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Table 5 Chi-squared test to calculate the associations between the parental haplotypes (T1, T2, C1 and C2) and the observed and expected number of resistant/susceptible trees

From: Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

QTL and haplotypes Total Observed Expected P-value % resistant
Resistant Suscept. Resistant Suscept.
QTL3.1_T1 242 154 88 121 121 2.21E-05 63.64
QTL3.1_T2 217 145 72 108.5 108.5 7.21E-07 66.82
QTL3.1_C1 211 147 64 105.5 105.5 1.10E-08 69.67
QTL3.1_C2 248 152 96 124 124 3.77E-04 61.29
QTL4.1_T1 244 144 100 122 122 4.85E-03 59.02
QTL4.1_T2 215 155 60 107.5 107.5 9.24E-11 72.09
QTL4.1_C1 259 167 92 129.5 129.5 3.16E-06 64.48
QTL4.1_C2 200 132 68 100 100 6.03E-06 66.00
QTL6.1_T1 221a 127 94 110.5 110.5 2.64E-02 57.47
QTL6.1_T2 232a 167 65 116 116 2.13E-11 71.98
QTL6.1_C1 228 135 93 114 114 5.41E-03 59.21
QTL6.1_C2 231 164 67 115.5 115.5 1.75E-10 71.00
QTL6.2_T1 221 125 96 110.5 110.5 5.11E-02 56.56
QTL6.2_T2 238 174 64 119 119 1.00E-12 73.11
QTL6.2_C1 216a 132 84 108 108 1.09E-03 61.11
QTL6.2_C2 239a 165 74 119.5 119.5 3.95E-09 69.04
QTL7.1_T1 234 174 60 117 117 9.16E-14 74.36
QTL7.1_T2 225 125 100 112.5 112.5 9.56E-02 55.56
QTL7.1_C1 230 138 92 115 115 2.42E-03 60.00
QTL7.1_C2 229 161 68 114.5 114.5 7.97E-10 70.31
QTL9.1_T1 230 111 119 115 115 5.98E-01 48.26
QTL9.1_T2 229 188 41 114.5 114.5 2.63E-22 82.10
QTL9.1_C1 236a 159 77 118 118 9.41E-08 67.37
QTL9.1_C2 218a 136 82 109 109 2.55E-04 62.39
QTL9.2_T1 224 127 97 112 112 4.50E-02 56.70
QTL9.2_T2 235 172 63 117.5 117.5 1.16E-12 73.19
QTL9.2_C1 219 159 60 109.5 109.5 2.23E-11 72.60
QTL9.2_C2 240 140 100 120 120 9.82E-03 58.33
  1. The threshold for susceptible trees was set for trees with more than ten total vegetative brooms over the whole period of 4 years
  2. ‘Total’ indicates the total number of trees in MP01 that have that particular haplotype for the specific QTL. ‘a’ indicates that certain haplotypes could not be exactly identified due to recombination at that particular locus, and the resulting haplotype could be one of both parental haplotypes
  3. P-value in bold indicates the highest association identified between the various QTL/haplotype combinations and WBD resistance