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Table 4 QTLs detected using a HMM

From: Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

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
  1. 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