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

pvalue

3B

.5

4

.

.03

3B

9

.

.

7 3B

.

.

8 3B 10.

7

9 3B

.4

.

.

.34

10 3B

9

.02

11 3B 11.559

3B 11.559

20.34

13 3B 11.559

9

.

14 3B

3B

7

16 3B

15

9

17 3B

19 3B

2

20 3B 13.7

40.85

21 3B

.

3B 14.105

23 3B 14.105

3B 14.105

3

4

25 3B 14.105

.05

0.27

3B 14.105

33.36

27 3B 14.105

3B 14.105

29 3B 14.105

9

30 3B

8

31 3B 24.406

31.93

3B

33 3B

34 3B

35 3B 32.21

6

36 3B

7.7

37 3B 34.62

38 3B

39 3B

37.46

40 3B 37.288

41 3B

42 3B

43 3B

3B

45 3B

46 3B

2

47 3B

3

49 3B

.251

3B 60.251

13.79

51 3B 60.251

1

8

52 3B

53 3B

38.86

3B 62.311

55 3B 62.311

6

5

56 3B 62.311 12.89 38.94

57 3B

38.86

58 3B 62.569 12.86

59 3B 62.569 12.89

17.01

60 3B 62.569 12.89 38.94 17.24
61 3B

6

38.94

62 3B 62.666

63 3B 62.666 12.89

64 3B 62.666

3B 62.666 12.72

66 3B 62.666 12.89 38.87 17.14

3B 62.666 12.72 38.93

68 3B

2

69 3B 63.962

3B

12.72

17.01

71 3B

13.37 38.82

72 3B

38.74

74 3B

13.81

75 3B

12.79 38.66

76 3B

38.76

77 3B

5

78 3B 67.455 11.52

79 3B 67.455 11.52 38.84 19.19

3B 67.455 11.52

19.1

81 3B 67.455 11.52 38.78

82 3B 67.455

38.66

83 3B

13.81

84 3B

85 3B 67.785

86 3B 67.785

87 3B

88 3B

11.59 38.6

89 3B 68.71

38.6 17

3B 68.71

38.73

91 3B

12.29 38.66

92 3B 68.87 12.11 38.73 17.57
93 3B 68.87 11.42 38.66

94 3B 68.87 11.59

18.42

95 3B 68.87 12.29 38.53 16.92
96 3B

38.73

98 3B 69.527

38.6

99 3B 69.527 11.59 38.67 18.64

3B 69.527 12.11

17.6

3B

38.67

102 3B 69.72

3B 69.72

3B 69.72

15.37

105 3B 69.72

38.7

3B

3B 70.088 13.03 37.65 12.83

3B

3B 70.118

3B

8

3B 70.698 14.18

3B 70.698 14.18

11.7

3B

3B 71

3B

3B

37.35

3B 71.123

3

118 3B

37.93

3B 71.34 13.19

8

3B

38.7

3B

37.75

3B

123 3B

13.83

3B 73.133

37.5

3B 73.133

3B 73.133 13.55 37.43 11.83

3B 73.133

3B

37.45

129 3B 73.353

37.65 12.79

3B 73.353

3B 73.353

37.46 12.26

3B 73.353

133 3B

16.9 37.2 7.73

3B

3B

13.6

3B 74.263

37.35

3B 74.263

3B 74.263

3B 74.263

37.4

3B 74.263

3B 74.263

37.41

3B

3B

3B

3B

4.2

3B

4.07

3B

9

36.72

3B 80.129

3B 80.129

4.69

3B 80.129 22.49 36.72 4.2

3B 80.129

4.08

3B 80.129 22.49

7

3B 80.129 22.21

4.5

3B

3.15

3B

2.79

3B 80.992

3B 80.992

2.66

3B 80.992

36.78 4.7

3B 80.992

37.36 2.8

161 3B 80.992 17.64

3B 80.992

37.39

3B 80.992

3.77

3B 80.992

3B 80.992

37.39

3B 80.992

3B 80.992

3B

3B 81.202

4.5

3B

2.66

3B 81.592

37.43 3.03

3B

27.27 37.39 2.92

3B

22.6

3.96

3B

37.45

3B 82.187

6.22

3B 82.187

3B

36.81

3B

36.5 4.39

187 3B 85.027

4.31

3B

36.72

3B 85.517

4.9

3B

3B

20.33

3B

36.38 3.9

3B 88.075

3.61

3B

4.27

3B 88.313

3B

197 3B

3.41

3B

33.59

3B 90.873

1.57

3B

33.5 0.12

3B 91.518

33.5 0.08

202 3B 91.518

0.09

3B

35

3B

3B

0.08

3B

3B

3B

3B 125.365

0.1

3B

7

0.1

3B 134.834

0.11

3B 134.834

0.75

3B 134.834

0

3B 134.834

33.8 0

3B 134.834

3B 134.834

3B 134.834

33.94 0.01

3B

0.01

3B

0.11

3B 137.845

3B

0.69

																																																																																																																																																																																																																																																																																																																																																																																																																										Marker number	Chromosome	cM	R Severity (%)	S Severity (%)	-log	1		0
5		8	9		30	82			35	0.	7
6	9.	69		34	68			33	36	0.	14
	10.5	27			17	63		38	59	9.	96
52	18.63	38.	46	8.	93
	11	64		13	16		40	83			20
			11.	55	13.46		41	20.	84
13.59	41.13	20.64
12		13.55		40.	85
	13.6	40.7		19	76
	11.8	37	14.	51	41.	21	18.	81
	15	11.83	14.		71	40.	72	17.	25
11.8	74	41.	23		17.6
12.064	15.19	40.	78	16.83
		13.	79	14.	58	40.	39			17.01
92	13.68	19.	98
								14.	105		29	86	3	4.08	0.4
22	14.04	40.	66	17.	95
1	3.41	4	0.27	18.11
24	3	4.7	33.4			0.1
	31	34.18
26	34.02			0.08
	34.	62	33.	56			0.11
28	33.	94	33.64	0.03
34.	47				33.5		0.09
	24.406	3	7.7		31.93	1.12
37.72	1.09
32	26.	129	17.84	38.1	9.24
28.409	18.9	37.84	7.66
	32.21	18.7	37.6	7.47
19.84				37.4	6.47
32.9	87	18.	75	37.82
19.	43	38.	42	8.41
35.768	19.81			37.43	6.63
		37.2	88	20.	57	5.98
20.96	37.23	5.51
37.405	19.	49		37.93	7.	53
51.08		18.42	39.34	10.31
52.	45	18.52	38.06	7.83
44	52.	99	18.09	37.98	8.29
53.32		18.64	37.85	7.	77
57.971			16.9	38.02	9.06
59.1	61	1	4.9	38.9	14.06
			60	1	3.15		38.93	16.61
50	14.	91	38.85
1	3.9				38.6	15.07
61.639			13.81			38.86		15.37
			62.311	13.99	15.34
54						12.	89				38.94		17.24
	1	2.8			38.7	16.78
17.23
			62.569	12.76	16.71
	38.84	16.86
	38.74
						6		2.66			1	2.79	17.05
12.62	38.91	17.43
	38.87		17.14
			12.72	39.07	17.79
65				38.73	16.96
67		17.64
	6	3.96		13.19		38.82	1	6.22
	13.37					38.66	15.66
70	64.354		38.76
64.787	15.82
65.554	13.63	15.42
65.722	38.61	14.92
66.782	16.15
67.	197	12.21	17.52
					67.455					11.52		38.78		19.1
38.83		19.19
80	38.77
19.15
	11.42	19.04
67.67		13.83	38.21
		67.785	11.68	39.01	18.92
13.28			38.67	14.94
	11.7	38.69	18.2
68.	102				11.59	38.64	18.59
		68.71	18.51
		12.29
90			12.11		17.57
				68.87	17.04
19.09
	38.53
			69.527	1	1.57	18.68
11.92	17.62
100	38.79
101					69.72	12.45	15.69
12.33	38.54	15.99
103	12.34	38.38	15.83
104	12.52	38.35
15.64	11.73
106		70.088		1	3.03			37.65		12.83
107
108		70.	118	13.21		37.75	13.24
109	1	4.69			37.35	10.28
110			7	0.69			14.18	37.67	11.72
111	3	7.73	11.77
112	37.63
113	70.715	13.58	38.09	13.18
114	14.11	37.96		12.26
115	71.075	12.9	37.44	13.36
116		71.	123	13.75	11.78
117	14.3		37.5	11.29
	71.34	13.65	12.65
119	38.47	1		4.2
120	71.65	14.33	13.66
121	72.018	13.97	12.17
122	72.238	14.78		36.78	8.57
				73.	133		37.36	11.74
124	1	4.07	10.95
125	14.75			37.45	10.98
126
127	1	3.77	37.56	11.54
128					73.353	13.09	12.18
13.33
130	1		4.5	37.77	11.09
131	13.53
132	13.39	37.53	12.68
73.938
134	74.226	1	4.27	37.38	10.65
135							74.263	37.21	11.56
136	15.53	9.38
137	14.55	37.62	10.81
138	15.86	37.48	9.44
139	14.17	11.07
140	14.53		37.41	10.66
141	15.03	9.83
142	74.433	14.98				37.39	10.03
143	74.758	1	4.31	37.47	11.05
144	78.	161	19.47		36.38	5.29
145	79.454			22.49				36.72
146	79.944		22.6	36.64
147							8	0.12		22.21		4.39
148	20.13	36.94	5.43
149	21.71	36.8
150
151	22.73	36.71
152		36.5	4.13
153	36.95
155	80.762	26.62	37.37
156												80.992	27.4	37.27
157	27.73	37.24	2.63
158	27.58	37.17
159	21.65
160	27.47
36.84	7.07
162		27.27		2.92
163	23.14	36.65
164	18.55	36.75	6.03
165	27.1	2.99
166	18.33	36.97	6.39
167	22.99	36.52	3.87
168		81.	202	18.71	36.93	6.08
169	21.91	36.73
170		81.592	27.6	37.22
171	27.05
172	81.599
173	81.797	36.55
175			82.	187	27.31	2.96
176	18.57		36.81
177	27.25	37.49	2.95
178	82.549	18.85	5.96
186		85.027	21.49
21.44	36.46
188		85.517	21.07	4.65
189		20.33	36.59
190	85.66	22.89	36.35		3.61
191	87.403	36.45	4.83
192		88.075	21.89
193	22.18	36.13
194		88.313	21.25	36.42
195	20.23	36.36	4.88
196	89.128	22.52	36.16	3.44
90.628	22.35	36.03
198		90.873		33.94	0.04
199	27.42	35.55
200			91.518	34.46
201	34.17
34.21	33.44
203	95.099	26.33	1.41
204	104.52	31.96	34.06	0.22
205	106.648	33.32	34.13
206	115.632	29.39	34.68		0.75
207	117.242	27.33	35.36	1.33
208		125.365	31.87	34.28	0.29
209	33.11	34.09
210								134.834	32.91		33.8
211	32.97	33.93
212	29.57	34.74
213	33.76	33.79
214	33.81
215	33.69	33.62			0.01
216	35.29	33.35	0.21
217	33.84
218	136.36	33.77	33.92
219		137.845	34.49	33.45
220	32.73	34.07	0.15
221	139.618	30.54	34.99