TABLE 5.
Quantitative trait nucleotides (QTNs) associated with resistance to Pst at adult plant stages in four environments in SYN-DER panel using 90K and GBS markers.
| Environment | SNP | Allelesa | Chr | Pos (Mb) | QTN effectb | LOD score | −log10(p) | r2 (%)c | MAFd |
| ISB.15 | IWB7628 | T/C | 1A | 3.1 | 2.3 | 6.34 | 7.19 | 6.83 | 0.47 |
| ISB.16 | 1A_3878168 | G/T | 1A | 3.9 | 2.18 | 6.71 | 7.57 | 6.95 | 0.3 |
| NWS.15 | IWB4201 | G/A | 1A | 4.0 | –2.96 | 3.95 | 4.7 | 5.72 | 0.1 |
| NWS.16 | IWB21700 | T/C | 1A | 534.3 | –7.22 | 3.53 | 4.26 | 8.13 | 0.29 |
| NWS.15 | 1A_560487941 | G/A | 1A | 560.5 | –2.35 | 4.52 | 5.29 | 5.98 | 0.17 |
| NWS.15 | IWB10188 | G/A | 1A | 581.5 | –3.08 | 5.11 | 5.91 | 9.09 | 0.15 |
| ISB.15 | 1B_8591698 | C/T | 1B | 8.6 | –2.92 | 3.4 | 4.12 | 5.97 | 0.1 |
| NWS.16 | IWB64963 | G/A | 1B | 86.8 | 7.81 | 5.69 | 6.51 | 11.1 | 0.48 |
| ISB.15 | IWB2120 | A/C | 1B | 106.8 | 2.92 | 3.84 | 4.58 | 6.85 | 0.15 |
| ISB.16 | IWB49173 | T/C | 1B | 327.8 | 3.11 | 5.19 | 6 | 10.57 | 0.19 |
| ISB.15 | 1B_633336851 | C/A | 1B | 633.3 | 2.65 | 3.74 | 4.48 | 3.26 | 0.09 |
| ISB.15 | 1B_683306760 | G/A | 1B | 683.3 | –2.58 | 6.16 | 7 | 8.16 | 0.36 |
| NWS.16 | 2A_566856454 | G/T | 2A | 566.9 | 11.57 | 4.08 | 4.83 | 9.06 | 0.12 |
| NWS.16 | 2B_163977776 | G/A | 2B | 164.0 | –9.38 | 5.72 | 6.55 | 8.33 | 0.18 |
| NWS.16 | 2B_360129171 | G/A | 2B | 360.1 | –13.81 | 7.83 | 8.72 | 6.89 | 0.06 |
| NWS.15 | IWB35566 | G/A | 2B | 783.2 | –2.85 | 4.6 | 5.38 | 5.11 | 0.1 |
| NWS.15 | 3A_130776756 | C/T | 3A | 130.8 | 3.81 | 5.81 | 6.64 | 6.5 | 0.06 |
| NWS.15 | 3A_503145562 | A/G | 3A | 503.1 | 2.12 | 3.75 | 4.49 | 3.88 | 0.13 |
| NWS.15 | 3A_736945971 | A/T | 3A | 736.9 | –2 | 5.46 | 6.28 | 7.22 | 0.41 |
| ISB.15 | IWA747 | G/A | 3B | 55.5 | –3.21 | 5.65 | 6.47 | 9.26 | 0.21 |
| ISB.15 | 3B_55514953 | T/C | 3B | 55.5 | –6.08 | 14.26 | 15.27 | 29.31 | 0.18 |
| NWS.16 | 3B_65339336 | G/A | 3B | 65.3 | –15.82 | 5.7 | 6.52 | 14.21 | 0.1 |
| ISB.16 | 3B_470866042 | A/G | 3B | 470.9 | –2.83 | 4.72 | 5.51 | 4.71 | 0.09 |
| ISB.16 | 3D_2620724 | C/T | 3D | 2.6 | –2.17 | 5.95 | 6.78 | 8.2 | 0.5 |
| NWS.15 | 3D_355163225 | T/C | 3D | 355.2 | –1.94 | 3.36 | 4.08 | 3.69 | 0.16 |
| ISB.16 | 3D_551073224 | T/C | 3D | 551.1 | –2.34 | 5.45 | 6.27 | 6.64 | 0.23 |
| NWS.16 | 4A_438964494 | C/T | 4A | 439.0 | 5.83 | 5.54 | 6.36 | 5.45 | 0.48 |
| NWS.16 | IWB68805 | C/T | 4A | 733.6 | 4.91 | 3.35 | 4.07 | 3.75 | 0.3 |
| ISB.16 | 4D_156687029 | G/A | 4D | 156.7 | –6.08 | 10.39 | 11.34 | 13.35 | 0.06 |
| NWS.15 | IWB33444 | C/T | 5A | 481.9 | –2.41 | 10.85 | 11.81 | 9.01 | 0.5 |
| ISB.16 | IWA4223 | C/T | 5A | 670.4 | –1.72 | 3.09 | 3.79 | 4.71 | 0.46 |
| ISB.15 | IWB7864 | G/A | 5B | 2.6 | –2.29 | 4.23 | 4.99 | 6.14 | 0.32 |
| NWS.16 | IWB65690 | G/A | 5B | 10.8 | 8.23 | 6.46 | 7.31 | 12.44 | 0.49 |
| NWS.15 | IWB8592 | G/A | 5B | 64.7 | 2.79 | 9.55 | 10.47 | 8.81 | 0.24 |
| NWS.16 | 5B_207483057 | G/A | 5B | 207.5 | 6.74 | 4 | 4.75 | 3.31 | 0.13 |
| ISB.16 | 5B_471381890 | A/G | 5B | 471.4 | 2.81 | 4.58 | 5.36 | 6.28 | 0.13 |
| NWS.16 | IWA2062 | G/A | 5B | 542.6 | –9.99 | 3.94 | 4.69 | 6.48 | 0.07 |
| NWS.15 | IWB65055 | T/C | 5B | 692.6 | –2.58 | 4.62 | 5.4 | 8.44 | 0.26 |
| NWS.15 | IWB14489 | G/A | 5D | 133.5 | –3.85 | 6.99 | 7.85 | 6.04 | 0.06 |
| ISB.16 | IWB9144 | G/A | 5D | 487.6 | –1.73 | 3.15 | 3.85 | 4.52 | 0.41 |
| ISB.15 | IWB30735 | T/C | 6A | 297.7 | –2.8 | 4.14 | 4.9 | 8.9 | 0.33 |
| NWS.15 | IWB66163 | T/C | 6A | 415.9 | –2.18 | 3.61 | 4.34 | 3.82 | 0.14 |
| ISB.16 | IWB40151 | A/G | 6A | 546.6 | –1.89 | 3.14 | 3.85 | 5.44 | 0.37 |
| ISB.16 | 6A_595332866 | T/C | 6A | 595.3 | –2.64 | 3.94 | 4.69 | 4.1 | 0.09 |
| ISB.16 | IWB37028 | T/C | 6B | 4.4 | –5.97 | 11.61 | 12.58 | 14.01 | 0.06 |
| NWS.16 | 6B_22858086 | A/G | 6B | 22.9 | –12.25 | 7.15 | 8.02 | 9.36 | 0.11 |
| NWS.15 | 6B_31867138 | C/T | 6B | 31.9 | –4.97 | 9.13 | 10.05 | 10.2 | 0.06 |
| ISB.15 | 6B_231490683 | G/A | 6B | 231.5 | 2.46 | 4.29 | 5.06 | 5.98 | 0.25 |
| NWS.16 | 6B_361469100 | C/T | 6B | 361.5 | –9.57 | 4.24 | 5.01 | 3.59 | 0.07 |
| ISB.15 | 6B_419133836 | G/A | 6B | 419.1 | –3.17 | 6.3 | 7.14 | 6.62 | 0.15 |
| NWS.15 | 6B_618067850 | G/C | 6B | 618.1 | –4.03 | 5.93 | 6.76 | 6.71 | 0.06 |
| NWS.15 | 6D_436810635 | G/A | 6D | 436.8 | –3.16 | 5.47 | 6.29 | 10.85 | 0.17 |
| ISB.16 | IWB74161 | C/T | 7A | 47.0 | –1.79 | 3.34 | 4.06 | 5.05 | 0.43 |
| NWS.16 | 7A_234640959 | C/T | 7A | 234.6 | 5.9 | 4.71 | 5.49 | 5.49 | 0.43 |
| ISB.16 | IWB21762 | C/T | 7A | 506.1 | –2.21 | 4.53 | 5.3 | 6.44 | 0.28 |
| ISB.16 | 7A_588284942 | G/A | 7A | 588.3 | 1.78 | 3.86 | 4.61 | 4.34 | 0.3 |
| NWS.16 | 7A_675526339 | G/C | 7A | 675.5 | –7.26 | 5.11 | 5.91 | 4.86 | 0.17 |
| NWS.15 | 7A_676996750 | G/A | 7A | 677.0 | –3.29 | 5.28 | 6.08 | 7.02 | 0.09 |
| ISB.16 | IWB26214 | C/T | 7B | 59.6 | –3.19 | 6.87 | 7.73 | 8.24 | 0.14 |
| NWS.15 | IWA5939 | T/C | 7B | 582.3 | 4.04 | 12.21 | 13.19 | 11.9 | 0.15 |
| ISB.15 | IWB13912 | T/C | 7B | 692.6 | –3.28 | 5.45 | 6.26 | 7.47 | 0.12 |
| NWS.16 | IWB48256 | T/C | 7B | 711.5 | –6.84 | 3.59 | 4.32 | 7.87 | 0.35 |
| ISB.16 | IWB12163 | G/A | 7B | 727.5 | –2.06 | 5.62 | 6.44 | 6.45 | 0.4 |
| ISB.16 | 7B_746448232 | A/G | 7B | 746.4 | –1.87 | 3.49 | 4.22 | 3.87 | 0.2 |
| NWS.16 | IWB42068 | A/G | 7D | 11.4 | –5.84 | 3.69 | 4.43 | 6.05 | 0.4 |
| ISB.15 | IWB74163 | A/C | 7D | 44.5 | –3.07 | 9.65 | 10.58 | 12.08 | 0.41 |
| ISB.15 | IWB59266 | A/G | 7D | 58.7 | –3.11 | 4.95 | 5.74 | 7.59 | 0.14 |
| ISB.16 | 7D_96173227 | G/T | 7D | 96.2 | 1.82 | 4 | 4.75 | 3.25 | 0.17 |
aResistance allele is underlined.
bQTN effect is negative if the minor allele is increasing phenotype and positive if the major allele is increasing phenotype value.
cPhenotypic variation explained by the QTN.
dMinor allele frequency.