Table 5.
Quantitative trait loci for stripe rust resistance identified at the seedling stage using pooled data.
| Pathotype | QTL | SNP | Chr | Position (Mb) | Allele | MAF | P-value | FDR P-value | R2 (%) | Allelic Effect |
|---|---|---|---|---|---|---|---|---|---|---|
| 47S103 | Qyr.stripe-1BS | AX-94839474* | 1BS | 92.87 | T/C | 0.194 | 4.95E-05 | 0.084702# | 27.7 | 1.84 |
| Qyr.stripe-2AL | AX-95174135 | 2AL | 591.62 | C/T | 0.363 | 2.52E-05 | 0.081406# | 28.1 | −1.05 | |
| Qyr.stripe-2BL.1 | AX-94848091 | 2BL | 756.70 | C/T | 0.232 | 6.53E-05 | 0.081406# | 27.6 | 1.02 | |
| Qyr.stripe-2BL.2 | AX-94490490 | 2BL | 759.82 | C/T | 0.378 | 3.54E-05 | 0.081406# | 27.9 | −1.03 | |
| AX-95175933 | 2BL | 760.12 | C/T | 0.203 | 1.46E-05 | 0.081406# | 28.3 | −2 | ||
| AX-94608940 | 2BL | 760.26 | A/G | 0.498 | 7.54E-05 | 0.081406# | 27.5 | 1.12 | ||
| AX-95142963 | 2BL | 760.89 | A/C | 0.387 | 1.79E-05 | 0.081406# | 28.2 | −1.07 | ||
| AX-95238626* | 2BL | 760.95 | G/A | 0.195 | 4.26E-05 | 0.084702# | 27.8 | 1.86 | ||
| AX-94497849 | 2BL | 761.98 | C/T | 0.31 | 5.47E-05 | 0.084702# | 27.7 | 1.91 | ||
| AX-94868242* | 2BL | 761.99 | A/C | 0.475 | 6.33E-06 | 0.084702# | 28.8 | −1.03 | ||
| Qyr.stripe-2DL.1 | AX-95007159 | 2DL | 619.60 | A/G | 0.441 | 6.80E-05 | 0.081406# | 27.6 | 1.16 | |
| Qyr.stripe-2DL.2 | AX-95166280 | 2DL | 621.02 | G/A | 0.194 | 8.98E-06 | 0.084702# | 28.6 | 1.97 | |
| Qyr.stripe-3B | AX-94877000* | 3B- | 3.24 | A/T | 0.427 | 4.10E-05 | 0.081406# | 27.8 | −0.98 | |
| Qyr.stripe-3DS.1 | AX-95098367 | 3DS | 3.98 | A/G | 0.256 | 7.54E-05 | 0.084702# | 27.5 | −0.96 | |
| Qyr.stripe-3DS.2 | AX-94417619 | 3DS | 12.45 | C/G | 0.435 | 9.85E-05 | 0.104201# | 27.4 | 0.94 | |
| Qyr.stripe-4BL | AX-94853722 | 4BL | 623.07 | C/A | 0.422 | 3.52E-05 | 0.081406# | 27.9 | −1.39 | |
| Qyr.stripe-6BL.1 | AX-94735973 | 6BL | 117.99 | C/T | 0.413 | 6.56E-05 | 0.081406# | 27.6 | 1.62 | |
| Qyr.stripe-6BL.2 | AX-94382687 | 6BL | 408.65 | G/A | 0.162 | 3.05E-05 | 0.084702# | 28 | 1.34 | |
| 46S119 | Qyr.stripe-1BL | AX-94482117 | 1BL | 486.48 | T/G | 0.134 | 6.69E-04 | 0.97075 | 11.8 | 1.14 |
| Qyr.stripe-3AL | AX-94419836* | 3AL | 374.73 | G/T | 0.182 | 8.77E-05 | 0.250823# | 13 | 1.02 | |
| Qyr.stripe-3AS | AX-95193648 | 3AS | 0.56 | A/G | 0.172 | 5.19E-05 | 0.278927# | 13.3 | −1.58 | |
| Qyr.stripe-3B.1 | AX-94486149 | 3B- | 3.23 | G/A | 0.221 | 6.66E-05 | 0.250823# | 13.2 | 1.24 | |
| AX-94904447 | 3B- | 3.24 | G/T | 0.197 | 3.86E-05 | 0.250823# | 13.5 | −1.53 | ||
| Qyr.stripe-3B.2 | AX-94702815* | 3B- | 542.74 | A/T | 0.199 | 4.12E-05 | 0.254159# | 13.5 | −1.94 | |
| AX-94701179* | 3B- | 542.90 | A/G | 0.373 | 9.24E-04 | 0.97075 | 11.7 | −0.86 | ||
| Qyr.stripe-4AL | AX-95630255 | 4AL | 602.25 | G/A | 0.199 | 4.55E-04 | 0.97075 | 12.1 | −0.95 | |
| Qyr.stripe-4DL | AX-94541083* | 4DL | 226.26 | T/C | 0.142 | 5.52E-04 | 0.97075 | 11.9 | 1.47 | |
| Qyr.stripe-5AS | AX-94797468 | 5AS | 253.60 | C/T | 0.454 | 8.48E-04 | 0.97075 | 11.7 | −0.82 | |
| Qyr.stripe-5BS.1 | AX-94706157 | 5BS | 38.36 | C/A | 0.486 | 5.26E-05 | 0.250823# | 13.3 | 0.85 | |
| Qyr.stripe-5BS.2 | AX-95145565* | 5BS | 45.24 | C/T | 0.154 | 9.01E-04 | 0.97075 | 11.7 | −1.22 | |
| Qyr.stripe-5DS | AX-94429414 | 5DS | 98.26 | C/T | 0.019 | 5.36E-04 | 0.97075 | 12 | −3.97 | |
| Qyr.stripe-6DL | AX-94859969 | 6DL | 462.86 | G/A | 0.306 | 4.11E-04 | 0.97075 | 12.1 | 0.85 | |
| 110S119 | Qyr.stripe-3B | AX-94883935 | 3B- | 816.28 | A/C | 0.291 | 9.76E-04 | 1 | 6.6 | 0.59 |
| Qyr.stripe-6AS | AX-94989376 | 6AS | 221.88 | T/G | 0.177 | 2.70E-04 | 1 | 7.4 | −1.01 | |
| Qyr.stripe-6DL | AX-94633926 | 6DL | 369.66 | C/G | 0.279 | 2.95E-04 | 1 | 7.4 | −0.48 | |
| Qyr.stripe-7AS | AX-94844913 | 7AS | 8.78 | A/G | 0.5 | 6.54E-04 | 1 | 6.9 | 0.4 | |
| Qyr.stripe-7DL | AX-95227592 | 7DL | 518.05 | A/G | 0.205 | 7.70E-04 | 1 | 6.8 | 0.48 | |
| Qyr.stripe-7DS.1 | AX-94943939 | 7DS | 14.17 | A/G | 0.234 | 4.39E-04 | 1 | 7.1 | 0.5 | |
| Qyr.stripe-7DS.2 | AX-94878859 | 7DS | 16.70 | A/G | 0.393 | 3.24E-04 | 1 | 7.3 | 0.51 | |
| 238S119 | Qyr.stripe-1AL | AX-95153545* | 1AL | 541.98 | G/A | 0.195 | 5.01E-04 | 0.993302 | 8.2 | 0.64 |
| AX-94381637 | 1AL | 542.87 | C/T | 0.14 | 3.37E-04 | 0.993302 | 8.4 | −0.82 | ||
| Qyr.stripe-1BL.1 | AX-94717933 | 1BL | 326.02 | C/T | 0.414 | 5.28E-04 | 0.993302 | 8.1 | 0.75 | |
| Qyr.stripe-1BL.2 | AX-95243592 | 1BL | 606.84 | G/T | 0.152 | 5.36E-04 | 0.993302 | 8.1 | −0.7 | |
| AX-95229302 | 1BL | 608.47 | C/T | 0.171 | 2.83E-04 | 0.993302 | 8.5 | −0.69 | ||
| AX-94850928 | 1BL | 608.53 | C/T | 0.168 | 6.11E-04 | 0.993302 | 8.1 | −0.66 | ||
| Qyr.stripe-4AS | AX-94398581 | 4AS | 176.88 | C/T | 0.229 | 8.25E-04 | 0.993302 | 7.9 | −0.55 | |
| Qyr.stripe-4DL | AX-94948233 | 4DL | 211.03 | T/C | 0.371 | 5.13E-04 | 0.993302 | 8.2 | −0.63 | |
| Qyr.stripe-5BL | AX-95258852 | 5BL | 499.12 | T/C | 0.422 | 3.79E-04 | 0.993302 | 8.3 | −0.82 | |
| Qyr.stripe-5BS | AX-94809513 | 5BS | 26.45 | T/C | 0.317 | 9.81E-04 | 0.993302 | 7.8 | 0.69 | |
| Qyr.stripe-5DL.1 | AX-95244380* | 5DL | 344.50 | C/G | 0.146 | 1.44E-04 | 0.993302 | 8.9 | −0.8 | |
| Qyr.stripe-5DL.2 | AX-95202253 | 5DL | 428.83 | G/A | 0.114 | 6.15E-04 | 0.993302 | 8.1 | −0.97 |
Here * denotes MTAs which were also found to be significant to both year (i.e. 2018 and 2019) association mapping results and # represents FDR adjusted p < 0.30.