TABLE 3.
Putative QTL significantly (p < 0.001) associated with seedling stage resistance against at least two pathotypes for each rust pathogen.
| Putative QTL* | Representative SNP |
Associated SNPs | No. of MTAs | −log10(p) |
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| YR pathotypes |
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| SNP (35K) | Chroma | Position (cM) | Allele# | MAFb | %PVE (R2)$ | YR_46S119 | YR_110S119 | YR_238S119 | YR_110S84 | YR_T | |||||
| QYr.ramp-1A.1 | AX-94448779 | 1A | 57.21–58.94 | T(128)/C(348) | 0.27 | 5.24 | AX-94838936 | 16 | – | – | – | 3.3448 | 8.2227 | ||
| QYr.ramp-1B.1 | AX-95119512 | 1B | 8.24–9.93 | T(94)/C(388) | 0.20 | 3.91 | AX-94741250 | 9 | – | 6.3342 | – | – | 6.3456 | ||
| QYr.ramp-1B.3 | AX-94768106 | 1B | 23.90–26.22 | T(106)/C(377) | 0.22 | 4.81 | AX-94500816 AX-94451305 | 75 | – | 5.6034 | 3.3111 | – | 7.6201 | ||
| QYr.ramp-1D.2 | AX-94911855 | 1D | 34.26–35.95 | A(387)/G(91) | 0.19 | 2.75 | AX-95173669 | 3 | – | – | – | 3.4822 | 4.6689 | ||
| QYr.ramp-2A.1 | AX-94691448 | 2A | 0.00–1.59 | A(29)/G(451) | 0.06 | 4.27 | AX-94448314 | 52 | – | 5.3691 | – | 4.7365 | – | ||
| QYr.ramp-2B.4 | AX-94637676 | 2B | 102.12–103.81 | T(86)/C(396) | 0.18 | 3.05 | AX-94670661 | 3 | – | – | 3.3727 | – | 5.1017 | ||
| QYr.ramp-3B.1 | AX-94573417 | 3B | 0.79–2.24 | A(394)/G(82) | 0.17 | 2.67 | AX-94632746 | 6 | 4.1367 | – | – | – | 4.5486 | ||
| QYr.ramp-5A.1 | AX-95229410 | 5A | 12.21–12.25 | A(177)/G(302) | 0.37 | 2.22 | AX-94592812 | 2 | 3.0734 | – | – | – | 3.8789 | ||
| QYr.ramp-6A.5 | AX-94926681 | 6A | 217.8–221.75 | T(367)/C(112) | 0.23 | 4.04 | AX-95094933 | 3 | 5.0844 | – | 3.6115 | – | – | ||
|
LR pathotypes |
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| LR_106 | LR_12-5 | LR_104-2 | LR_77-9 | LR_77-5 | LR_77-1 | ||||||||||
| QLr.ramp-1A.2 | AX-94979481 | 1A | 69.85–74.11 | A(203)/G(277) | 0.42 | 1.96 | AX-94449010 AX-94897502 | 7 | 3.0647 | – | – | 3.2634 | 3.2910 | – | |
| QLr.ramp-1B.3 | AX-94904215 | 1B | 24.64–26.22 | C(158)/G(319) | 0.33 | 2.30 | AX-94908596 AX-94899483 | 6 | 3.0970 | 3.1977 | – | 3.2543 | – | – | |
| QLr.ramp-2B.3 | AX-94441179 | 2B | 76.24–76.62 | T(213)/C(267) | 0.44 | 3.72 | AX-94838738 | 11 | 3.1461 | – | – | – | – | 5.3291 | |
| QLr.ramp-2B.7 | AX-94554810 | 2B | 103.81–104.59 | T(172)/C(306) | 0.36 | 1.56 | AX-94705091 AX-94492853 | 8 | 4.2393 | 3.1461 | 3.1748 | – | – | – | |
| QLr.ramp-3A.6 | AX-95226287 | 3A | 239.09 | T(50)/C(426) | 0.11 | 3.54–9.37 | - | 5 | – | 7.0931 | 7.5785 | 10.5717 | 12.9567 | 5.1067 | |
| QLr.ramp-3A.7 | AX-94883935 | 3A | 250.41 | A(428)/C(54) | 0.11 | 3.73–10.34 | AX-94477684 | 7 | 3.3933 | 5.5415 | 7.2823 | 12.1087 | 14.0301 | 5.6772 | |
| QLr.ramp-3B.5 | AX-95176613 | 3B | 83.69–85.27 | T(452)/C(25) | 0.05 | 2.83 | AX-94852024 | 22 | – | 3.8968 | – | – | 4.5076 | – | |
| QLr.ramp-3B.8 | AX-94871275 | 3B | 202.68–204.37 | C(424)/G(53) | 0.11 | 3.06–8.87 | AX-94915269 | 23 | – | 4.6575 | 6.5729 | 7.7139 | 12.3379 | 5.0884 | |
| QLr.ramp-3B.9 | AX-94977862 | 3B | 226.84 | T(106)/C(372) | 0.22 | 2.38–3.05 | – | 3 | – | – | 3.5205 | 3.4349 | 4.8088 | – | |
| QLr.ramp-3B.11 | AX-94805563 | 3B | 245.19–245.57 | T(47)/C(434) | 0.10 | 4.39–12.32 | – | 19 | – | 6.3846 | 9.1131 | 12.3215 | 16.503 | 6.2255 | |
| QLr.ramp-3D.3 | AX-94968108 | 3D | 158.35 | A(151)/G(326) | 0.32 | 2.45–3.20 | – | 3 | – | – | 3.5997 | 3.8469 | 5.0179 | – | |
| QLr.ramp-3D.4 | AX-94874313 | 3D | 160.44–167.71 | A(414)/G(67) | 0.14 | 3.51–7.84 | – | 10 | – | 5.2404 | 7.6624 | 9.1212 | 11.0555 | 5.205 | |
| QLr.ramp-3D.5 | AX-94436339 | 3D | 169.4 | T(416)/G(47) | 0.12 | 3.41–10.97 | – | 10 | – | 5.1111 | 8.178 | 11.0265 | 14.8984 | 5.9561 | |
| QLr.ramp-3D.6 | AX-95224631 | 3D | 174.29–178.60 | A(55)/G(422) | 0.12 | 2.56–10.09 | AX-94681641 | 94 | – | 5.6468 | 8.0652 | 9.9604 | 13.8254 | 5.8167 | |
| QLr.ramp-3D.7 | AX-95082799 | 3D | 191.16–194.75 | T(255)/C(220) | 0.46 | 3.64 | AX-94958018 | 11 | – | – | 3.252 | – | 5.6019 | – | |
| QLr.ramp-5B.2 | AX-94673667 | 5B | 163.54 | A(332)/G(149) | 0.31 | 2.15–3.94 | – | 4 | – | 3.4472 | 4.3824 | 4.8432 | 6.0107 | – | |
| QLr.ramp-5B.7 | AX-94480370 | 5B | 270.33–272.82 | T(433)/C(40) | 0.09 | 2.10–3.75 | – | 14 | – | – | – | 3.0122 | 5.7506 | – | |
| QLr.ramp-7A | AX-95233333 | 7A | 27.21–29.90 | T(444)/C(36) | 0.08 | 3.45 | AX-94644716 | 11 | – | – | 3.6353 | 4.6082 | – | – | |
|
SR pathotypes |
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| SR_40-3 | SR_21A2 | SR_122 | SR_117-6 | SR_40A | SR_11 | SR_34-1 | |||||||||
| QSr.ramp-1A.1 | AX-94448779 | 1A | 58.79–61.06 | T(128)/C(348) | 0.27 | 2.57 | AX-94432182 AX-94979364 AX-94405956 AX-94963297 | 17 | – | – | 3.3467 | 3.8465 | 4.7283 | 4.6978 | 3.0231 |
| QSr.ramp-1A.2 | AX-94467908 | 1A | 72.25–74.86 | A(91)/C(387) | 0.19 | 3.26 | AX-94845461 AX-95080736 AX-94627776 | 24 | 3.6987 | – | 3.3512 | – | 3.1361 | 4.2983 | 7.2645 |
| QSr.ramp-1A.3 | AX-94976474 | 1A | 86.34–88.71 | A(374)/C(100) | 0.21 | 1.75 | AX-94601315 | 2 | – | – | 3.4656 | 3.9451 | – | – | – |
| QSr.ramp-1B.3 | AX-94567638 | 1B | 15.65 | A(391)/G(91) | 0.19 | 2.05 | AX-94518139 | 6 | – | – | – | – | 3.0735 | 3.5196 | – |
| QSr.ramp-1B.4 | AX-94608698 | 1B | 23.90–24.64 | A(333)/G(145) | 0.30 | 2.20–4.01 | AX-95166367 AX-95124337 | 52 | – | – | 3.674 | – | 5.4927 | 6.2792 | – |
| QSr.ramp-1D.2 | AX-95015596 | 1D | 30.82–35.95 | A(90)/C(392) | 0.19 | 1.59–2.89 | AX-94722864 | 6 | – | – | – | – | 3.6869 | 4.7119 | – |
| QSr.ramp-1D.3 | AX-94546280 | 1D | 72.10–76.08 | T(91)/C(368) | 0.20 | 2.61 | AX-94693694 | 2 | – | – | 3.344 | – | – | 4.3155 | – |
| QSr.ramp-2A.1 | AX-94850836 | 2A | 1.59 | A(136)/G(344) | 0.28 | 1.93–2.83 | AX-94856367 | 59 | – | 3.5327 | – | – | – | – | 6.4025 |
| QSr.ramp-2B.5 | AX-95180258 | 2B | 89.05 | A(395)/G(84) | 0.18 | 1.92–3.37 | AX-94621294 | 11 | – | 4.0995 | – | – | – | – | 7.4726 |
| QSr.ramp-2B.6 | AX-94778579 | 2B | 102.12–104.59 | C(108)/G(370) | 0.23 | 1.71 | AX-94425581 AX-95017376 AX-94492853 | 11 | – | 3.3367 | - | 3.5125 | - | 3.8347 | 4.1357 |
| QSr.ramp-3A.1 | AX-94407346 | 3A | 70.27–74.06 | T(388)/G(87) | 0.18 | 2.55 | AX-94518742 | 6 | – | – | – | 3.0052 | – | – | 5.8434 |
| QSr.ramp-3A.6 | AX-95226287 | 3A | 239.09 | T(50)/C(426) | 0.11 | 1.38–2.93 | – | 6 | 3.2747 | 3.032 | 3.1341 | 3.5889 | 4.0977 | 4.7693 | – |
| QSr.ramp-3A.7 | AX-94883935 | 3A | 250.41 | A(428)/C(54) | 0.11 | 1.80–2.53 | – | 2 | – | 3.0239 | – | – | – | 4.2038 | – |
| QSr.ramp-3B.1 | AX-94573417 | 3B | 0.79 | A(394)/G(82) | 0.17 | 1.79–2.55 | – | 2 | – | – | – | – | 3.4756 | 4.2301 | – |
| QSr.ramp-3B.3 | AX-94779453 | 3B | 83.69–85.27 | T(348)/C(125) | 0.26 | 1.40 | AX-94902398 | 2 | – | – | – | – | – | 3.2842 | 3.4922 |
| QSr.ramp-3B.6 | AX-94871275 | 3B | 202.68–204.37 | C(424)/G(53) | 0.11 | 1.53–2.54 | AX-94978418 | 4 | – | – | – | 3.5242 | 4.6767 | 3.5767 | – |
| QSr.ramp-3B.7 | AX-94805563 | 3B | 245.19–245.57 | T(47)/C(434) | 0.10 | 1.67–3.46 | AX-94989774 | 8 | – | 3.7911 | 3.6742 | 4.1798 | 4.2937 | 5.5216 | – |
| QSr.ramp-3D.2 | AX-94874313 | 3D | 160.44–167.71 | A(414)/G(67) | 0.14 | 1.51–3.51 | AX-94391473 | 6 | 3.2765 | – | 3.5944 | 3.4926 | 4.161 | 4.1827 | – |
| QSr.ramp-3D.3 | AX-94436339 | 3D | 169.4 | T(416)/G(47) | 0.12 | 1.39–3.25 | AX-94962712 | 8 | 3.7705 | – | 3.525 | 3.2463 | 4.0488 | 5.2282 | – |
| QSr.ramp-3D.4 | AX-94681641 | 3D | 174.67–178.60 | C(415)/G(54) | 0.12 | 1.33–3.10 | AX-94862539 | 29 | – | – | 3.3016 | 4.0116 | 3.7167 | 5.0067 | – |
| QSr.ramp-5A.3 | AX-94472861 | 5A | 90.15–91.37 | A(49)/G(432) | 0.10 | 1.88 | AX-95107770 | 2 | – | – | – | 3.1316 | 3.6164 | – | – |
| QSr.ramp-5B.10 | AX-94459834 | 5B | 233.87 | C(79)/G(393) | 0.17 | 2.40 | AX-95100204 | 2 | – | – | 3.197 | – | – | 4.0229 | – |
| QSr.ramp-5B.11 | AX-94677476 | 5B | 270.33 | T(114)/C(366) | 0.24 | 1.61–3.11 | – | 2 | – | – | – | – | 3.1796 | 5.0269 | – |
| QSr.ramp-6B.2 | AX-94426734 | 6B | 61.67–62.83 | T(395)/C(88) | 0.18 | 2.38 | AX-94735973 AX-95023059 | 15 | – | 3.8498 | – | – | – | 3.9954 | 3.6213 |
| QSr.ramp-6D | AX-94409568 | 6D | 17.65–18.61 | C(97)/G(386) | 0.20 | 2.18 | AX-94413225 AX-94803211 | 4 | – | – | 3.7012 | – | 3.2614 | 3.7021 | – |
| QSr.ramp-7A.1 | AX-95092895 | 7A | 29.86–33.34 | T(290)/C(191) | 0.40 | 2.66 | AX-94634646 AX-95251246 | 3 | 3.0999 | – | 3.0966 | – | – | 4.3851 | – |
*Remaining QTL associated with single pathotype is provided in Supplementary Table S9. #The numbers in parenthesis indicate the frequency of the allele in the panel;$percentage of phenotypic variation explained (PVE, R2). aChrom, Chromosome. bMAF, Minor allele frequency.