAF | GC_120_sal_Lf11 | LFRes11-3 | At1g44446 | 1.87/1.61 | 0.12 | |
| GC_120 p7629 STEM | GC_120_p76_St11 | STRes11-4 | cLEX4G10 | 3.06/1.68 | 0.18 | |
| GC-3_120 Sal10 STEM | GC-3_120_sal_St11-1 | STRes11-3 | At1g21690 | 1.87/1.61 | 0.10 | |
| GC-3_120_sal_St11-2 | STRes11-5 | At4g10050 | 3.35/1.61 | 0.21 |
| Chr | Trait | QTL | Allele Dirb | 1-LOD Interval | Flanking Markers |
|---|---|---|---|---|---|
| Chr5 | 09FD_120 Loc1 LEAF | 09FD_120_L1_Lf5 | (−) | 8.7-9.4 | At2g31970-At4g12590 |
| 09FD_120 Loc2 LEAF | 09FD_120_L2_Lf5 | (−) | 5.9-8.7 | At3g17210-At4g12590 | |
| 09FD_120 Loc1&2 STEM | 09FD_120_L12_St5 | (−) | 9.9-12.3 | T1541-At3g55360 | |
| 10FD-early_83 Loc1&2 LEAF | 10FDe_83_L12_Lf5-1 | (−) | 0.0-0.3 | TG358-T0536 | |
| 10FDe_83_L12_Lf5-2 | (−) | 7.3-9.4 | At5g49510-At4g12590 | ||
| 10FD-early_83 Loc1 STEM | 10FDe_83_L1_St5 | (+) | 9.9-12.3 | T1541-At3g55360 | |
| 10FD-early_83 Loc2 STEM | 10FDe_83_L2_St5 | (+) | 9.9-12.3 | T1541-At3g55360 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St5 | (−) | 0.0-0.3 | TG358-T0536 | |
| GC_120 p10353 STEM | GC_120_p10_St5-1 | (−) | 5.0-6.3 | At2g33950-At5g49510 | |
| GC_120_p10_St5-2 | (+) | 7.7-9.9 | At2g31970-T1541 | ||
| Chr11 | 09FD_120 Loc1&2 LEAF | 09FD_120_L12_Lf11-1 | (−) | 4.3-5.5 | CT182-At1g21690 |
| 09FD_120_L12_Lf11-2 | (−) | 9.0-9.4 | At4g10050-TG400 | ||
| 10FD-early_83 Loc1&2 LEAF | 10FDe_83_L12_Lf11-1 | (−) | 0.0-0.7 | TG194-T0408 | |
| 10FDe_83_L12_Lf11-2 | (−) | 9.0-9.4 | At5g04590-TG400 | ||
| 10FD-early_83 Loc1 STEM | 10FDe_83_L1_St11-1 | (−) | 0.0-1.4 | TG194-J1 | |
| 10FDe_83_L1_St11-2 | (+) | 3.4-4.3 | At5g16710-CT182 | ||
| 10FD-early_83 Loc2 STEM | 10FDe_83_L2_St11-1 | (−) | 0.0-0.7 | TG194-T0408 | |
| 10FDe_83_L2_St11-2 | (+) | 3.0-4.3 | At5g16710-CT182 | ||
| 10FD-late_83 Loc1 LEAF | 10FDl_83_L1_Lf11-1 | (−) | 6.9-7.6 | cLEX4G10-TG147 | |
| 10FDl_83_L1_Lf11-2 | (−) | 9.0-9.4 | At5g04590-TG400 | ||
| 10FD-late_83 Loc2 LEAF | 10FDl_83_L2_Lf11-1 | (−) | 4.8-5.6 | At4g22260-At1g44790 | |
| 10FDl_83_L2_Lf11-2 | (−) | 6.9-7.6 | cLEX4G10-TG147 | ||
| 10FDl_83_L2_Lf11-3 | (−) | 9.0-9.4 | At5g04590-TG400 | ||
| 10FD-late_83 Loc1 STEM | 10FDl_83_L1_St11 | (−) | 9.0-9.4 | At5g04590-TG400 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St11-1 | (+) | 3.0-4.3 | AAt5g04590-TG400 | |
| 10FD-late_83 Loc2 STEM | 10FDl_83_L2_St11-2 | (−) | 9.0-9.4 | At5g04590-TG400 | |
| GC_120 p7629 LEAF | GC_120_p76_Lf11 | (−) | 6.9-7.5 | cLEX4G10-cLEB7L1 | |
| GC_120 Sal10 LEAF | GC_120_sal_Lf11 | (−) | 5.5-6.9 | At1g21690-cLEX4G10 | |
| GC_120 p7629 STEM | GC_120_p76_St11 | (−) | 6.6-7.5 | At1g44790-cLEB7L1 | |
| GC-3_120 Sal10 STEM | GC-3_120_sal_St11-1 | (−) | 5.5-5.6 | At1g21690-At1g44790 | |
| GC-3_120_sal_St11-2 | (+) | 8.4-9.0 | At4g10050-At5g04590 |
Trait and QTL names are given according to the dataset, location or isolate, and trait evaluated. QTL names also include the chromosome, and if multiple QTL were detected for a single trait, a dash and number was included to differentiate among QTL (see Materials and Methods). 1-LOD interval positions refer to the cM distances on the linkage map for each introgressed region from S. habrochaites on chromosome 5 or 11. The R2 values are the proportion of phenotypic variation explained by the marker-trait association.
a
Group indicates coincident QTL, as defined by trait measured, directionality of the S. habrochaites allele effect, and coincidence of the 1-LOD intervals.
b
Allele directionality is the direction of the effect of the S. habrochaites allele at that QTL: a minus sign (−) indicates a decrease in AUDPC and thus an increase in resistance.