Table 3.
P. nodorum resistance/sensitivity QTL identified in the ‘NIAB Elite MAGIC’ population from field trials, seedling culture filtrate infiltration, ToxA infiltration and seedling inoculation
| QTL | Ref. | Trait | Year | Chr | Interval (cM) | Flanking markers | Peak marker | −log10 (p) | IWGSC RefSeq v1.0 start (bp) | IWGSC RefSeq v1.0 end (bp) | R2 (%) | Detected by QTL methods |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| QSnb.niab-2A.1 | 1 | Inoc_203649 | 2A | 0–1.01 | RAC875_c44680_90 and BS00111318_51 | BS00111318_51 | 3.00 | 2378473 | 2378574 | 5.11 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.2 | LB (Norway) | 2017 | 2A | 100.36–109.94 | Kukri_c24852_466 and BS00008805_51 | Excalibur_c637_1078 | 3.19 | 78844360 | 111457371 | 3.88 | IM,CIM (cov5, cov10) | |
| QSnb.niab-2A.3 | LB (Norway) | 2014 | 2A | 121.07–138.24 | JD_c2056_506 and Kukri_c7825_288 | BS00059475_51 | 5.82 | 410872779 | 588258104 | 16.00 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.3 | LB (Norway) | 2018 | 2A | 135.19–146.82 | Excalibur_c1793_97 and BS00022241_51 | RAC875_c9372_94 | 4.67 | 558953000 | 663329017 | 6.80 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.3 | LB (Norway) | 2016 | 2A | 130.65–146.82 | BS00059475_51 and BS00022241_51 | Ku_c5710_312 | 6.20 | 574172945 | 663329017 | 6.57 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.3 | GB (Norway) | 2016 | 2A | 141.26–142.77 | RAC875_c20247_398 and BS00062679_51 | BS00062679_51 | 4.21 | 611946675 | 615287757 | 4.12 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.3 | Infil_203649 (ncov1)† | 2A | 142.2–150.6 | BS00022641_51 and IAAV4015 | BS00090569_51 | 3.49 | 612422267 | 677529836 | 2.98 | CIM (cov1, cov5, cov10) | ||
| QSnb.niab-2A.3 | LB (UK) | 2017 | 2A | 144.81–145.31 | RAC875_c9372_94 and BS00012320_51 | RAC875_c9372_94 | 3.17 | 635606922 | 647927416 | 3.87 | IM,CIM (cov5, cov10) | |
| QSnb.niab-2A.4 | LB (Norway) | 2016 | 2A | 229.02–241.18 | wsnp_Ra_c6586_11477949 and BS00022252_51 | wsnp_Ra_c17622_26522072 | 4.41 | 755929525 | 775619939 | 3.74 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-2A.4 | LB (Norway) | 2017 | 2A | 234.62–237.63 | JD_c11825_1135 and Tdurum_contig8350_350 | Excalibur_c4372_363 | 3.97 | 758396871 | 780714672 | 4.53 | IM,CIM (cov5, cov10) | |
| QSnb.niab-2A.4 | Inoc_203649 | 2A | 252.80–256.82 | BS00064836_51 and Kukri_c365_345 | BS00101944_51 | 3.17 | 761248555 | 765269621 | 5.06 | IM,IBD | ||
| QSnb.niab-2D.1 | 2 | LB (UK) | 2018 | 2D | 32.58–50.83 | wsnp_JD_rep_c63957_40798083 and BobWhite_c59161_181 | BS00029208_51 | 3.51 | 14897896 | 27859806 | 3.91 | IM,CIM (cov5, cov10),IBD |
| QSnb.niab-2D.2 | Inoc_203649 | 2D | 188.01–198.36 | RFL_Contig1128_620 and Kukri_c36328_419 | Excalibur_c42413_442 | 4.61 | 635950166 | 637636412 | 11.42 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-2D.2 | Inoc_202579 | 2D | 188.01–198.86 | RFL_Contig1128_620 and BS00010685_51 | Ra_c19051_1446 | 4.33 | 635950166 | 638147754 | 4.86 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-3A | LB (Norway) | 2016 | 3A | 0–9.55 | RAC875_c46403_277 and Kukri_rep_c69028_347 | Tdurum_contig83209_316 | 3.95 | 1031134 | 10300906 | 4.37 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-3A | LB (Norway) | 2017 | 3A | 7.04–16.64 | Kukri_rep_c89183_282 and BS00066230_51 | wsnp_Ex_c6833_11782875 | 4.09 | 8685996 | 32325166 | 4.31 | IM,CIM (cov5, cov10) | |
| QSnb.niab-3A | Infil_202579 | 3A | 14.63–31.02 | TA003589_0518 and RAC875_c20134_535 | BS00055211_51 | 3.49 | 8865639 | 14851061 | 5.09 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-3B | Infil_203649 | 3B | 147.39–156.96 | BS00076872_51 and Excalibur_c5977_1409 | BobWhite_c13099_755 | 3.47 | 566843633 | 578616694 | 4.69 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-4A | LB (UK) | 2017 | 4A | 110.56–112.09 | BS00072025_51 and IAAV6581 | Kukri_c96129_147 | 3.68 | 598590361 | 605713556 | 3.56 | IM,CIM (cov5, cov10) | |
| QSnb.niab-5B.1(Snn3-B1) | 3, 4 | Infil_202579 | 5B | 0–13.16 | Tdurum_contig44048_276 and wsnp_Ex_c26252_35497729 | Tdurum_contig44048_276 | 5.48 | 13428116 | 27830730 | 8.10 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-5B.1(Snn3-B1) | Infil_203667 | 5B | 0–13.16 | Tdurum_contig44048_276 and wsnp_Ex_c26252_35497729 | BS00022336_51 | 8.90 | 13428116 | 27830730 | 10.40 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-5B.1 (Snn3-B1) | Inoc_202579 | 5B | 0–6.88 | Tdurum_contig44048_276 and Kukri_c60322_490 | Excalibur_rep_c104354_205 | 3.59 | 13428116 | 19438610 | 4.84 | IM,CIM (cov10), IBD | ||
| QSnb.niab-5B.2(Tsn1) | 4, 5 | Inoc_202579 | 5B | 123.06–138.93 | IACX7649 and wsnp_Ex_c6695_11577150 | Kukri_c54078_114 | 7.93 | 539294940 | 547404553 | 8.54 | IM,CIM (cov5, cov10),IBD | |
| Tsn1 | Infil_ToxA | 5B | 124.06–142.56 | IACX11840 and Excalibur_c33675_201 | Kukri_c54078_114 | Inf | 539935182 | 550847459 | 73.43 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-5D | 6 | GB (Norway) | 2017 | 5D | 49.43–66.08 | BobWhite_c7263_337 and BS00063971_51 | BS00110475_51 | 3.57 | 389934855 | 431201019 | 4.44 | IM,CIM (cov10),IBD |
| QSnb.niab-6A.1 | LB (Norway) | 2016 | 6A | 123.39–135.99 | IAAV5188 and RFL_Contig3088_949 | TA004558_1018 | 4.85 | 74025753 | 249160705 | 3.85 | IM,CIM (cov5, cov10),IBD | |
| QSnb.niab-6A.2 | 7, 8 | GB (Norway) | 2016 | 6A | 229.10 | BS00096240_51 and GENE_4028_152 | GENE_4028_152 | 3.68 | 600395629 | 600406208 | 3.56 | IM,CIM (cov5, cov10),IBD |
| QSnb.niab-7B.1 | Inoc_203649 | 7B | 100.24–110.66 | BS00067599_51 and Excalibur_rep_c67475_1420 | BS00067599_51 | 4.31 | 115244415 | 498523237 | 4.06 | IM,CIM (cov5, cov10), IBD | ||
| QSnb.niab-7B.2 | Infil_203649 | 7B | 168.06–184.77 | Kukri_c15912_860 and Excalibur_c50612_409 | BS00077956_51 | 2.91 | 673961429 | 700551772 | 5.83 | IM,CIM (cov5, cov10), IBD | ||
| QSnb.niab-7D.1 | Inoc_203649 | 7D | 69.65–81.20 | GENE_4292_204 and BS00049220_51 | GENE_4292_204 | 9.90 | 174445641 | 458015017 | 7.89 | IM,CIM (cov5, cov10),IBD | ||
| QSnb.niab-7D.2 | Infil_203649 | 7D | 116.86–118.37 | BS00023150_51 and BS00070188_51 | BS00070188_51 | 3.03 | 554596126 | 559460390 | 4.13 | IM,IBD | ||
| QSnb.niab-7D.3 | LB (Norway) | 2016 | 7D | 215.78–218.30 | RAC875_c10022_23 and JD_c2708_1512 | JD_c2708_1512 | 3.49 | 629325776 | 724128709 | 4.06 | IM,CIM (cov5, cov10),IBD |
Significance values and proportion of the variance explained (R2) for all QTL reported are derived from IM analysis and the intervals determined via CIM-cov10, unless otherwise indicated. References of studies where QTL were found in similar positions: 1—Rybak et al. (2017), 2—Phan et al. (2016), 3—Liu et al. (2009), 4—Downie et al. (2018), 5—Faris et al. (2010), 6—Liu et al. (2015), 7—Gao et al. (2015), 8—Arseniuk et al. (2004). QTL with − log10(p) value > 3 are presented, with QTL above the permutated trait-specific significance threshold highlighted in bold. Reference (Ref.), Chromosome (Chr.), IM (interval mapping), CIM (composite interval mapping), IBD (identity by descent). The − log10(p) value for Tsn1 is recorded as ‘Inf,’ as the p value was 0, resulting in an error when converted to the log10 scale
†Detected via CIM-cov1, -cov5 and -cov10