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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