Table 3. Most significant (top 10) QTLs and representative SNPs for field and seedling traits.
| Trait | QTL | Marker | blast | Chr | Position | p.MLM | p.QGLM | RSQ | eff | R | Sub pop1 | Sub pop2 | Sub pop3 | postulation | reference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Race.1 | 1B_2 | IWB13336 | NA | 1B | 85.57 | 7.84E-05 | 1.39E-06 | 0.05 | 2.76 | C | 78 | 99 | 108 | Lr26? | Kolmer 2003 |
| Race.1 | 1D_t1 | IWB14612 | 1DS_1885467 | 1D | 45.44 | 3.85E-04 | 2.77E-05 | 0.04 | 2.48 | A | 77 | 107 | 101 | Lr42? | Liu et al 2013 |
| Race.1 | 4A_t2 | IWB3569 | 4AL_v2_7176180 | 4A | 144.38 | 5.59E-04 | 1.08E-05 | 0.04 | 2.32 | A | 10 | 107 | 83 | Lr28? | Bipinraj et al 2011 |
| Race.1 | 5B_2 | IWB9055 | NA | 5B | 49.65 | 5.08E-05 | 1.44E-06 | 0.06 | 2.35 | G | 76 | 101 | 78 | QLr. cdl-5BL? | Kolmer 2015 |
| Race.1 | 5D_1 | IWB53861 | NA | 5D | 203.88 | 1.17E-04 | 2.32E-05 | 0.05 | -2.58 | A | 3 | 16 | 30 | Lr1 | Kolmer 2003 |
| Race.1 | 6A_2 | IWB625.2 | NA | 6A | 100.62 | 2.23E-04 | 5.76E-06 | 0.05 | 1.97 | G | 75 | 57 | 87 | Lr64? | - |
| Race.1 | 6B_1 | IWB65148 | NA | 6B | 16.76 | 9.43E-04 | 4.82E-06 | 0.04 | 2.51 | G | 9 | 114 | 102 | - | - |
| Race.1 | 6B_3 | IWB65914 | 6BL_4378239 | 6B | 66.36 | 2.33E-03 | 3.06E-04 | 0.03 | 1.83 | G | 43 | 110 | 112 | Lr9? | Kolmer 2003 |
| Race.1 | 6B_4 | IWB3292 | 6BL_4278271 | 6B | 122.92 | 6.02E-07 | 1.18E-07 | 0.09 | -3.43 | C | 4 | 14 | 23 | Lr3 | Kolmer 2003 |
| Race.1 | 7B_3 | IWA306 | 7BL_6747122 | 7B | 76.31 | 2.09E-04 | 9.56E-07 | 0.05 | 3.16 | G | 75 | 115 | 115 | Lr14? | Kolmer 2003 |
| Race.CA1.2 | 1B_1 | IWB19584 | NA | 1B | 63.91 | 9.21E-03 | 3.24E-04 | 0.02 | -2.46 | G | 4 | 3 | 20 | QLr.cimmyt-1BS | Rosewarne 2012 |
| Race.CA1.2 | 1D_3 | IWB35520 | 1DL_2290849 | 1D | 89.58 | 3.96E-04 | 5.16E-08 | 0.04 | 2.42 | A | 79 | 113 | 94 | Lr21? | |
| Race.CA1.2 | 2A_3 | IWA3151 | 2AL_6426630 | 2A | 108.46 | 5.61E-03 | 2.97E-05 | 0.03 | -1.40 | T | 4 | 49 | 104 | Lr11.Lr38? | Darino 2015 |
| Race.CA1.2 | 2B_2 | IWB37811 | 2BS_5186722 | 2B | 93.47 | 9.08E-05 | 8.75E-08 | 0.05 | 1.91 | G | 73 | 47 | 82 | Lr13.Lr23.Lr16? | Oelke & Kolmer 2005 |
| Race.CA1.2 | 4A_2 | IWB40915 | 4AS_v2_6008166 | 4A | 48.52 | 6.04E-03 | 1.13E-04 | 0.03 | 1.95 | T | 79 | 116 | 95 | - | - |
| Race.CA1.2 | 4A_t2 | IWB3569 | 4AL_V2_7176180 | 4A | 144.38 | 7.94E-03 | 1.86E-04 | 0.02 | 1.57 | A | 10 | 107 | 83 | Lr28? | Bipinraj et al 2011 |
| Race.CA1.2 | 6B_3 | IWB65914 | 6BL_4378239 | 6B | 66.36 | 5.05E-04 | 1.16E-06 | 0.04 | 1.89 | G | 43 | 110 | 112 | Lr9? | Kolmer 2003 |
| Race.CA1.2 | 6B_4 | IWB6474 | NA | 6B | 119.73 | 8.78E-05 | 1.53E-05 | 0.06 | 2.27 | G | 9 | 110 | 95 | Lr3 | Kolmer 2003 |
| Race.CA1.2 | 7B_1 | IWB39492 | 7BS_3168118 | 7B | 58.17 | 4.03E-03 | 1.60E-02 | 0.03 | 1.76 | A | 72 | 111 | 113 | Lr72? | Herrera-Foessel et al. 2014 |
| Race.CA1.2 | 7B_2 | IWB68484 | 7BS_3079273 | 7B | 66.62 | 1.22E-04 | 3.19E-07 | 0.05 | 4.06 | T | 80 | 111 | 126 | Lr14? | Singh et al. 2009 |
| Race.Mix | 1A_3 | IWB48030 | 1AL_3976804 | 1A | 149.82 | 3.55E-03 | 5.99E-04 | 0.03 | 1.72 | G | 10 | 113 | 103 | QLr.umn-1AL | * |
| Race.Mix | 1B_1 | IWB19584 | NA | 1B | 63.91 | 3.77E-04 | 2.67E-07 | 0.05 | -3.44 | G | 4 | 3 | 20 | QLr.cimmyt-1BS | Rosewarne et al 2012 |
| Race.Mix | 1D_1 | IWB44021 | 1DS_1912623 | 1D | 8.71 | 1.46E-03 | 9.51E-07 | 0.04 | -3.22 | T | 4 | 3 | 17 | Lr42? | Liu et al 2013 |
| Race.Mix | 2A_1 | IWB74529 | NA | 2A | 20.14 | 2.58E-04 | 4.56E-06 | 0.05 | 2.10 | C | 79 | 36 | 121 | Lr17? | Kolmer 2003 |
| Race.Mix | 3A_t2 | IWB34789 | 3AL_4449581 | 3A | 169.89 | 1.16E-03 | 3.57E-05 | 0.04 | 1.57 | G | 8 | 61 | 105 | QLr.fcu-3AL? | Chu et al. 2009 |
| Race.Mix | 3B_t2 | IWB74350 | 3B_10762316 | 3B | 51.07 | 6.69E-04 | 8.56E-05 | 0.04 | 1.74 | A | 73 | 83 | 85 | - | - |
| Race.Mix | 4B_3 | IWB72129 | 4BL_7035179 | 4B | 86.55 | 2.93E-03 | 4.75E-06 | 0.03 | 1.55 | G | 76 | 80 | 103 | Lr30? | Draz et al 2015 |
| Race.Mix | 4D_1 | IWB17540 | 4DS_2288313 | 4D | 70.59 | 2.31E-04 | 1.78E-07 | 0.05 | -3.35 | T | 6 | 3 | 19 | ? | |
| Race.Mix | 6A_3 | IWA7764 | 6AL_5772638 | 6A | 119.64 | 2.28E-04 | 1.13E-06 | 0.06 | 2.12 | C | 74 | 60 | 83 | - | - |
| Race.Mix | 6B_3 | IWB11702 | 6BL_4398818 | 6B | 66.36 | 7.02E-04 | 5.60E-05 | 0.04 | 1.86 | T | 43 | 111 | 125 | Lr9? | Kolmer 2003 |
| Field.COI | 1A_3 | IWB48030 | 1AL_3976804 | 1A | 149.82 | 1.11E-04 | 7.23E-06 | 0.05 | 12.98 | G | 10 | 113 | 103 | QLr.umn-1AL | * |
| Field.COI | 2A_3 | IWA3151 | 2AL_6426630 | 2A | 108.46 | 4.38E-04 | 1.17E-06 | 0.04 | -10.14 | T | 4 | 49 | 104 | Lr11? | Darino et al 2015 |
| Field.COI | 2B_2 | IWB22236 | 2BS_5202128 | 2B | 88.44 | 4.52E-04 | 6.65E-06 | 0.04 | 10.02 | T | 13 | 79 | 104 | Lr13.Lr23.Lr16? | Oelke & Kolmer 2005 |
| Field.COI | 3A_t2 | IWB34789 | 3AL_4449581 | 3A | 169.89 | 4.31E-04 | 8.19E-06 | 0.04 | 9.48 | G | 8 | 61 | 105 | QLr.fcu-3AL? | Chu et al. 2009 |
| Field.COI | 4A_1 | IWB59410 | 4AS_v2_5925149 | 4A | 37.05 | 4.17E-05 | 7.73E-06 | 0.05 | 11.23 | T | 7 | 74 | 99 | QLr.umn-4AS | * |
| Field.COI | 4A_3 | IWB7998 | NA | 4A | 51.7 | 6.67E-04 | 1.11E-04 | 0.04 | -9.63 | T | 38 | 38 | 16 | - | - |
| Field.COI | 4B_3 | IWB7278 | 4BL_6967384 | 4B | 78.96 | 1.56E-04 | 6.47E-06 | 0.04 | 13.46 | T | 81 | 108 | 103 | QLr.cimmyt-4BL? | William et al 2006 |
| Field.COI | 5B_2 | IWB39735 | 5BL_10794137 | 5B | 49.01 | 1.69E-04 | 6.69E-06 | 0.04 | 20.17 | C | 80 | 115 | 124 | QLr. cdl-5BL? | Kolmer 2015 |
| Field.COI | 6A_t1 | IWB40242 | NA | 6A | 48.09 | 4.97E-04 | 3.26E-04 | 0.04 | -11.69 | T | 4 | 10 | 61 | - | - |
| Field.COI | 7B_4 | IWB64015 | 7BL_6699942 | 7B | 166.99 | 5.03E-04 | 9.98E-05 | 0.04 | 10.87 | T | 75 | 107 | 81 | Lr68 | Herrera-Foessel et al 2012 |
Column "Marker", underlining indicates SNPs detected by or significant in stepwise regression models.
Columns "p.MLM" and "p.QGLM" reflect p-values from the MLM and QGLM methods, underlining indicates p-values passing the simpleM threshold.
Column R indicates resistance (or favorable) allele.
Columns “RSQ” and “eff” indicate marker R2 and effects based on MLM models.
Columns “Sub pop1”, “Sub pop2” and “Sub pop3” indicate number of favorable allele within each sub-populations. Column "postulation" are postulated genes or QTLs based on position, infection type, and donor parents or pedigree information. Some of the loci names were adopted from Li et al [41]. The postulated gene or QTLs followed by questions marks "?" are primarily based on position and infection type (pedigree or donor line information was unobtainable).
Column "reference" shows literature reports that support our loci postulation. Dash "-" signs indicate that the corresponding p-values are below the simpleM threshold and loci identity were not postulated. Asterisks "*" indicate potentially novel loci identified through this study.