Table 4.
QTLs detected using a HMM
| Env | LG | Trait | Pos. (cM) | Mean_AC | Mean_AD | Mean_BC | Mean_BD | %var | LOD | se_AC | se_AD | se_BC | se_BD | Nearest SNP | Detected previously | Key parent |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Field | 2 | Red | 57 | 46.02 | 46.31 | 46.59 | 47.09 | 9.10 | 4.57 | 0.163 | 0.156 | 0.177 | 0.180 | s986_p33227_R52 | No | Both |
| Field | 2 | PCO1 | 63 | −0.10 | 0.03 | −0.04 | 0.10 | 10.27 | 5.42 | 0.029 | 0.029 | 0.032 | 0.032 | s1650_p8516_R1 | Yes | Both |
| Field | 2 | Open | 85 | 13.36 | 15.03 | 13.69 | 15.16 | 9.99 | 5.03 | 0.309 | 0.336 | 0.335 | 0.338 | s976_p36734_R52 | No | Moy |
| Field | 2 | %late | 86 | 0.06 | 0.09 | 0.27 | 0.28 | 11.58 | 5.91 | 0.036 | 0.039 | 0.038 | 0.039 | s3294_p23887_F36 | Yes | Latham |
| Field | 2 | PCO4 | 88 | −0.01 | −0.05 | 0.03 | 0.03 | 15.22 | 7.46 | 0.010 | 0.012 | 0.011 | 0.011 | s22199_p1017_F46 | Yes | Latham |
| Field | 3 | Red | 8 | 46.17 | 45.97 | 46.81 | 46.89 | 9.64 | 4.70 | 0.161 | 0.174 | 0.167 | 0.169 | s2456_p19264_F31 | No | Latham |
| Poly | 3 | Red | 9 | 50.68 | 51.00 | 51.73 | 51.77 | 14.70 | 5.25 | 0.171 | 0.210 | 0.197 | 0.196 | s2456_p19264_F31 | No | Latham |
| Field | 3 | PCO1 | 16 | −0.11 | −0.08 | 0.05 | 0.12 | 17.07 | 8.91 | 0.027 | 0.032 | 0.029 | 0.029 | s88_p165011_R50 | Yes | Latham |
| Field | 3 | Open | 17 | 13.22 | 13.64 | 14.76 | 15.46 | 12.95 | 6.64 | 0.306 | 0.347 | 0.319 | 0.325 | s88_p165011_R50 | Yes | Latham |
| Field | 3 | Green | 49 | 25.76 | 25.89 | 26.46 | 26.27 | 10.20 | 5.17 | 0.108 | 0.131 | 0.118 | 0.127 | s59561_p275_R31 | Yes | Latham |
| Poly | 3 | PCO1 | 56 | −0.06 | −0.09 | 0.06 | 0.08 | 12.06 | 4.95 | 0.025 | 0.033 | 0.026 | 0.036 | s4830_p9111_R31 | Yes | Latham |
| Poly | 3 | Open | 62 | 21.10 | 20.03 | 22.55 | 22.42 | 8.68 | 3.91 | 0.368 | 0.554 | 0.427 | 0.524 | s3246_p13440_F35 | Yes | Latham |
| Poly | 3 | %flower | 66 | 49.80 | 62.33 | 41.67 | 41.96 | 11.96 | 5.02 | 2.371 | 3.681 | 2.790 | 3.619 | s2005_p3000_F19 | Yes | Both |
| Field | 3 | PCO4 | 76 | 0.02 | 0.01 | −0.04 | −0.01 | 6.99 | 3.75 | 0.010 | 0.013 | 0.011 | 0.013 | s4615_p65_R31 | No | Latham |
| Poly | 3 | Set | 76 | 24.96 | 25.17 | 26.88 | 25.96 | 8.51 | 3.73 | 0.314 | 0.451 | 0.376 | 0.462 | s4615_p65_R31 | Yes | Latham |
| Field | 3 | PCO2 | 94 | 0.06 | 0.00 | −0.05 | −0.05 | 9.98 | 5.10 | 0.017 | 0.019 | 0.018 | 0.022 | s37694_p610_F60 | Yes | Latham |
| Field | 3 | Set | 102 | 21.33 | 22.15 | 22.72 | 22.92 | 11.17 | 5.96 | 0.215 | 0.252 | 0.251 | 0.293 | s4_p124533_F28 | Yes | Both |
| Field | 3 | Green | 105 | 25.75 | 25.95 | 26.40 | 26.49 | 11.21 | 5.66 | 0.102 | 0.119 | 0.124 | 0.143 | s65_p181620_R20 | Yes | Both |
| Field | 4 | PCO2 | 35 | 0.01 | 0.02 | −0.08 | 0.02 | 8.80 | 4.50 | 0.019 | 0.017 | 0.020 | 0.020 | s2217_p870_F28 | No | Both |
| Field | 4 | Green/Red | 39 | 41.31 | 41.56 | 43.88 | 40.40 | 10.28 | 5.41 | 0.526 | 0.475 | 0.508 | 0.550 | s702_p32282_F17 | No | Both |
| Field | 4 | Red | 42 | 46.52 | 46.45 | 46.94 | 45.90 | 7.49 | 3.81 | 0.172 | 0.155 | 0.172 | 0.181 | s39775_p439_F60 | No | Both |
| Field | 5 | Set | 1 | 21.40 | 21.62 | 22.43 | 23.20 | 14.96 | 7.34 | 0.232 | 0.249 | 0.258 | 0.238 | s376_p49208_R48 | Yes | Both |
| Field | 5 | Green | 1 | 25.70 | 25.95 | 26.27 | 26.45 | 10.15 | 5.08 | 0.114 | 0.123 | 0.128 | 0.118 | s376_p49208_R48 | Yes | Both |
| Field | 5 | PCO4 | 17 | 0.03 | 0.02 | −0.03 | −0.01 | 7.69 | 3.95 | 0.011 | 0.012 | 0.012 | 0.011 | s54868_p407_F20 | Yes | Latham |
| Field | 5 | PCO1 | 40 | −0.07 | −0.06 | 0.00 | 0.09 | 6.99 | 3.74 | 0.031 | 0.031 | 0.033 | 0.029 | s608_p18443_F46 | Yes | Both |
| Field | 5 | Open | 40 | 13.46 | 13.57 | 14.23 | 15.64 | 13.08 | 6.62 | 0.318 | 0.328 | 0.346 | 0.307 | s608_p18443_F46 | Yes | Both |
| Field | 5 | PCO2 | 72 | −0.05 | −0.03 | −0.01 | 0.08 | 10.87 | 5.42 | 0.020 | 0.017 | 0.018 | 0.020 | s1838_p21919_F22 | No | Both |
| Field | 6 | PCO2 | 3 | 0.06 | 0.07 | −0.08 | −0.04 | 19.26 | 9.48 | 0.019 | 0.019 | 0.018 | 0.016 | s4321_p5696_R54 | Yes | Latham |
| Field | 6 | Green/Red | 3 | 40.48 | 39.57 | 43.35 | 43.14 | 17.75 | 8.76 | 0.521 | 0.531 | 0.492 | 0.436 | s4321_p5696_R54 | Yes | Latham |
| Field | 6 | PCO4 | 5 | 0.01 | 0.05 | −0.04 | −0.01 | 11.72 | 5.89 | 0.012 | 0.012 | 0.011 | 0.010 | s5202_p10092_F12 | Yes | Latham |
| Field | 6 | Set | 9 | 22.02 | 21.11 | 22.85 | 22.44 | 10.47 | 5.44 | 0.263 | 0.268 | 0.251 | 0.225 | s666_p20259_R9 | No | Latham |
| Field | 6 | Green | 9 | 26.06 | 25.53 | 26.38 | 26.24 | 11.61 | 6.04 | 0.126 | 0.128 | 0.120 | 0.107 | s666_p20259_R9 | No | Latham |
| Poly | 6 | Green/Red | 46 | 47.03 | 47.46 | 49.35 | 49.05 | 11.69 | 4.43 | 0.452 | 0.430 | 0.416 | 0.455 | s75795_p432_F40 | No | Latham |
| Field | 7 | Set | 20 | 21.65 | 21.45 | 22.66 | 22.62 | 7.70 | 4.00 | 0.271 | 0.267 | 0.240 | 0.240 | s21_p135135_R49 | No | Latham |
Env environment, LG linkage group, Pos is the position of the maximum LOD in cM, Mean_AC etc. are the means of the four offspring genotype classes AC, AD, BC, BD (assuming a QTL model of Latham having genotype AB and Moy having genotype CD), se_AC etc. are the corresponding standard errors, %var. is the % trait variance explained by this QTL, ‘Detected previously’ indicates whether it was reported by Graham et al. (2009b) and ‘Key parent’ indicates whether one or both parents’ alleles are significant, based on pairwise t-tests of the estimated genotype means