Phenotypic traits diversity and cluster analysis
Phenotypic diversity analysis
Data of the 15 phenotypic traits of the 93 samples are summarized in Table 1. The basic statistical analysis and diversity of the 15 phenotypic traits based on phenotypic data is shown in Table 2. The coefficient of variation (CV) was 29.72% on average and ranged from 3.07% (brown rice rate) to 137.43% (chalkiness). The average diversity index (He) was 1.92 and ranged from 1.55 to 2.08, with brown rice rate and chalkiness having lower He, indicating that there were relatively few phenotypes in these two traits. Overall, the Indica rice materials tested had relatively more phenotypes on these 15 traits; the distribution in each phenotype was uneven.
Table 1: Phenotypic data of 93 samples
Name
|
Type
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
W1
|
R
|
115
|
128.2
|
46.26
|
2.58
|
6.17
|
28.95
|
241.36
|
217.64
|
28.57
|
79.14
|
67.47
|
58.60
|
17.50
|
4.00
|
2.40
|
W298
|
S
|
115
|
128.2
|
46.26
|
2.58
|
6.17
|
28.95
|
241.36
|
217.64
|
28.57
|
79.14
|
67.47
|
58.60
|
17.50
|
4.00
|
2.40
|
W2
|
R
|
114
|
121.8
|
53.3
|
2.46
|
7.83
|
27.94
|
219.00
|
181.75
|
28.82
|
92.16
|
60.35
|
54.90
|
51.50
|
12.00
|
2.30
|
W300
|
S
|
81
|
111
|
47.38
|
1.96
|
5.50
|
25.42
|
184.07
|
177.53
|
24.78
|
77.77
|
58.56
|
57.00
|
100.00
|
79.80
|
2.40
|
W352
|
S
|
102
|
112.4
|
30.76
|
2.22
|
7.50
|
24.22
|
140.43
|
135.00
|
26.31
|
76.33
|
55.36
|
43.90
|
58.60
|
22.20
|
2.50
|
W353
|
S
|
115
|
127.8
|
42.62
|
1.96
|
6.82
|
28.30
|
128.45
|
112.14
|
31.81
|
77.24
|
64.10
|
46.30
|
54.40
|
15.1
|
2.3
|
W354
|
S
|
122
|
120.2
|
29.94
|
2.01
|
6.35
|
27.21
|
169.50
|
157.10
|
29.52
|
76.80
|
59.29
|
29.60
|
21.70
|
5.9
|
2.5
|
W355
|
S
|
117
|
117.6
|
45.82
|
2.11
|
8.13
|
23.93
|
162.30
|
146.11
|
27.34
|
75.68
|
63.34
|
51.00
|
3.30
|
0.9
|
2.9
|
W357
|
S
|
100
|
106
|
48.78
|
2.4
|
5.17
|
26.72
|
200.93
|
180.00
|
22.23
|
77.18
|
52.41
|
43.80
|
72.70
|
24.70
|
2.00
|
W359
|
S
|
96
|
135.8
|
32.28
|
2.48
|
6.67
|
25.98
|
213.56
|
188.56
|
24.14
|
77.90
|
59.42
|
58.70
|
23.10
|
7.30
|
2.40
|
W361
|
S
|
109
|
113.2
|
44.52
|
2.06
|
4.83
|
27.93
|
187.31
|
175.19
|
33.51
|
74.70
|
50.25
|
48.40
|
91.20
|
58.80
|
2.10
|
W366
|
S
|
105
|
124.6
|
40.42
|
1.72
|
9.00
|
23.71
|
159.72
|
133.33
|
19.46
|
69.03
|
50.18
|
49.10
|
97.20
|
79.00
|
1.50
|
W367
|
S
|
103
|
110
|
55.36
|
1.8
|
3.33
|
25.96
|
247.25
|
237.00
|
27.73
|
81.64
|
51.28
|
48.60
|
95.60
|
42.60
|
1.70
|
W369
|
S
|
105
|
109.2
|
37.22
|
2.1
|
6.33
|
24.41
|
221.87
|
195.00
|
20.51
|
77.39
|
49.92
|
37.30
|
18.40
|
5.40
|
2.40
|
W370
|
S
|
110
|
129.2
|
45.26
|
2.16
|
10.33
|
28.80
|
221.94
|
208.17
|
23.60
|
77.30
|
53.29
|
48.20
|
18.80
|
7.90
|
2.50
|
W375
|
S
|
85
|
98.6
|
36.3
|
2.02
|
6.67
|
25.90
|
231.06
|
214.29
|
19.30
|
77.54
|
50.08
|
41.40
|
38.90
|
13.20
|
2.30
|
W377
|
S
|
103
|
123
|
35.88
|
2.38
|
3.83
|
26.47
|
236.86
|
216.71
|
23.07
|
77.72
|
47.80
|
53.30
|
12.50
|
3.80
|
2.20
|
W380
|
S
|
100
|
98
|
36.76
|
2
|
7.17
|
25.96
|
216.39
|
196.94
|
20.21
|
77.23
|
48.00
|
24.60
|
49.80
|
18.60
|
2.20
|
W381
|
S
|
98
|
99.6
|
28.8
|
2
|
4.50
|
31.31
|
228.86
|
203.93
|
22.10
|
75.31
|
53.19
|
48.00
|
19.90
|
4.80
|
2.50
|
W3
|
R
|
116
|
133.2
|
45.34
|
2.38
|
6.33
|
29.28
|
216.14
|
201.36
|
36.22
|
79.87
|
51.44
|
28.90
|
37.60
|
9.30
|
2.40
|
W4
|
R
|
115
|
121.8
|
46.98
|
2.14
|
7.17
|
27.94
|
176.63
|
168.94
|
30.67
|
79.44
|
60.83
|
60.30
|
23.00
|
4.90
|
2.40
|
W5
|
R
|
113
|
125.6
|
46
|
2.28
|
6.00
|
31.35
|
254.55
|
247.36
|
26.83
|
78.58
|
56.36
|
46.70
|
17.70
|
4.10
|
2.50
|
W666
|
R
|
105
|
109.8
|
39.5
|
1.68
|
10.17
|
22.25
|
127.20
|
122.50
|
23.10
|
79.66
|
56.12
|
55.60
|
2.80
|
0.70
|
2.40
|
W667
|
R
|
101
|
105
|
35.6
|
2.43
|
6.83
|
22.04
|
175.00
|
168.50
|
24.41
|
78.62
|
60.95
|
55.90
|
25.70
|
7.70
|
2.10
|
W668
|
R
|
109
|
116.4
|
39.14
|
2.2
|
8.17
|
25.90
|
142.90
|
130.59
|
30.20
|
77.87
|
63.30
|
62.60
|
10.50
|
2.50
|
2.40
|
W669
|
R
|
109
|
110.8
|
37.56
|
1.78
|
10.33
|
24.84
|
140.95
|
115.29
|
21.67
|
78.60
|
64.80
|
64.10
|
4.00
|
0.80
|
2.70
|
W670
|
R
|
104
|
132
|
38.52
|
2.26
|
5.50
|
26.93
|
176.40
|
166.28
|
32.35
|
77.20
|
53.32
|
50.00
|
56.80
|
15.6
|
2.4
|
W671
|
R
|
110
|
128.6
|
45.76
|
2.62
|
6.17
|
28.33
|
190.31
|
176.38
|
31.60
|
80.06
|
60.73
|
59.40
|
53.70
|
15.60
|
2.30
|
W672
|
R
|
104
|
121.8
|
41.98
|
2.12
|
6.83
|
23.69
|
143.73
|
127.64
|
34.36
|
78.55
|
60.60
|
59.90
|
7.10
|
1.10
|
2.60
|
W673
|
R
|
106
|
119.6
|
37.83
|
2.15
|
8.00
|
26.10
|
128.07
|
120.21
|
30.95
|
72.24
|
55.13
|
52.70
|
7.80
|
2.10
|
2.40
|
W674
|
R
|
110
|
135.8
|
43.4
|
2.08
|
5.17
|
28.33
|
190.31
|
176.38
|
34.66
|
76.61
|
58.74
|
58.30
|
13.80
|
3.10
|
2.50
|
W675
|
R
|
110
|
118.6
|
30.84
|
1.98
|
8.00
|
27.53
|
154.08
|
141.33
|
29.10
|
78.89
|
57.35
|
55.20
|
22.80
|
5.00
|
2.40
|
W676
|
R
|
109
|
106
|
30.12
|
2.2
|
6.17
|
25.65
|
165.25
|
153.00
|
23.64
|
76.92
|
54.06
|
53.90
|
1.20
|
0.30
|
2.10
|
W677
|
R
|
110
|
112.2
|
30.12
|
2.1
|
8.17
|
24.23
|
174.44
|
159.63
|
29.13
|
79.80
|
58.10
|
56.60
|
18.10
|
3.50
|
2.30
|
W678
|
R
|
110
|
112
|
39.24
|
2.14
|
10.83
|
24.91
|
131.57
|
111.38
|
30.99
|
80.68
|
58.13
|
53.10
|
10.60
|
1.90
|
2.60
|
W679
|
R
|
112
|
108.8
|
38.18
|
2.3
|
7.83
|
24.72
|
133.44
|
120.94
|
29.62
|
78.82
|
60.50
|
59.60
|
19.90
|
4.50
|
2.60
|
W680
|
R
|
107
|
121.6
|
43.76
|
2.08
|
6.83
|
27.08
|
151.26
|
141.86
|
31.99
|
78.55
|
63.99
|
61.40
|
28.30
|
7.60
|
2.70
|
W681
|
R
|
111
|
116.8
|
37.56
|
2.3
|
5.17
|
24.72
|
130.73
|
119.00
|
30.08
|
76.89
|
54.86
|
54.00
|
1.60
|
0.20
|
2.30
|
W684
|
R
|
111
|
116.6
|
36.6
|
2.3
|
7.33
|
26.56
|
168.31
|
163.13
|
31.26
|
79.58
|
61.82
|
60.00
|
5.80
|
1.70
|
2.30
|
W685
|
R
|
110
|
121.4
|
31.94
|
2.44
|
8.17
|
23.98
|
176.87
|
169.53
|
33.26
|
79.48
|
56.74
|
54.50
|
35.20
|
10.00
|
2.10
|
W686
|
R
|
110
|
121
|
38.8
|
2.48
|
6.83
|
24.97
|
184.50
|
172.92
|
25.40
|
78.90
|
60.28
|
59.80
|
23.40
|
5.00
|
2.00
|
W687
|
R
|
110
|
108.4
|
38.22
|
2.12
|
7.33
|
25.07
|
142.33
|
128.87
|
28.74
|
78.56
|
56.34
|
54.10
|
29.50
|
6.90
|
2.20
|
W688
|
R
|
108
|
114.6
|
43.2
|
2
|
7.83
|
26.27
|
147.40
|
139.27
|
34.58
|
78.12
|
60.78
|
59.80
|
13.10
|
2.30
|
2.60
|
W689
|
R
|
109
|
105.2
|
36.54
|
2.54
|
8.67
|
25.75
|
131.06
|
86.86
|
30.03
|
80.33
|
54.00
|
39.80
|
29.40
|
5.80
|
2.20
|
W690
|
R
|
113
|
104.8
|
33.14
|
2.04
|
10.17
|
24.06
|
96.70
|
84.85
|
26.11
|
76.74
|
59.39
|
58.10
|
4.40
|
0.80
|
2.90
|
W691
|
R
|
108
|
115.6
|
44.72
|
2.02
|
8.83
|
28.18
|
135.40
|
130.30
|
34.40
|
78.35
|
56.20
|
51.50
|
9.40
|
1.90
|
2.60
|
W692
|
R
|
108
|
116.8
|
45.8
|
2.66
|
6.50
|
26.02
|
262.85
|
212.18
|
24.50
|
78.72
|
65.00
|
62.70
|
3.70
|
1.10
|
3.00
|
W693
|
R
|
114
|
122
|
39.16
|
2.52
|
7.17
|
24.98
|
234.75
|
208.13
|
27.27
|
77.99
|
58.61
|
57.20
|
23.90
|
8.90
|
2.20
|
W694
|
R
|
110
|
103.8
|
33.52
|
1.6
|
10.67
|
23.33
|
137.54
|
129.04
|
22.59
|
80.13
|
56.70
|
48.00
|
9.60
|
3.00
|
2.60
|
W697
|
R
|
105
|
90.8
|
27.32
|
1.82
|
7.33
|
22.96
|
114.19
|
101.31
|
21.27
|
79.24
|
62.57
|
61.80
|
2.60
|
0.70
|
2.40
|
W698
|
R
|
107
|
115.8
|
41.6
|
2.04
|
9.67
|
25.65
|
158.88
|
153.17
|
25.75
|
79.04
|
59.82
|
58.70
|
14.20
|
3.70
|
2.40
|
W699
|
R
|
102
|
108.8
|
80.7
|
2.22
|
3.83
|
26.27
|
428.50
|
394.60
|
20.63
|
78.94
|
61.29
|
58.80
|
9.50
|
2.40
|
2.60
|
W6
|
R
|
117
|
125.2
|
44.12
|
2.32
|
6.17
|
23.90
|
236.15
|
211.31
|
29.18
|
82.15
|
56.04
|
47.20
|
25.60
|
5.20
|
2.20
|
W700
|
R
|
101
|
121.8
|
35.6
|
2.72
|
7.17
|
24.09
|
166.38
|
153.81
|
25.17
|
79.40
|
63.40
|
62.00
|
1.60
|
0.30
|
2.60
|
W701
|
R
|
113
|
141.2
|
45.16
|
1.68
|
9.50
|
28.70
|
188.70
|
181.15
|
22.20
|
77.79
|
60.04
|
58.60
|
17.50
|
4.00
|
2.40
|
W702
|
R
|
107
|
126.6
|
33.08
|
1.78
|
10.83
|
21.27
|
127.13
|
118.13
|
23.38
|
78.85
|
63.27
|
61.40
|
0.70
|
0.20
|
2.60
|
W703
|
R
|
107
|
108.6
|
35.32
|
1.66
|
8.00
|
23.84
|
162.30
|
147.04
|
20.43
|
79.58
|
63.86
|
63.50
|
2.50
|
0.40
|
2.70
|
W704
|
R
|
114
|
133.4
|
45.7
|
1.9
|
5.40
|
24.22
|
206.46
|
196.77
|
25.36
|
78.24
|
56.96
|
56.20
|
5.80
|
1.10
|
2.40
|
W707
|
R
|
106
|
116.6
|
38.02
|
1.76
|
8.33
|
23.91
|
141.78
|
134.67
|
18.61
|
77.21
|
62.43
|
61.80
|
5.00
|
1.10
|
2.90
|
W708
|
R
|
104
|
117.4
|
33.16
|
2.26
|
8.17
|
26.06
|
235.25
|
216.00
|
23.70
|
76.51
|
61.23
|
59.10
|
7.41
|
1.23
|
2.60
|
W710
|
R
|
104
|
116.4
|
30.1
|
1.86
|
7.33
|
23.69
|
177.88
|
168.25
|
29.56
|
81.48
|
60.29
|
59.30
|
91.10
|
23.20
|
1.80
|
W711
|
R
|
102
|
115
|
32.88
|
1.82
|
8.17
|
22.98
|
159.88
|
153.24
|
28.85
|
81.24
|
67.08
|
65.80
|
89.10
|
21.20
|
1.80
|
W713
|
R
|
108
|
114.2
|
35.7
|
1.64
|
7.67
|
24.48
|
232.19
|
201.19
|
20.37
|
79.93
|
64.68
|
64.20
|
1.20
|
0.20
|
2.80
|
W714
|
R
|
100
|
120.2
|
26.94
|
1.9
|
7.33
|
21.90
|
200.82
|
181.59
|
19.69
|
79.96
|
59.60
|
57.70
|
3.00
|
0.70
|
2.40
|
W715
|
R
|
104
|
118.6
|
35.08
|
1.8
|
8.50
|
26.41
|
233.60
|
219.87
|
22.28
|
78.34
|
62.90
|
62.70
|
2.00
|
0.50
|
2.70
|
W716
|
R
|
92
|
104.4
|
39.22
|
2.08
|
6.67
|
24.20
|
175.50
|
145.70
|
28.09
|
78.25
|
62.24
|
56.80
|
13.70
|
3.40
|
2.70
|
W717
|
R
|
105
|
135
|
41.06
|
2.32
|
6.67
|
28.69
|
192.38
|
180.15
|
25.76
|
79.01
|
63.85
|
57.50
|
52.50
|
14.50
|
2.30
|
W718
|
R
|
113
|
141.4
|
36.28
|
2.1
|
10.17
|
26.83
|
153.96
|
137.42
|
27.43
|
79.26
|
61.09
|
59.90
|
2.20
|
0.30
|
2.70
|
W719
|
R
|
97
|
125.4
|
32.66
|
1.88
|
7.83
|
22.45
|
145.20
|
138.60
|
28.62
|
79.48
|
60.49
|
53.40
|
0.70
|
0.10
|
3.10
|
W720
|
R
|
99
|
122.4
|
32.56
|
2.04
|
9.17
|
24.35
|
112.14
|
104.83
|
29.21
|
77.50
|
58.73
|
54.70
|
2.00
|
0.30
|
2.90
|
W721
|
R
|
105
|
98.2
|
35.22
|
2.4
|
5.67
|
25.36
|
183.46
|
178.54
|
27.12
|
77.43
|
56.51
|
52.60
|
48.70
|
39.20
|
2.20
|
W722
|
R
|
96
|
123.6
|
37.06
|
2.18
|
6.17
|
26.69
|
159.75
|
110.56
|
24.65
|
79.20
|
55.98
|
15.30
|
39.50
|
10.30
|
2.90
|
W723
|
R
|
105
|
129.2
|
37.64
|
2.62
|
6.67
|
28.06
|
255.29
|
245.93
|
22.96
|
80.44
|
62.13
|
60.80
|
14.00
|
4.20
|
2.30
|
W724
|
M
|
84
|
93.4
|
41.5
|
1.54
|
8.67
|
22.65
|
148.47
|
126.25
|
20.37
|
80.37
|
61.14
|
58.80
|
15.30
|
4.90
|
2.40
|
W725
|
M
|
89
|
99.2
|
44.26
|
1.74
|
7.67
|
23.71
|
196.28
|
182.00
|
24.47
|
83.39
|
62.30
|
51.30
|
13.40
|
3.70
|
2.40
|
W726
|
M
|
78
|
76.2
|
33.46
|
1.38
|
13.67
|
21.25
|
99.33
|
80.42
|
28.09
|
82.26
|
64.04
|
59.70
|
85.90
|
33.00
|
2.70
|
W727
|
M
|
80
|
88.6
|
40.52
|
1.76
|
8.00
|
23.10
|
120.29
|
112.19
|
29.70
|
79.21
|
60.38
|
56.20
|
30.68
|
12.79
|
2.50
|
W728
|
M
|
75
|
82.6
|
36.14
|
1.42
|
10.33
|
20.88
|
98.26
|
90.37
|
26.50
|
80.29
|
61.90
|
57.32
|
16.97
|
6.70
|
2.60
|
W730
|
M
|
86
|
95.6
|
36.22
|
1.42
|
11.33
|
22.60
|
128.52
|
124.67
|
24.01
|
77.68
|
53.86
|
40.40
|
59.50
|
22.50
|
2.30
|
W732
|
M
|
89
|
90.2
|
29.7
|
1.4
|
7.67
|
20.20
|
125.82
|
119.68
|
25.93
|
79.99
|
56.99
|
43.30
|
81.00
|
23.50
|
1.90
|
W733
|
M
|
81
|
75.8
|
29.3
|
1.28
|
10.83
|
18.17
|
70.53
|
63.07
|
28.11
|
80.07
|
58.88
|
52.40
|
80.80
|
26.90
|
2.50
|
W734
|
M
|
91
|
90.2
|
34.44
|
2.22
|
9.33
|
21.92
|
165.61
|
150.83
|
24.90
|
80.61
|
60.13
|
57.80
|
93.80
|
41.10
|
1.70
|
W735
|
M
|
87
|
89.2
|
37.42
|
1.54
|
9.67
|
20.91
|
131.59
|
128.12
|
26.67
|
79.86
|
58.57
|
43.30
|
89.90
|
30.70
|
2.00
|
W736
|
M
|
84
|
86
|
31.12
|
1.5
|
12.00
|
20.20
|
100.84
|
94.72
|
29.44
|
78.64
|
51.84
|
38.50
|
94.70
|
41.50
|
2.10
|
W737
|
M
|
81
|
92
|
28.28
|
1.54
|
9.17
|
19.37
|
127.92
|
123.28
|
27.59
|
80.10
|
56.71
|
49.80
|
97.10
|
48.40
|
2.40
|
W738
|
M
|
100
|
105.8
|
41.8
|
1.72
|
9.67
|
25.33
|
154.27
|
149.68
|
24.63
|
80.55
|
64.13
|
63.20
|
73.10
|
21.00
|
2.40
|
W739
|
M
|
100
|
110.6
|
44.86
|
2.36
|
6.17
|
24.10
|
146.10
|
133.24
|
23.69
|
79.56
|
62.05
|
61.60
|
34.20
|
8.90
|
2.00
|
W740
|
M
|
81
|
85.8
|
29.18
|
1.52
|
14.00
|
26.22
|
253.15
|
230.23
|
29.85
|
81.05
|
63.60
|
58.50
|
86.00
|
39.50
|
2.20
|
W741
|
M
|
85
|
86.6
|
34.18
|
1.54
|
10.83
|
19.78
|
82.93
|
71.67
|
30.37
|
76.67
|
57.31
|
52.30
|
93.40
|
45.20
|
2.20
|
W742
|
M
|
104
|
132.8
|
36.88
|
2.44
|
7.50
|
27.73
|
262.47
|
253.33
|
22.38
|
79.80
|
62.17
|
61.20
|
12.30
|
3.10
|
2.40
|
W743
|
M
|
100
|
91.4
|
34.34
|
1.98
|
6.83
|
21.83
|
135.57
|
125.77
|
29.02
|
78.89
|
55.50
|
50.40
|
40.20
|
7.90
|
2.10
|
W744
|
M
|
95
|
92.8
|
50.86
|
1.74
|
7.00
|
24.79
|
133.40
|
127.07
|
31.90
|
77.38
|
57.72
|
52.90
|
27.60
|
5.50
|
2.10
|
W7
|
R
|
114
|
131.2
|
36.94
|
2.16
|
6.00
|
26.41
|
218.94
|
202.63
|
28.25
|
77.60
|
55.92
|
51.90
|
1.20
|
0.30
|
2.30
|
Note: M, R and S in the table refer to the maintainer line and restorer line of rice CMS Lines, and special rice. Phenotypic trait number (1 to 15) in first row correspond from left to the right to The period from seeding to heading (d); Plant heights (cm); Leaf length (cm); Leaf width (cm); Average single plant valid spike number; Spike lengths (cm); Kernel numbers per spike; Grain numbe; 1000-seed weights (g); Brown rice rate (100%); Milled rice rate (100%); Head rice rate (100%); Chalky rice rate; Chalkiness; Length-width ratio.
Table 2: Basic statistical analysis and diversity of the 15 phenotypic traits
Phenotypic traits
|
Mean±SD
|
Median
|
Mode
|
Rang
|
CV (%)
|
He
|
The period from seeding to heading(d)
|
102.95±10.543
|
105
|
110
|
47
|
10.24
|
1.91
|
Plant heights (cm)
|
112.766±14.994
|
115.600
|
121.8
|
65.6
|
13.30
|
2.05
|
Leaf length (cm)
|
38.6727±7.51025
|
37.5600
|
30.12
|
53.76
|
19.42
|
1.89
|
Leaf width (cm)
|
2.0423±0.33795
|
2.0800
|
1.54
|
1.44
|
16.55
|
2.08
|
Average single plant valid spike number
|
7.74±2.007
|
7.50
|
6
|
11
|
25.83
|
2.03
|
Spike lengths (cm)
|
25.07±2.593
|
24.98
|
24
|
13
|
10.34
|
2.02
|
Kernel numbers per spike
|
174.42±52.668
|
165.61
|
190
|
358
|
30.20
|
1.92
|
Grain number
|
159.68±49.365
|
153.17
|
176
|
332
|
30.91
|
1.92
|
1000-seed weights (g)
|
26.75±4.129
|
27.12
|
20
|
17
|
15.44
|
2.06
|
Brown rice rate (100%)
|
78.76±2.414
|
78.85
|
79
|
23
|
3.07
|
1.79
|
Milled rice rate (100%)
|
58.80±4.439
|
59.42
|
67
|
19
|
7.59
|
2.04
|
Head rice rate (100%)
|
53.61±8.955
|
56.20
|
59
|
51
|
16.70
|
1.89
|
Chalky rice rate
|
32.17±31.064
|
19.90
|
1
|
99
|
96.56
|
1.68
|
Chalkiness
|
11.97±16.45
|
5
|
0
|
80
|
137.43
|
1.55
|
Length-width ratio
|
2.39±0.293
|
2.40
|
2
|
1
|
12.26
|
1.96
|
Most phenotypic traits were correlated or significantly correlated. The most significant correlation was between kernel numbers per spike and grain number, followed by that between chalky rice rate and chalkiness. However, the correlation between chalky rice rate and length-width ratio was the least significant, followed by that between leaf width and average single plant valid spike number (Table 3).
Table 3: Pearson correlation coefficient analysis of the 15 phenotypic traits
Traits
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
1
|
1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2
|
0.726**
|
1
|
|
s
|
|
|
|
|
|
|
|
|
|
|
|
3
|
0.224*
|
0.249*
|
1
|
|
|
|
|
|
|
|
|
|
|
|
|
4
|
0.567**
|
0.582**
|
.261*
|
1
|
|
|
|
|
|
|
|
|
|
|
|
5
|
-0.358**
|
-0.398**
|
-0.394**
|
-0.564**
|
1
|
|
|
|
|
|
|
|
|
|
|
6
|
0.574**
|
0.634**
|
0.398**
|
0.571**
|
-0.469**
|
1
|
|
|
|
|
|
|
|
|
|
7
|
0.268**
|
0.391**
|
0.509**
|
0.460**
|
-0.520**
|
0.554**
|
1
|
|
|
|
|
|
|
|
|
8
|
0.260*
|
0.393**
|
0.501**
|
0.428**
|
-0.519**
|
0.545**
|
0.984**
|
1
|
|
|
|
|
|
|
|
9
|
0.179
|
0.111
|
0.074
|
0.159
|
-0.024
|
0.147
|
-0.272**
|
-0.250*
|
1
|
|
|
|
|
|
|
10
|
-0.107
|
-0.130
|
0.098
|
-0.013
|
0.156
|
-0.116
|
0.085
|
0.067
|
0.078
|
1
|
|
|
|
|
|
11
|
0.053
|
0.095
|
0.049
|
0.014
|
0.222*
|
-0.037
|
-0.014
|
-0.022
|
0.012
|
0.336**
|
1
|
|
|
|
|
12
|
0.076
|
0.125
|
0.058
|
0.055
|
0.115
|
-0.054
|
0.031
|
0.065
|
-0.045
|
0.155
|
0.680**
|
1
|
|
|
|
13
|
-0.491**
|
-0.414**
|
-0.053
|
-0.322**
|
0.152
|
-0.268**
|
-0.158
|
-0.140
|
0.145
|
0.077
|
-0.239*
|
-0.270**
|
1
|
|
|
14
|
-0.466**
|
0.353**
|
-0.017
|
-0.301**
|
0.116
|
-0.240*
|
-0.116
|
-0.099
|
0.036
|
-0.143
|
-0.295**
|
-0.208*
|
0.891**
|
1
|
|
15
|
0.095
|
0.171
|
0.005
|
0-.015
|
0.156
|
0.104
|
-0.047
|
-0.084
|
-0.042
|
0.001
|
0.360**
|
0.134
|
-0.604**
|
-0.518**
|
1
|
Note: Asterisk indicates significant difference between phenotypic traits using two-tailed t-tests. *P<0.05; **P<0.01.
Principal components were extracted based on the criterion that the eigenvalue was greater than 1.0. The eigenvalues of the first four PCs in 15 phenotypic traits were greater than 1.0, and together accounted for 70.693% of the phenotypic variation (Table 4). The first PC accounted for 31.527%; the most important traits were spike lengths (0.167), plant heights (0.165) and leaf width (0.159). The second PC accounted for 18.137%, the most important traits being length-width ratio (0.252), milled rice rate (0.244) and head rice rate (0.195).
Table 4: Eigenvalue and contributive percentage of principal components and component scores coefficient matrix of the 15 phenotypic traits
Traits code
|
First principal
component
|
Second principal
component
|
Third principal
component
|
Fourth principal
component
|
The period from seeding to heading(d)
|
0.155
|
0.052
|
-0.212
|
0.135
|
Plant heights (cm)
|
0.165
|
0.029
|
-0.138
|
0.106
|
Leaf length (cm)
|
0.108
|
-0.098
|
0.188
|
0.130
|
Leaf width (cm)
|
0.159
|
-0.038
|
-0.091
|
0.156
|
Average single plant valid spike number
|
-0.136
|
0.155
|
0.050
|
0.020
|
Spike lengths (cm)
|
0.167
|
-0.066
|
-0.083
|
0.081
|
Kernel numbers per spike
|
0.155
|
-0.136
|
0.262
|
-0.151
|
Grain number
|
0.152
|
-0.141
|
0.264
|
-0.137
|
1000-seed weights (g)
|
0.001
|
0.002
|
-0.224
|
0.565
|
Brown rice rate (100%)
|
-0.007
|
0.071
|
0.305
|
0.267
|
Milled rice rate (100%)
|
0.023
|
0.244
|
0.279
|
0.232
|
Head rice rate (100%)
|
0.030
|
0.195
|
0.272
|
0.194
|
Chalky rice rate
|
-0.121
|
-0.242
|
0.099
|
0.244
|
Chalkiness
|
-0.110
|
-0.248
|
0.077
|
0.142
|
Length-width ratio
|
0.043
|
0.252
|
-0.039
|
-0.194
|
Eigenvalue
|
4.729
|
2.721
|
1.763
|
1.391
|
Contributive percentage (%)
|
31.527
|
18.137
|
11.756
|
9.272
|
Cumulative contributive percentage (%)
|
31.527
|
49.665
|
61.420
|
70.693
|
Phenotypic traits clustering
Average Euclidean distance was 5.19, ranging from 0.90 (between W723 and W742) to 13.73 (between W699 and W733). Clustering result based on the 15 phenotypic traits was shown in Fig.1, which demonstrated that the 92 samples were clustered together in addition to W669 and showed a single genetic basis for the population.
SSR marker analysis
Polymorphism of SSR markers
A total of 378 bands was detected using 48 core SSRs primer pairs (Table 5). Among these, 336 polymorphic bands were detected. The average number of polymorphic fragments was 7, ranging from 1 to 14. The highest number (14) of polymorphic bands was detected by RM278 while RM311 is the least bands. The average value of PPB (Percentage of polymorphic bands) was 88.87%, ranging from 50% to 100%. The average value of PIC (Polymorphism information content) was 0.77, ranging from 0.19 to 0.88. Data showed that core SSR in rice can produce rich bands and high polymorphic rate.
Table 5: Information and polymorphism of 48 SSR primers
Primer name
|
Chr.
|
Sequence(5’-3’)
|
Annealing temperature (℃)
|
TNB
|
NPB
|
PPB (%)
|
PIC
|
RM583
|
1
|
F:agatccatccctgtggagag; R:gcgaactcgcgttgtaatc
|
55
|
10
|
10
|
100
|
0.86
|
RM71
|
2
|
F:ctagaggcgaaaacgagatg; R:gggtgggcgaggtaataatg
|
55
|
8
|
8
|
100
|
0.84
|
RM85
|
3
|
F:ccaaagatgaaacctggattg; R:gcacaaggtgagcagtcc
|
55
|
9
|
9
|
100
|
0.85
|
RM471
|
4
|
F:acgcacaagcagatgatgag; R:gggagaagacgaatgtttgc
|
55
|
8
|
6
|
75
|
0.86
|
RM274
|
5
|
F:cctcgcttatgagagcttcg; R:cttctccatcactcccatgg
|
55
|
12
|
12
|
100
|
0.84
|
RM190
|
6
|
F:ctttgtctatctcaagacac; R:ttgcagatgttcttcctgatg
|
55
|
5
|
5
|
100
|
0.74
|
RM336
|
7
|
F:cttacagagaaacggcatcg; R:gctggtttgtttcaggttcg
|
55
|
7
|
7
|
100
|
0.79
|
RM72
|
8
|
F:ccggcgataaaacaatgag; R:gcatcggtcctaactaaggg
|
55
|
12
|
9
|
75
|
0.86
|
RM219
|
9
|
F:cgtcggatgatgtaaagcct; R:catatcggcattcgcctg
|
55
|
2
|
2
|
100
|
0.36
|
RM311
|
10
|
F:tggtagtataggtactaaacat; R:tcctatacacatacaaacatac
|
55
|
2
|
1
|
50
|
0.37
|
RM209
|
11
|
F:atatgagttgctgtcgtgcg; R:caacttgcatcctcccctcc
|
55
|
4
|
3
|
75
|
0.67
|
RM19
|
12
|
F:caaaaacagagcagatgac; R:ctcaagatggacgccaaga
|
55
|
12
|
9
|
75
|
0.86
|
RM1195
|
1
|
F:atggaccacaaacgaccttc; R:cgactcccttgttcttctgg
|
55
|
8
|
8
|
100
|
0.84
|
RM208
|
2
|
F:tctgcaagccttgtctgatg; R:taagtcgatcattgtgtggacc
|
55
|
5
|
4
|
80
|
0.75
|
RM232
|
3
|
F:ccggtatccttcgatattgc; R:ccgacttttcctcctgacg
|
55
|
10
|
10
|
100
|
0.87
|
RM119
|
4
|
F:catccccctgctgctgctgctg; R:cgccggatgtgtgggactagcg
|
67
|
7
|
4
|
57.14
|
0.79
|
RM267
|
5
|
F:tgcagacatagagaaggaagtg; R:agcaacagcacaacttgatg
|
55
|
9
|
5
|
56.56
|
0.85
|
RM253
|
6
|
F:tccttcaagagtgcaaaacc; R:gcattgtcatgtcgaagcc
|
55
|
6
|
6
|
100
|
0.75
|
RM481
|
7
|
F:tagctagccgattgaatggc; R:ctccacctcctatgttgttg
|
55
|
7
|
7
|
100
|
0.80
|
RM339
|
8
|
F:gtaatcgatgctgtgggaag; R:gagtcatgtgatagccgatatg
|
55
|
8
|
8
|
100
|
0.79
|
RM278
|
9
|
F:gtagtgagcctaacaataatc; R:tcaactcagcatctctgtcc
|
55
|
14
|
14
|
100
|
0.85
|
RM258
|
10
|
F:tgctgtatgtagctcgcacc; R:tggcctttaaagctgtcgc
|
55
|
7
|
6
|
85.71
|
0.80
|
RM224
|
11
|
F:atcgatcgatcttcacgagg; R:tgctataaaaggcattcggg
|
55
|
8
|
8
|
100
|
0.84
|
RM17
|
12
|
F:tgccctgttattttcttctctc; R:ggtgatcctttcccatttca
|
55
|
9
|
9
|
100
|
0.78
|
RM493
|
1
|
F:tagctccaacaggatcgacc; R:gtacgtaaacgcggaaggtg
|
55
|
7
|
7
|
100
|
0.83
|
RM561
|
2
|
F:gagctgttttggactacggc; R:gagtagctttctcccacccc
|
55
|
8
|
5
|
62.50
|
0.85
|
RM8277
|
3
|
F:agcacaagtaggtgcatttc; R:atttgcctgtgatgtaatagc
|
55
|
7
|
7
|
100
|
0.75
|
RM551
|
4
|
F:agcccagactagcatgattg; R:gaaggcgagaaggatcacag
|
55
|
6
|
6
|
100
|
0.68
|
RM598
|
5
|
F:gaatcgcacacgtgatgaac; R:atgcgactgatcggtactcc
|
55
|
9
|
5
|
55.56
|
0.75
|
RM176
|
6
|
F:cggctcccgctacgacgtctcc; R:agcgatgcgctggaagaggtgc
|
67
|
10
|
7
|
70
|
0.88
|
RM432
|
7
|
F:ttctgtctcacgctggattg; R:agctgcgtacgtgatgaatg
|
55
|
5
|
5
|
100
|
0.71
|
RM331
|
8
|
F:gaaccagaggacaaaaatgc; R:catcatacatttgcagccag
|
55
|
8
|
7
|
87.50
|
0.82
|
OSR28
|
9
|
F:agcagctatagcttagctgg; R:actgcacatgagcagagaca
|
55
|
10
|
9
|
90
|
0.80
|
RM590
|
10
|
F:catctccgctctccatgc; R:ggagttggggtcttgttcg
|
55
|
9
|
6
|
66.67
|
0.87
|
RM21
|
11
|
F:acagtattccgtaggcacgg; R:gctccatgagggtggtagag
|
55
|
11
|
11
|
100
|
0.87
|
RM3331
|
12
|
F:cctcctccatgagctaatgc; R:aggaggagcggatttctctc
|
50
|
6
|
4
|
66.67
|
0.80
|
RM443
|
1
|
F:gatggttttcatcggctacg; R:agtcccagaatgtcgtttcg
|
55
|
10
|
7
|
70
|
0.75
|
RM490
|
1
|
F:atctgcacactgcaaacacc; R:agcaagcagtgctttcagag
|
55
|
9
|
9
|
100
|
0.82
|
RM424
|
2
|
F:tttgtggctcaccagttgag; R:tggcgcattcatgtcatc
|
55
|
5
|
5
|
100
|
0.72
|
RM423
|
2
|
F:agcacccatgccttatgttg; R:cctttttcagtagccctccc
|
55
|
7
|
7
|
100
|
0.82
|
RM571
|
3
|
F:ggaggtgaaagcgaatcatg; R:cctgctgctctttcatcagc
|
55
|
7
|
7
|
100
|
0.67
|
RM231
|
3
|
F:ccagattatttcctgaggtc; R:cacttgcatagttctgcattg
|
55
|
12
|
12
|
100
|
0.84
|
RM567
|
4
|
F:atcagggaaatcctgaaggg; R:ggaaggagcaatcaccactg
|
55
|
10
|
10
|
100
|
0.78
|
RM289
|
5
|
F:ttccatggcacacaagcc; R:ctgtgcacgaacttccaaag
|
55
|
10
|
10
|
100
|
0.88
|
RM542
|
7
|
F:tgaatcaagcccctcactac; R:ctgcaacgagtaaggcagag
|
55
|
8
|
7
|
87.50
|
0.84
|
RM316
|
9
|
F:ctagttgggcatacgatggc; R:acgcttatatgttacgtcaac
|
55
|
2
|
2
|
100
|
0.19
|
RM332
|
11
|
F:gcgaaggcgaaggtgaag; R:catgagtgatctcactcaccc
|
55
|
10
|
8
|
80
|
0.88
|
RM7102
|
12
|
F:taggagtgtttagagtgcca; R:tcggtttgcttatacatcag
|
55
|
3
|
3
|
100
|
0.43
|
Clustering based on SSR
PC, in which the first three PC (eigenvalue) to select and their cumulative contribution of variance accounted for 15.76%, and the unweighted pair-group method with arithmetic means (UPGMA) were performed, which demonstrated that the 93 genotypes could be divided into 2 subgroups (Fig. 2)
Bayesian clustering based on SSR markers
A total of 378 SSR bands was used to elucidate the population structure of the entire pool of 93 rice germplasms. The best K was K = 2, suggesting that the 93 rice germplasms were best divided into two subgroups (Fig. 3).
SNPs marker analysis
A total of 39,872 SNPs-NlaIII and 35,547 SNPs-MseI passed the minor allele frequency (MAF) lower limit of 0.05 using NlaIII and MseI digestion, respectively. Merged data of SNPs-NlaIII and SNPs-MseI, with a total of 72,824 SNPs including 67,621 SNPs that aligned to specific chromosomes and 5,023 SNPs unlocalized, were then obtained.
Linkage disequilibrium (LD) and haplotype analysis
From the total of 6,288,753 loci (93 samples × 67,621SNPs), 326,873 (5.198%) were heterozygous. The 67,621 SNPs were unevenly distributed on the 12 chromosomes (Fig.4a); chromosome 1 contained the largest number of makers (8,425), while chromosome 8 included the least (3,953). LD, as represented by inter-loci R2 values, was calculated for the 84,255 SNP pairs. R2 value had a minimum of 0.2 and an average of 0.73. 46,322 SNP pairs (54.98%) had R2 values higher than 0.8, while 7,841 pairs (9.31%) were in complete LD (R2=1). The 12 chromosomes yielded a total of 6,568 predicted haplotypes (Fig.4b), with chromosome 1 possessing the most haplotypes (776) and chromosome 10 possessing the least (349). The largest haplotype was composed of 95 SNPs. The longest haplotype spanned over 200.0 kb; the average haplotype length was 33.71kb.
AMOVA and gene flow
The average MAF of the 93 samples was 0.21. Tajima’s D value was 1.66, which suggests low levels of both low- and high-frequency polymorphisms, indicating a decrease in population size and/or balancing selection that resulted in more haplotypes and lacked rare alleles in this population. Analysis of molecular variance (AMOVA) showed that the genetic variation was 98% within the population and 2% between populations, which indicated the existence of slight genetic variation among 93 samples. The genetic differentiation coefficient (FST) between the two populations was 0.61, and gene flow (Nm) was 0.16. Further investigation showed that the gene flow of selfing crops was the smallest, and that of annual herbaceous plants was the lowest. If Nm > 1, which indicates that the level of gene flow between populations is high, then genetic differentiation among populations is small; if Nm > 4, then gene communication between populations is more adequate and genetic differentiation is smaller; and Nm < 1 indicates that population differentiation may have occurred due to genetic drift. The gene flow was 0.16, which indicates that the gene flow among populations in the Qinba region is lower, but nearly 2.5-fold higher than that of conventional inbred plants, which may result in long-term artificial selection, leading to reduced genetic differentiation.
Clustering based on SNPs
PC clustering
Principal component analysis was performed to select the first three PCs (based on eigenvalue). Their cumulative contribution of variance accounted for 40.69%, 39.76% and 40.10% for SNPs-NlaIII, SNPs-MseI, merged data of SNPs-NlaIII and SNPs-MseI, respectively, which demonstrated that the 93 genotypes could be clustered into two subgroups by the first three PCs (Fig.5), with W366 and W367 being always separated from other samples.
UPGMA clustering
The unweighted pair-group method with arithmetic means (UPGMA) algorithm was performed and demonstrated that the 93 genotypes could be divided into 2 subgroups (Fig. 6), which was consistent with the PC results. Group I included 1 to 3 samples, while group II contained 92 to 90 samples. The average genetic distance was 0.29, ranging from 0.02 to 0.55 based on merged SNPs-NlaIII and SNPs-MseI data. The two most closely related materials were W710 and W711, and the two most furthest materials were W366 and W740.
Bayesian clustering
72,824 SNPs (MAF <5%) were used to assess the population structure of the entire pool of 93 samples. Delta K reached a maximum value at K=2, suggesting that the 93 samples were divided into two subgroups (consisting of 70 and 23 samples) (Fig. 7). In the population structure analysis, the results from K = 2 to K = 5 revealed the occurrence of gene introgression between groupІ and groupII, accounting for approximately 76.34% of the observed variations (calculated with K = 2).
Clustering of different category materials
Population genetic information of different category samples, including 57 restoring lines, 19 maintainer lines and 17 special rice lines was analyzed (Table 6) and clustered (Fig 8. 8a, 8b, 8c, respectively). Results showed that the genetic basis of the restorer line was more abundant than that of the maintainer line, and that the genetic basis of the special rice was wider than that of the conventional rice.
Table 6 Population genetic analysis of different category materials
Samples
|
Tajima’ D
|
Range of IBS genetic distance
|
The average genetic distance
|
Two samples with the closest genetic distance
|
Two samples with the farthest genetic distance
|
Whole materials (93)
|
1.66
|
0.0229-0.5452
|
0.3007
|
W710/W711
|
W366/W740
|
Restoring lines (57)
|
1.36672
|
0.0229-0.3927
|
0.2666
|
W710/W711
|
W685/W697
|
Maintainer lines (19)
|
0.43533
|
0.0242-0.3745
|
0.2293
|
W740/W741
|
W725/W738
|
Special rice (17)
|
0.62542
|
0.0285-0.5315
|
0.3280
|
W375/W380
|
W300/W366
|
Correlation analysis of genetic distance matrices based on 3 types of genetic markers
All cluster analyses were based on the genetic distance or genetic similarity coefficient generated by genetic markers between samples; in the present study, the coefficients of correlation (R2) between the genetic distance matrices were 0.0914, 0.1726, 0.198, 0.876, 0.3478, 0.2713, respectively (Fig. 9). These results may be due to the use of different number of markers.