Quantitative Trait Loci
The file Homework 6 Data.xlsx contains the results of a QTL analysis of stem rust severity (%) for wheat chromosome 3B. The analysis used homozygous inbred lines from a resistant parent susceptible parent cross, and a SNP-based chip for wheat. The mean disease severities for both parental genotypes at each of >200 marker locations, as well as the significance (-log10 p-value) of the marker-phenotype associations, are provided.
How many quantitative loci can be identified? What is their estimated location and effect size?
3B
Marker number Chromosome cM R Severity (%) S Severity (%) -log10pvalue
5 3B 8.594 30.82 35.03 0.7
6 3B 9.699 34.68 33.36 0.14
7 3B 10.527 17.63 38.59 9.96
8 3B 10.527 18.63 38.46 8.93
9 3B 11.464 13.16 40.83 20.34
10 3B 11.559 13.46 41.02 20.84
11 3B 11.559 13.59 41.13 20.64
12 3B 11.559 13.55 40.85 20.34
13 3B 11.559 13.69 40.7 19.76
14 3B 11.837 14.51 41.21 18.81
15 3B 11.837 14.71 40.72 17.25
16 3B 11.874 15 41.23 17.69
17 3B 12.064 15.19 40.78 16.83
19 3B 13.792 14.58 40.39 17.01
20 3B 13.792 13.68 40.85 19.98
21 3B 14.105 29.86 34.08 0.4
22 3B 14.105 14.04 40.66 17.95
23 3B 14.105 13.41 40.27 18.11
24 3B 14.105 34.73 33.4 0.14
25 3B 14.105 31.05 34.18 0.27
26 3B 14.105 34.02 33.36 0.08
27 3B 14.105 34.62 33.56 0.11
28 3B 14.105 33.94 33.64 0.03
29 3B 14.105 34.47 33.59 0.09
30 3B 24.406 37.78 31.93 1.12
31 3B 24.406 37.72 31.93 1.09
32 3B 26.129 17.84 38.1 9.24
33 3B 28.409 18.9 37.84 7.66
34 3B 32.21 18.7 37.6 7.47
35 3B 32.21 19.84 37.46 6.47
36 3B 32.987 18.75 37.82 7.7
37 3B 34.62 19.43 38.42 8.41
38 3B 35.768 19.81 37.43 6.63
39 3B 37.288 20.57 37.46 5.98
40 3B 37.288 20.96 37.23 5.51
41 3B 37.405 19.49 37.93 7.53
42 3B 51.08 18.42 39.34 10.31
43 3B 52.45 18.52 38.06 7.83
44 3B 52.99 18.09 37.98 8.29
45 3B 53.32 18.64 37.85 7.77
46 3B 57.971 16.92 38.02 9.06
47 3B 59.161 14.93 38.9 14.06
49 3B 60.251 13.15 38.93 16.61
50 3B 60.251 14.91 38.85 13.79
51 3B 60.251 13.91 38.68 15.07
52 3B 61.639 13.81 38.86 15.37
53 3B 62.311 13.99 38.86 15.34
54 3B 62.311 12.89 38.94 17.24
55 3B 62.311 12.86 38.75 16.78
56 3B 62.311 12.89 38.94 17.23
57 3B 62.569 12.76 38.86 16.71
58 3B 62.569 12.86 38.84 16.86
59 3B 62.569 12.89 38.74 17.01
60 3B 62.569 12.89 38.94 17.24
61 3B 62.666 12.79 38.94 17.05
62 3B 62.666 12.62 38.91 17.43
63 3B 62.666 12.89 38.87 17.14
64 3B 62.666 12.72 39.07 17.79
65 3B 62.666 12.72 38.73 16.96
66 3B 62.666 12.89 38.87 17.14
67 3B 62.666 12.72 38.93 17.64
68 3B 63.962 13.19 38.82 16.22
69 3B 63.962 13.37 38.66 15.66
70 3B 64.354 12.72 38.76 17.01
71 3B 64.787 13.37 38.82 15.82
72 3B 65.554 13.63 38.74 15.42
74 3B 65.722 13.81 38.61 14.92
75 3B 66.782 12.79 38.66 16.15
76 3B 67.197 12.21 38.76 17.52
77 3B 67.455 11.52 38.78 19.15
78 3B 67.455 11.52 38.83 19.19
79 3B 67.455 11.52 38.84 19.19
80 3B 67.455 11.52 38.77 19.1
81 3B 67.455 11.52 38.78 19.15
82 3B 67.455 11.42 38.66 19.04
83 3B 67.67 13.83 38.21 13.81
84 3B 67.785 11.68 39.01 18.92
85 3B 67.785 13.28 38.67 14.94
86 3B 67.785 11.7 38.69 18.2
87 3B 68.102 11.59 38.64 18.59
88 3B 68.71 11.59 38.6 18.51
89 3B 68.71 12.29 38.6 17
90 3B 68.71 12.11 38.73 17.57
91 3B 68.87 12.29 38.66 17.04
92 3B 68.87 12.11 38.73 17.57
93 3B 68.87 11.42 38.66 19.09
94 3B 68.87 11.59 38.53 18.42
95 3B 68.87 12.29 38.53 16.92
96 3B 69.527 11.57 38.73 18.68
98 3B 69.527 11.92 38.6 17.62
99 3B 69.527 11.59 38.67 18.64
100 3B 69.527 12.11 38.79 17.6
101 3B 69.72 12.45 38.67 15.69
102 3B 69.72 12.33 38.54 15.99
103 3B 69.72 12.34 38.38 15.83
104 3B 69.72 12.52 38.35 15.37
105 3B 69.72 15.64 38.7 11.73
106 3B 70.088 13.03 37.65 12.83
107 3B 70.088 13.03 37.65 12.83
108 3B 70.118 13.21 37.75 13.24
109 3B 70.118 14.69 37.35 10.28
110 3B 70.698 14.18 37.67 11.72
111 3B 70.698 14.18 37.73 11.77
112 3B 70.698 14.18 37.63 11.7
113 3B 70.715 13.58 38.09 13.18
114 3B 71 14.11 37.96 12.26
115 3B 71.075 12.9 37.44 13.36
116 3B 71.123 13.75 37.35 11.78
117 3B 71.123 14.3 37.53 11.29
118 3B 71.34 13.65 37.93 12.65
119 3B 71.34 13.19 38.47 14.28
120 3B 71.65 14.33 38.7 13.66
121 3B 72.018 13.97 37.75 12.17
122 3B 72.238 14.78 36.78 8.57
123 3B 73.133 13.83 37.36 11.74
124 3B 73.133 14.07 37.5 10.95
125 3B 73.133 14.75 37.45 10.98
126 3B 73.133 13.55 37.43 11.83
127 3B 73.133 13.77 37.56 11.54
128 3B 73.353 13.09 37.45 12.18
129 3B 73.353 13.33 37.65 12.79
130 3B 73.353 14.5 37.77 11.09
131 3B 73.353 13.53 37.46 12.26
132 3B 73.353 13.39 37.53 12.68
133 3B 73.938 16.9 37.2 7.73
134 3B 74.226 14.27 37.38 10.65
135 3B 74.263 13.6 37.21 11.56
136 3B 74.263 15.53 37.35 9.38
137 3B 74.263 14.55 37.62 10.81
138 3B 74.263 15.86 37.48 9.44
139 3B 74.263 14.17 37.4 11.07
140 3B 74.263 14.53 37.41 10.66
141 3B 74.263 15.03 37.41 9.83
142 3B 74.433 14.98 37.39 10.03
143 3B 74.758 14.31 37.47 11.05
144 3B 78.161 19.47 36.38 5.29
145 3B 79.454 22.49 36.72 4.2
146 3B 79.944 22.6 36.64 4.07
147 3B 80.129 22.21 36.72 4.39
148 3B 80.129 20.13 36.94 5.43
149 3B 80.129 21.71 36.8 4.69
150 3B 80.129 22.49 36.72 4.2
151 3B 80.129 22.73 36.71 4.08
152 3B 80.129 22.49 36.57 4.13
153 3B 80.129 22.21 36.95 4.5
155 3B 80.762 26.62 37.37 3.15
156 3B 80.992 27.4 37.27 2.79
157 3B 80.992 27.73 37.24 2.63
158 3B 80.992 27.58 37.17 2.66
159 3B 80.992 21.65 36.78 4.7
160 3B 80.992 27.47 37.36 2.8
161 3B 80.992 17.64 36.84 7.07
162 3B 80.992 27.27 37.39 2.92
163 3B 80.992 23.14 36.65 3.77
164 3B 80.992 18.55 36.75 6.03
165 3B 80.992 27.1 37.39 2.99
166 3B 80.992 18.33 36.97 6.39
167 3B 80.992 22.99 36.52 3.87
168 3B 81.202 18.71 36.93 6.08
169 3B 81.202 21.91 36.73 4.5
170 3B 81.592 27.6 37.22 2.66
171 3B 81.592 27.05 37.43 3.03
172 3B 81.599 27.27 37.39 2.92
173 3B 81.797 22.6 36.55 3.96
175 3B 82.187 27.31 37.45 2.96
176 3B 82.187 18.57 36.81 6.22
177 3B 82.187 27.25 37.49 2.95
178 3B 82.549 18.85 36.81 5.96
186 3B 85.027 21.49 36.5 4.39
187 3B 85.027 21.44 36.46 4.31
188 3B 85.517 21.07 36.72 4.65
189 3B 85.517 20.33 36.59 4.9
190 3B 85.66 22.89 36.35 3.61
191 3B 87.403 20.33 36.45 4.83
192 3B 88.075 21.89 36.38 3.9
193 3B 88.075 22.18 36.13 3.61
194 3B 88.313 21.25 36.42 4.27
195 3B 88.313 20.23 36.36 4.88
196 3B 89.128 22.52 36.16 3.44
197 3B 90.628 22.35 36.03 3.41
198 3B 90.873 33.94 33.59 0.04
199 3B 90.873 27.42 35.55 1.57
200 3B 91.518 34.46 33.5 0.12
201 3B 91.518 34.17 33.5 0.08
202 3B 91.518 34.21 33.44 0.09
203 3B 95.099 26.33 35 1.41
204 3B 104.52 31.96 34.06 0.22
205 3B 106.648 33.32 34.13 0.08
206 3B 115.632 29.39 34.68 0.75
207 3B 117.242 27.33 35.36 1.33
208 3B 125.365 31.87 34.28 0.29
209 3B 125.365 33.11 34.09 0.1
210 3B 134.834 32.91 33.87 0.1
211 3B 134.834 32.97 33.93 0.11
212 3B 134.834 29.57 34.74 0.75
213 3B 134.834 33.76 33.79 0
214 3B 134.834 33.81 33.8 0
215 3B 134.834 33.69 33.62 0.01
216 3B 134.834 35.29 33.35 0.21
217 3B 134.834 33.84 33.94 0.01
218 3B 136.36 33.77 33.92 0.01
219 3B 137.845 34.49 33.45 0.11
220 3B 137.845 32.73 34.07 0.15
221 3B 139.618 30.54 34.99 0.69
