Table 2.
Significant associations between single nucleotide polymorphism (SNP) markers (marker trait association—MTA) and different Parastagonospora nodorum culture filtrate (CF) infiltrations or infections (whole plant spray, WPS).
| Treatment | SNP marker | Allele | Chra | Position (Mbp) | Genomic region ID | P-value | Effect | R2 |
|---|---|---|---|---|---|---|---|---|
| Tox3 | AX.95632742 | A/G | 2A | 675.90 | 2A1 | 4.72E−05 | 1.13 | 0.80 |
| AX.94610974 | C/T | 5BS* | 6.65 | 5B1 | 3.31E−20 | 1.95 | 0.98 | |
| AX.94457982 | A/C | 5BL | 584.07 | 5B4 | 1.19E−06 | − 1.32 | 0.82 | |
| AX.95126753 | C/T | 5DS* | 4.34 | 5D | 2.09E−14 | − 1.39 | 0.90 | |
| AX.94978939 | C/T | 7A | 652.61 | 7A | 1.98E−06 | 1.20 | 0.82 | |
| CF-16FG168 | AX.94774467 | G/T | 2B | 213.25 | 2B2 | 4.37E−04 | 0.62 | 0.44 |
| AX.95165387 | A/C | 2B | 747.82 | 2B3 | 7.50E−04 | 0.57 | 0.44 | |
| AX.94753171 | A/G | 2D | 612.46 | 2D | 6.13E−04 | 1.14 | 0.44 | |
| AX.94828722 | A/G | 4B | 665.35 | 4B | 3.83E−04 | − 1.05 | 0.45 | |
| AX.94610974 | C/T | 5BS* | 6.65 | 5B1 | 1.99E−05 | 0.86 | 0.47 | |
| AX.95126753 | C/T | 5DS* | 4.34 | 5D | 4.03E−04 | − 0.65 | 0.44 | |
| AX.95019005 | A/G | 6A | 595.18 | 6A2 | 2.92E−04 | − 0.43 | 0.45 | |
| AX.94681771 | A/T | 7A | 657.09 | 7A | 9.69E−04 | 0.56 | 0.40 | |
| CF-15FG114 | AX.94429024 | A/T | 3A | 47.82 | 3A1 | 7.07E−04 | 0.83 | 0.49 |
| AX.94531841 | A/C | 4B | 611.51 | 4B | 7.76E−04 | − 1.82 | 0.49 | |
| AX.94610974 | C/T | 5BS* | 6.65 | 5B1 | 2.40E−10 | 1.45 | 0.64 | |
| AX.94457982 | A/C | 5BL | 584.07 | 5B4 | 2.93E−05 | − 1.33 | 0.52 | |
| AX.95126753 | C/T | 5DS* | 4.34 | 5D | 1.01E−08 | − 1.23 | 0.58 | |
| AX.94407285 | C/T | 6B | 239.87 | 6B2 | 2.12E−04 | − 1.81 | 0.51 | |
| CF-Sn15 | AX.94950274 | C/T | 1B | 566.84 | 1B | 3.97E−05 | − 0.95 | 0.40 |
| AX.95253275 | G/T | 1D | 203.32 | 1D2 | 2.04E−04 | − 0.81 | 0.39 | |
| AX.95171319 | G/T | 2A | 761.76 | 2A2 | 8.37E−04 | 1.05 | 0.37 | |
| AX.94610974 | C/T | 5BS* | 6.65 | 5B1 | 6.70E−08 | 0.97 | 0.48 | |
| AX.95010548 | C/G | 5B | 64.63 | 5B2 | 3.84E−05 | 1.20 | 0.40 | |
| AX.94457982 | A/C | 5BL | 584.07 | 5B4 | 2.32E−04 | − 0.89 | 0.39 | |
| AX.95126753 | C/T | 5DS* | 4.34 | 5D | 4.85E−06 | − 0.72 | 0.42 | |
| AX.94459459 | C/T | 6A | 555.58 | 6A2 | 8.38E−04 | 2.45 | 0.37 | |
| AX.94407285 | C/T | 6B | 239.87 | 6B2 | 3.86E−04 | − 1.36 | 0.38 | |
| AX.94535772 | A/G | 7B | 47.00 | 7B | 2.72E−04 | − 1.24 | 0.38 | |
| AX.94860625 | A/G | 7D | 632.34 | 7D | 2.78E−04 | 0.58 | 0.38 | |
| WPS_WAC13404 | AX.94935613 | C/T | 2A | 758.39 | 2A2 | 1.66E−04 | 1.25 | 0.23 |
| AX.95255981 | C/T | 2B | 744.69 | 2B3 | 3.35E−04 | 0.99 | 0.21 | |
| AX.94526408 | A/G | 3B | 117.59 | 3B | 3.68E−04 | − 0.66 | 0.22 | |
| AX.94948233 | C/T | 3D | 480.83 | 3D | 7.06E−04 | − 1.08 | 0.21 | |
| AX.94428968 | C/T | 4A | 736.15 | 4A | 9.62E−04 | 1.02 | 0.16 | |
| WPS_16FG168 | AX.94694976 | C/T | 1D | 7.61 | 1D1 | 9.07E−04 | − 1.28 | 0.19 |
| AX.95632742 | A/G | 2A | 675.90 | 2A1 | 8.56E−04 | 1.13 | 0.49 | |
| AX.94935613 | C/T | 2A | 758.39 | 2A2 | 3.76E−04 | 0.87 | 0.26 | |
| AX.95133018 | C/G | 2D | 636.07 | 2D | 6.28E−05 | 0.49 | 0.28 | |
| AX.94792356 | C/T | 4D | 50.64 | 4D | 2.49E−04 | 0.76 | 0.21 | |
| AX.94610974 | C/T | 5BS* | 6.65 | 5B1 | 1.05E−05 | 0.79 | 0.31 | |
| AX.95629214 | A/G | 6A | 544.48 | 6A2 | 4.65E−04 | 0.50 | 0.20 | |
| AX.94436382 | C/T | 7D | 632.01 | 7D | 1.44E−04 | − 0.89 | 0.21 | |
| WPS_15FG114 | AX.94427355 | A/C | 1D | 379.59 | 1D3 | 7.93E−04 | − 0.83 | 0.17 |
| AX.95007069 | A/G | 2B | 134.04 | 2B1 | 2.24E−04 | 0.42 | 0.19 | |
| AX.94699167 | C/T | 5A | 586.60 | 5A | 3.30E−05 | − 0.83 | 0.21 | |
| AX.94575839 | C/T | 6A | 570.00 | 6A2 | 8.09E–−04 | − 0.58 | 0.17 | |
| 0.00 | ||||||||
| WPS_Sn15 | AX.94723571 | C/T | 1D | 362.01 | 1D3 | 6.59E−04 | − 1.40 | 0.14 |
| AX.94954416 | A/G | 3A | 705.31 | 3A2 | 6.74E−04 | − 1.27 | 0.14 | |
| AX.94804165 | A/G | 5B | 548.33 | 5B3 | 4.55E−04 | − 1.41 | 0.14 | |
| AX.95097189 | C/T | 6B | 47.14 | 6B1 | 3.26E−04 | − 1.58 | 0.15 | |
| WPS_WAC13443 | AX.94935613 | C/T | 2A | 758.39 | 2A2 | 7.70E−04 | 1.06 | 0.17 |
| AX.94772629 | A/G | 4A | 636.97 | 4A | 8.32E−04 | 0.88 | 0.17 | |
| AX.95086097 | C/T | 6A | 50.00 | 6A1 | 7.18E−04 | 1.16 | 0.17 | |
| AX.94750259 | C/G | 7D | 613.62 | 7D | 7.88E-04 | 0.94 | 0.17 |
aChromosome; asterisk indicates that this marker corresponds to Snn3-5B (5BS) or Snn3-5D (5DS).