Table 2. Common quantitative trait loci (QTL) detected between the joint inclusive composite interval mapping (JICIM) in nested association mapping of 10 RIL populations, and inclusive composite interval mapping (ICIM) methods in individual populations for stem rust adult plant resistance in four environments.
Chra | Pos (cM)b | Populationc | Env | Left Marker | Right Marker | LODd | R2 (%)e | Addf |
---|---|---|---|---|---|---|---|---|
1A | 33 | Joint | SA12 | 1A_53256976 | 1A_214244842 | 10.26 | 3.05 | |
35 | Kulungu | Ken13 | 1A_64961094 | 1A_101708352 | 4.12 | 1.84 | -0.15 | |
36 | Fahari | SA12 | 1A_184159449 | 1A_50973716 | 15.36 | 38.71 | 0.22 | |
36 | Joint | StP12 | 1A_168260073 | 1A_50914673 | 5.86 | 4.22 | ||
37 | Romany | SA12 | 1A_39856840 | 1A_235277072 | 3.22 | 2.20 | 0.09 | |
1D | 20 | Gem | StP12 | 1D_96967944 | 1D_11687876 | 4.01 | 1.26 | 0.15 |
23 | Joint | Ken13 | 1D_95968008 | 1D_62309262 | 5.01 | 8.16 | ||
2A | 16 | Joint | StP12 | 2A_13651965 | 2A_195408664 | 4.49 | 8.78 | |
17 | Romany | SA12 | 2A_11044893 | 2A_152187592 | 3.06 | 1.31 | -0.04 | |
17 | Joint | Ken13 | 2A_118236938 | 2A_152187592 | 6.68 | 10.63 | ||
20 | Romany | SA12 | 2A_85264302 | 2A_96999682 | 13.96 | 6.54 | -0.16 | |
144 | Joint | StP12 | 2A_254280385 | 2A_226128547 | 5.31 | 2.40 | ||
145 | Ada | StP12 | 2A_254280385 | 2A_226128547 | 3.52 | 7.86 | 0.05 | |
2B | 53 | Joint | SA12 | 2B_295548243 | 2B_4526688 | 18.27 | 1.52 | |
55 | Romany | SA12 | 2B_14347146 | 2B_326925659 | 3.57 | 2.21 | 0.07 | |
60 | Ada | StP13 | 2B_328392028 | 2B_344339504 | 3.00 | 3.15 | -0.14 | |
60 | Joint | StP13 | 2B_309579404 | 2B_313124463 | 6.62 | 6.73 | ||
60 | Joint | StP12 | 2B_309579404 | 2B_313124463 | 4.68 | 6.91 | ||
3B | 108 | Pasa | StP13 | 3B_647995685 | 3B_584832142 | 9.82 | 10.93 | -0.05 |
108 | Joint | StP12 | 3B_673326253 | 3B_82601403 | 4.90 | 3.16 | ||
108 | Joint | StP13 | 3B_673326253 | 3B_82601403 | 6.89 | 5.00 | ||
109 | Pasa | StP12 | 3B_647995685 | 3B_584832142 | 7.12 | 9.91 | -0.05 | |
121 | Gem | StP13 | 3B_496875398 | 3B_554937272 | 5.70 | 19.89 | -0.07 | |
121 | Joint | SA12 | 3B_538190692 | 3B_554937272 | 13.40 | 4.43 | ||
121 | Joint | StP12 | 3B_538190692 | 3B_554937272 | 5.75 | 6.24 | ||
124 | Kudu | StP12 | 3B_591992271 | 3B_909961 | 3.65 | 17.15 | -0.12 | |
124 | Kudu | StP13 | 3B_591992271 | 3B_909961 | 4.21 | 29.22 | -0.09 | |
124 | Kudu | Ken13 | 3B_591992271 | 3B_909961 | 3.10 | 10.93 | -0.12 | |
4B | 51 | Romany | StP13 | 4B_299160842 | 4B_210047150 | 3.57 | 1.06 | 0.14 |
51 | Joint | StP13 | 4B_282191767 | 4B_203809435 | 5.89 | 8.27 | ||
4D | 21 | Kulungu | Ken13 | 4D_50470445 | 4D_59436083 | 3.51 | 1.93 | -0.16 |
21 | Joint | StP12 | 4D_61244682 | 4D_58434790 | 4.62 | 7.73 | ||
5B | 51 | Joint | StP13 | 5B_258358007 | 5B_233185212 | 7.69 | 8.42 | |
53 | Gem | StP12 | 5B_257695597 | 5B_155513783 | 4.94 | 1.28 | -0.14 | |
5D | 47 | Joint | Ken13 | 5D_145713577 | 5D_101495576 | 6.28 | 13.20 | |
48 | Kulungu | Ken13 | 5D_27462012 | 5D_91682679 | 3.33 | 1.88 | -0.16 | |
6A | 21 | Pasa | SA12 | 6A_41412787 | 6A_49007339 | 11.68 | 6.71 | -0.02 |
21 | Joint | StP13 | 6A_12874936 | 6A_16883183 | 4.87 | 4.33 | ||
7A | 3 | Gem | StP12 | 7A_92272971 | 7A_134846357 | 3.94 | 1.05 | -0.15 |
3 | Joint | StP13 | 7A_5990339 | 7A_2150377 | 5.96 | 3.15 |
a Chromosome location of the QTL.
b Position (centiMorgan) of the detected QTL peak in Chromosome ‘Chr’. Positions are sorted in ascending order.
c Result of JICIM is shown in bold; result of ICIM is shown in italics.
d Logarithm of odds scores for the QTL detected at position ‘Pos’, based on joint mapping.
e Percentage of phenotypic variation explained by the observed QTL, based on joint mapping.
f Additive effect for JICIM is not shown as JICIM reports additive effect for each parent individually; see S1 File for more information.