TABLE 4.
Putative QTL significantly (p < 0.001) associated with resistance at the adult plant stage observed in at least two environments corresponding to the three rust diseases.
| Putative QTL* | Representative SNP | Associated SNPs | No. of MTAs | −log10(p) | ||||||||
| SNP (35K) | Chroma | Position (cM) | Allele# | MAFb | %PVE (R2)$ | YR_E1 | YR_E2 | YR_E3 | YR_E4 | |||
| QYr.ramp-1B.3 | AX-95222999 | 1B | 24.64 | A(405)/C(77) | 0.16 | 2.15 | AX-94903617 | 2 | 3.0259 | 3.3988 | – | – |
| QYr.ramp-1B.4 | AX-94515822 | 1B | 61.73 | C(36)/G(440) | 0.08 | 2.42–3.55 | AX-94765876 | 6 | – | – | 4.1825 | 5.0791 |
| QYr.ramp-1D.1 | AX-94508418 | 1D | 3.38 | T(448)/C(26) | 0.06 | 2.14–2.44 | – | 2 | 3.4973 | 3.7765 | – | – |
| QYr.ramp-1D.3 | AX-94444583 | 1D | 95.56–95.70 | A(93)/G(386) | 0.20 | 2.19 | AX-94918964 | 4 | – | – | 3.6071 | 3.0063 |
| QYr.ramp-2B.3 | AX-94761935 | 2B | 88.33 | C(43)/G(440) | 0.09 | 1.87–2.09 | – | 2 | 3.4389 | – | 3.1554 | – |
| QYr.ramp-2D.1 | AX-94842790 | 2D | 25.72 | T(22)/C(453) | 0.05 | 1.81–2.59 | – | 5 | 3.0408 | 3.4617 | 3.4908 | 3.8662 |
| QYr.ramp-3B.3 | AX-94541758 | 3B | 85.27 | A(123)/G(348) | 0.26 | 2.10–2.59 | – | 3 | 4.1191 | 3.333 | – | – |
| QYr.ramp-3B.4 | AX-94680284 | 3B | 245.57 | T(255)/C(221) | 0.46 | 2.08–2.62 | – | 2 | 3.4187 | 4.0166 | – | – |
| QYr.ramp-4A.1 | AX-94437374 | 4A | 56.59 | A(33)/G(442) | 0.07 | 2.19–2.27 | – | 4 | – | – | 3.6111 | 3.4591 |
| QYr.ramp-5A.2 | AX-95684352 | 5A | 70.36–73.80 | A(76)/G(400) | 0.16 | 1.85–1.99 | AX-95002679 | 3 | 3.2955 | – | 3.2128 | – |
| QYr.ramp-6B.4 | AX-95209190 | 6B | 147.99 | C(24)/G(401) | 0.10 | 2.53–3.55 | AX-94777981 | 4 | 4.5647 | 5.2201 | – | – |
| QYr.ramp-6D.1 | AX-94953259 | 6D | 0 | T(274)/G(192) | 0.41 | 1.93–2.02 | – | 2 | – | – | 3.2415 | 3.1352 |
| QYr.ramp-6D.2 | AX-95215612 | 6D | 17.65 | C(87)/G(385) | 0.18 | 1.80–2.39 | AX-95632341 | 12 | – | – | 3.5407 | 3.6068 |
| QYr.ramp-6D.3 | AX-94385810 | 6D | 173.03–175.55 | T(37)/C(436) | 0.09 | 2.20–2.53 | – | 4 | – | – | 3.6192 | 3.786 |
| QYr.ramp-6D.4 | AX-95176310 | 6D | 183.03 | A(415)/G(62) | 0.13 | 2.09–2.22 | – | 2 | – | – | 3.4617 | 3.3988 |
| QYr.ramp-7D.2 | AX-95205886 | 7D | 6.96–10.82 | T(369)/C(107) | 0.22 | 1.20–2.09 | – | 3 | – | – | 3.4674 | 3.1032 |
| LR_E1 | LR_E2 | LR_E3 | LR_E4 | |||||||||
| QLr.ramp-1A.2 | AX-95080736 | 1A | 72.25–74.11 | A(428)/G(45) | 0.10 | 2.50–2.72 | – | 11 | 4.5164 | 4.098 | – | 4.5249 |
| QLr.ramp-1B.1 | AX-95092361 | 1B | 0.79 | A(296)/C(185) | 0.38 | 1.77–2.59 | AX-94456747, AX-95222141 | 5 | – | 3.5824 | 3.8295 | 3.7671 |
| QLr.ramp-1B.2 | AX-94692514 | 1B | 8.24 | C(266)/G(212) | 0.44 | 2.55 | AX-94997422 | 4 | – | – | 3.776 | 3.089 |
| QLr.ramp-1B.3 | AX-94517050 | 1B | 24.64–26.22 | C(425)/G(48) | 0.10 | 5.03 | AX-94571235, AX-94538509 | 26 | 5.8111 | – | 6.8053 | 3.0183 |
| QLr.ramp-1D | AX-94541931 | 1D | 3.38 | A(360)/G(113) | 0.24 | 2.35–3.37 | AX-94641589 | 6 | 4.0322 | 5.3001 | – | 3.0538 |
| QLr.ramp-2B.7 | AX-94962080 | 2B | 103.81–104.59 | T(297)/G(181) | 0.38 | 2.22 | AX-95019501, AX-95149329 | 7 | 3.8429 | 3.7829 | – | 3.0912 |
| QLr.ramp-2B.8 | AX-94481202 | 2B | 126.67 | A(29)/G(448) | 0.06 | 2.48–3.62 | – | 3 | 5.0863 | 5.6499 | 3.69 | – |
| QLr.ramp-3A.1 | AX-94394356 | 3A | 30.91 | A(340)/C(136) | 0.29 | 1.90–1.94 | – | 2 | – | 3.3009 | – | 3.3312 |
| QLr.ramp-3B.6 | AX-94925132 | 3B | 117.54 | T(359)/C(105) | 0.23 | 1.75–1.99 | – | 2 | 3.1401 | – | 3.0643 | – |
| QLr.ramp-4A.4 | AX-94708164 | 4A | 214.72 | A(131)/G(343) | 0.28 | 2.44–3.61 | – | 4 | 5.8523 | 4.0148 | 3.9499 | 4.7453 |
| QLr.ramp-5A | AX-94889598 | 5A | 12.25–16.13 | A(226)/C(256) | 0.47 | 2.08 | AX-95168494 | 2 | 3.6276 | – | – | 3.1295 |
| QLr.ramp-5B.2 | AX-94515669 | 5B | 161.41–161.85 | T(316)/C(156) | 0.33 | 2.26 | AX-94996993 | 4 | – | 3.7482 | 3.1212 | – |
| QLr.ramp-6A.1 | AX-94653398 | 6A | 0.00–0.82 | T(157)/G(316) | 0.33 | 1.74–2.67 | AX-94585745, AX-94800842 | 14 | 3.9121 | 3.5047 | 3.9293 | 3.7568 |
| QLr.ramp-6A.4 | AX-95147877 | 6A | 217.80–221.75 | T(87)/C(385) | 0.19 | 1.83–2.04 | AX-94411794, AX-95014734 | 6 | 3.1277 | 3.3368 | – | 3.5439 |
| QLr.ramp-6B.5 | AX-94638655 | 6B | 142.73 | T(265)/C(215) | 0.45 | 1.75–2.53 | – | 2 | 4.294 | 3.027 | – | – |
| QLr.ramp-6B.6 | AX-94877284 | 6B | 147.99–150.38 | T(393)/C(76) | 0.16 | 1.84–2.73 | – | 4 | 3.1583 | 4.5831 | – | – |
| QLr.ramp-7B.1 | AX-95109168 | 7B | 1.72–2.51 | A(286)/G(174) | 0.38 | 1.69–2.21 | AX-94767893, AX-94617870 | 5 | 3.8311 | 3.3579 | 3.0418 | 3.1978 |
| QLr.ramp-7D.2 | AX-94674448 | 7D | 18.37 | T(69)/C(408) | 0.15 | 1.94–2.79 | – | 4 | 3.4277 | – | 4.0777 | – |
| SR_E1 | SR_E2 | SR_E3 | SR_E4 | |||||||||
| QSr.ramp-1A.1 | AX-94629244 | 1A | 54.04–58.94 | T(355)/C(122) | 0.26 | 2.76–4.07 | AX-94831912 | 16 | – | 5.5236 | 3.8788 | 3.9088 |
| QSr.ramp-1A.2 | AX-95092467 | 1A | 74.11–74.86 | T(389)/C(92) | 0.19 | 3.80 | AX-94739433, AX-94845461 | 17 | – | 3.6209 | 3.579 | 5.1442 |
| QSr.ramp-1B.2 | AX-95108068 | 1B | 8.24–9.93 | A(376)/G(87) | 0.19 | 2.19–2.63 | AX-94602901 | 12 | 3.6636 | 3.7892 | 3.7174 | 3.5776 |
| QSr.ramp-1B.3 | AX-94518139 | 1B | 15.65 | C(384)/G(92) | 0.19 | 2.06–2.46 | – | 3 | – | 3.5756 | 3.5198 | 3.0799 |
| QSr.ramp-1B.4 | AX-94608698 | 1B | 24.64–26.22 | A(333)/G(145) | 0.30 | 1.81–2.83 | AX-94414930, AX-94538509 | 34 | 4.4578 | 4.1201 | 4.6302 | 3.7215 |
| QSr.ramp-1D.1 | AX-94842940 | 1D | 1.69 | A(88)/G(394) | 0.18 | 1.96–2.60 | – | 3 | – | 3.7503 | 3.3773 | 3.3816 |
| QSr.ramp-1D.2 | AX-94911855 | 1D | 30.82–35.95 | A(387)/G(91) | 0.19 | 1.68–2.57 | AX-94722864 | 8 | 3.1839 | 3.9222 | 4.0705 | 3.4796 |
| QSr.ramp-1D.3 | AX-94546280 | 1D | 76.08 | T(91)/C(368) | 0.20 | 1.57–3.24 | – | 4 | 3.0095 | 3.3603 | 5.209 | 4.1243 |
| QSr.ramp-1D.4 | AX-94842331 | 1D | 95.7 | T(395)/C(88) | 0.18 | 1.88–2.52 | – | 3 | – | 3.6553 | 3.2692 | 3.3673 |
| QSr.ramp-2B.6 | AX-94637676 | 2B | 102.12–104.59 | T(86)/C(396) | 0.18 | 2.07–2.26 | AX-94623285 | 5 | 3.2455 | 3.3308 | – | 3.0644 |
| QSr.ramp-2B.7 | AX-94784324 | 2B | 126.67 | T(215)/C(265) | 0.45 | 1.71 | AX-94481202 | 2 | 3.461 | 3.465 | – | – |
| QSr.ramp-3A.6 | AX-95226287 | 3A | 239.09 | T(50)/C(426) | 0.11 | 1.83–3.83 | – | 4 | 3.4185 | 4.0281 | 6.0299 | 4.1187 |
| QSr.ramp-3A.7 | AX-94883935 | 3A | 250.41 | A(428)/C(54) | 0.11 | 2.39–3.16 | – | 3 | – | 3.4977 | 5.1024 | 3.4855 |
| QSr.ramp-3B.1 | AX-94479164 | 3B | 0.79 | A(106)/G(375) | 0.22 | 1.89 | AX-94573417, AX-94581339 | 5 | 3.5179 | 3.3687 | 3.2188 | 3.439 |
| QSr.ramp-3B.6 | AX-94915269 | 3B | 204.37 | C(428)/G(50) | 0.10 | 2.43–2.67 | – | 5 | – | 3.5456 | 4.4059 | 3.7619 |
| QSr.ramp-3B.7 | AX-94805563 | 3B | 245.19–245.57 | T(47)/C(434) | 0.10 | 1.96–4.18 | – | 5 | 3.6265 | 4.5159 | 6.5041 | 4.532 |
| QSr.ramp-3D.1 | AX-94901185 | 3D | 76.05 | T(374)/C(88) | 0.20 | 2.02–2.06 | – | 2 | – | 3.0328 | – | 3.0419 |
| QSr.ramp-3D.2 | AX-94874313 | 3D | 160.44–167.71 | A(414)/G(67) | 0.14 | 2.09–2.40 | AX-94391473 | 6 | 4.1716 | – | 5.2554 | 3.4058 |
| QSr.ramp-3D.3 | AX-94436339 | 3D | 167.71–169.40 | T(416)/G(47) | 0.12 | 2.28–3.79 | – | 9 | 4.1324 | 4.7983 | 5.9778 | 4.2819 |
| QSr.ramp-3D.4 | AX-95224631 | 3D | 175.97–178.60 | A(55)/G(422) | 0.12 | 1.83–3.53 | AX-94681641, AX-94724171 | 52 | 4.1038 | 4.3769 | 5.6016 | 4.3799 |
| QSr.ramp-4A.2 | AX-94897136 | 4A | 188.85 | A(72)/G(392) | 0.16 | 2.27–3.33 | – | 3 | – | 4.646 | 3.8328 | 4.3236 |
| QSr.ramp-4A.3 | AX-94508043 | 4A | 214.31 | T(67)/C(415) | 0.14 | 2.31 | AX-94630583 | 2 | 3.1965 | 3.387 | – | – |
| QSr.ramp-4D.1 | AX-94516693 | 4D | 0 | T(352)/C(125) | 0.26 | 1.79–2.10 | – | 2 | – | – | 3.137 | 3.0959 |
| QSr.ramp-5A.1 | AX-94560538 | 5A | 59.99 | T(441)/G(35) | 0.08 | 2.93 | AX-94519690 | 9 | 3.2318 | – | – | 4.1142 |
| QSr.ramp-5B.10 | AX-94459834 | 5B | 233.87 | C(79)/G(393) | 0.17 | 1.70–3.06 | – | 3 | – | 4.3091 | 3.0007 | 3.4288 |
| QSr.ramp-6B.2 | AX-94426734 | 6B | 62.83 | T(395)/C(88) | 0.18 | 1.88–2.52 | – | 3 | – | 3.6553 | 3.2692 | 3.3673 |
| QSr.ramp-6D | AX-94805944 | 6D | 18.24–18.61 | T(68)/C(413) | 0.14 | 2.56 | AX-94409568 | 3 | 4.5629 | 3.6741 | 3.9384 | – |
∗Remaining QTL associated with single environment are provided in Supplementary Table S11. #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.