Table 2.
Major QTL in the MAGIC population identified in both MLM-based GWAS and QTL analysis optimized for complex populations. QTL are listed that were significant in both analyses and show clear peaks in GWAS. A complete list of significant marker trait associations is available for GWAS (Additional file 10) and QTL mapping (Additional file 11)
| QTL name | Trial | GWAS | QTL Mapping | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Most significant markera | p value | MAF | Effectb | Pos. (cM) | Nearest marker | LOD | PVE (%)c | ||
| DF1.1 | 2013 | Pv2.1_01_4147947_C/G | 5.46E-07 | 0.37 (G) | −0.46 | 32 | Pv2.1_01_5474208_C/T | 9.30 | 4.30 |
| DPM1.1 | 2013 | Pv2.1_01_763904_G/A | 1.60E-06 | 0.27 (A) | 0.43 | 36.5 | Pv2.1_01_6773375_T/A | 21.70 | 15.90 |
| DF1.2 | 2013 | Pv2.1_01_14672594_C/T | 1.05E-35 | 0.34 (C) | 1.63 | 38 | Pv2.1_01_11238077_T/A | 58.85 | 35.76 |
| 2014 | Pv2.1_01_17627372_A/G | 2.36E-12 | 0.35 (G) | −0.28 | 40 | Pv2.1_01_14582969_G/C | 34.42 | 16.50 | |
| DPM1.2 | 2013 | Pv2.1_01_14672594_C/T | 2.77E-09 | 0.34 (C) | 0.82 | 38.5 | Pv2.1_01_13085941_C/A | 8.19 | 5.47 |
| 2014 | Pv2.1_01_11567887_T/TA | 2.13E-07 | 0.18 (T) | 0.61 | |||||
| Yd1.1 | 2013 | Pv2.1_01_11250640_A/G | 3.11E-08 | 0.16 (A) | −52.81 | 38 | Pv2.1_01_11238077_T/A | 8.76 | 2.03 |
| 2014 | Pv2.1_01_11221702_T/A | 3.57E-07 | 0.21 (T) | −28.79 | |||||
| PHI2.1 | 2013 | Pv2.1_02_47566148_G/A | 2.61E-08 | 0.37 (G) | −1.08 | 71 | Pv2.1_02_47643879_G/T | 10.73 | 7.62 |
| DF3.1 | 2013 | Pv2.1_03_39652029_G/A | 5.23E-07 | 0.14 (A) | 0.62 | 50 | Pv2.1_03_39061112_G/C | 7.50 | 3.43 |
| 2014 | 50 | Pv2.1_03_39061112_G/C | 8.11 | 3.54 | |||||
| DPM3.1 | 2013 | Pv2.1_03_39534987_C/A | 2.08E-08 | 0.16 (C) | −0.75 | 48 | Pv2.1_03_37341462_T/C | 11.41 | 8.36 |
| 2014 | 51.5 | Pv2.1_03_39819948_G/A | 10.24 | 5.11 | |||||
| 100SdW4.1 | 2014 | Pv2.1_04_1328790_G/A | 4.08E-08 | 0.27 (A) | 0.51 | 3 | Pv2.1_04_522512_A/T | 8.36 | 4.74 |
| SdFe6.1 | 2014 | Pv2.1_06_5311627_C/T | 2.77E-07 | 0.17 (C) | 2.09 | 2 | Pv2.1_06_8725963_G/A | 7.33 | 4.06 |
| SdFe6.2 | 2016 | Pv2.1_06_22844368_T/G | 3.36E-07 | 0.08 (G) | −2.67 | 35 | Pv2.1_06_23945432_T/C | 6.46 | 8.68 |
| DPM8.1 | 2013 | Pv2.1_08_1070342_C/T | 2.54E-09 | 0.11 (T) | −1.45 | 5 | Pv2.1_08_1091562_T/G | 7.92 | 5.56 |
| 2014 | Pv2.1_08_706882_A/G | 3.58E-11 | 0.13 (G) | −1.77 | 4 | Pv2.1_08_946243_C/T | 18.15 | 9.09 | |
| SdZn8.1 | 2014 | Pv2.1_08_60922896_C/G | 4.39E-07 | 0.06 (C) | 0.85 | 83 | Pv2.1_08_60982396_C/G | 6.81 | 2.65 |
aMarker ID contains the physical position of the polymorphism in the reference version 2.1 and the genotype of the reference / alternative allele
bEffect of alternative allele
cPVE = Phenotypic variation explained