Genotype x Environment Interaction and stability of performance of Lowland NERICA.
The result of the combined analysis of variance for flowering days, maturity days, plant height, panicle/m2, and yield of 48 rice genotypes at 12 environments is presented in Table 4. Significant replicate effects were observed for flowering days, maturity days, plant height, panicle/m2 and yield. Also, the result indicates that the rice genotypes varied significantly for all traits. The location, genotype x location were highly significant to all traits except panicle/m2. The two years differed significantly for all traits meaning that climatic changes were observed during the study. Significant genotype x year effects were observed for flowering days and maturity days, but non-significant G x E effects were observed for plant height, panicle/m2 and yield meaning that the last three traits remained similar over the two years. Location x year interaction reported highly significant effects for all the five traits meaning that the location of experiments differed in the two years of the study.
Table 4. Mean squares of the combined analysis of variance for yield and related characters of rice genotypes at 12 environments (6-locations by 2-seasons).
Source
|
DF
|
Flowering days
|
Maturity days
|
Plant
Height
|
Panicle/m2
|
Yld (Kg)
|
Rep
|
2
|
405.57**
|
320.90*
|
935.73*
|
17802.79**
|
3172332.00*
|
Genotype
|
47
|
573.99**
|
445.64**
|
2510.16**
|
3224.97*
|
4241473.00**
|
Location
|
5
|
3415.67**
|
3293.76**
|
16468.86**
|
58159.07**
|
478999838.00**
|
Genotype x Location
|
235
|
39.00**
|
59.01**
|
431.84**
|
1640.01ns
|
2045861.00**
|
Year
|
1
|
598.55**
|
987.06**
|
11891.26**
|
2518782.18**
|
214102592.00**
|
Genotype x Year
|
47
|
55.59**
|
74.22*
|
60.48ns
|
1076.35ns
|
1323782.00ns
|
Location x Year
|
5
|
11053.14**
|
4314.64**
|
6147.59**
|
662751.43**
|
337035964.00**
|
Genotype x Location x Year
|
235
|
56.47**
|
48.14ns
|
60.66ns
|
1267.41ns
|
1876652.00*
|
Error
|
1150
|
23.14
|
39.26
|
107.85
|
1895.73
|
1411702.00
|
*, ** Significant at 5% and 1% probability levels, respectively
This suggests that rice genotypes performed differently in every location in each year. Genotype x location x year was significant for days to flowering and yield and non-significant effects were observed for maturity days, plant height, and panicle/m2.
Table 5 shows the mean of twenty-two characters measured in forty-eight rice genotypes in the six locations in two years. The highest mean grain yield of 4469.0Kg/ha was recorded in NERICA-L-28 while the lowest yield (2148.0Kg/ha) was observed in TOG 5681. The tallest genotype was NERICA-L-39 with a height of 123.0cm while NERICA-L-12 was the shortest with a height of 89.0cm. TOX 4004-43-1-2-1 had the highest number of panicles per meter square (219) while NERICA-L-60 had the lowest (172). FKR 19 (Check) was the earliest maturing among the genotypes with the number of days to heading of 81 days, while SUAKOKO 8 was the latest to head with the number of days to heading of 101 days. The genotype with the earliest maturity was FKR 19 with the number of days to maturity of 112 days while the latest to mature was SUAKOKO 8 with a number of days to maturity of 129 days.
Table 5. The means of twenty-two characters measured in forty-eight rice genotypes in 12 environments (6-locations by 2-seasons)
Plot/No
|
Designation
|
Flwdays
|
Matdays
|
PltHght
|
NmTiller
|
Pan_m
|
Yld
|
Panlght
|
PanExt
|
Pltvigor
|
PSht
|
1
|
BW 348-1
|
93
|
122
|
111
|
16
|
197
|
3976
|
26.80
|
6
|
2
|
3
|
2
|
FARO 44 (SIPI-692033)
|
87
|
117
|
95
|
11
|
190
|
4275
|
33.93
|
6
|
3
|
5
|
3
|
FARO 51(CISADANE)
|
98
|
124
|
109
|
12
|
200
|
3900
|
24.33
|
6
|
3
|
4
|
4
|
IR 75866-18-30-19-WAB1
|
90
|
121
|
108
|
12
|
194
|
4019
|
26.50
|
6
|
3
|
4
|
5
|
IR 75866-2-18-23-WAB1
|
91
|
122
|
97
|
12
|
206
|
4027
|
25.83
|
6
|
3
|
3
|
6
|
IR 75871-4-29-13-WAB1
|
93
|
123
|
106
|
13
|
189
|
3920
|
25.24
|
6
|
2
|
4
|
7
|
IR 75871-8-14-21-WAB1
|
94
|
123
|
114
|
12
|
208
|
3926
|
23.62
|
7
|
3
|
3
|
8
|
NERICA-L6
|
88
|
118
|
99
|
12
|
193
|
3652
|
25.94
|
6
|
3
|
3
|
9
|
NERICA-L7
|
87
|
117
|
95
|
12
|
205
|
4160
|
25.00
|
6
|
3
|
5
|
10
|
NERICA-L8
|
89
|
120
|
96
|
12
|
207
|
3921
|
26.38
|
6
|
3
|
3
|
11
|
NERICA-L9
|
85
|
116
|
98
|
12
|
210
|
4060
|
24.70
|
6
|
4
|
3
|
12
|
NERICA-L12
|
82
|
113
|
89
|
13
|
213
|
3779
|
24.37
|
5
|
3
|
4
|
13
|
NERICA-L14
|
89
|
120
|
102
|
12
|
202
|
4382
|
25.45
|
6
|
3
|
3
|
14
|
NERICA-L15
|
90
|
119
|
103
|
11
|
188
|
4231
|
26.22
|
7
|
3
|
3
|
15
|
NERICA-L17
|
90
|
119
|
105
|
12
|
195
|
4060
|
25.92
|
7
|
2
|
4
|
16
|
NERICA-L18
|
85
|
116
|
93
|
13
|
202
|
3888
|
25.84
|
6
|
3
|
3
|
17
|
NERICA-L19
|
88
|
118
|
106
|
12
|
202
|
4086
|
26.51
|
6
|
2
|
4
|
18
|
NERICA-L20
|
89
|
119
|
103
|
12
|
193
|
4300
|
26.55
|
5
|
3
|
4
|
19
|
NERICA-L26
|
91
|
121
|
101
|
13
|
186
|
4086
|
25.72
|
6
|
3
|
5
|
20
|
NERICA-L28
|
87
|
118
|
92
|
13
|
190
|
4469
|
26.18
|
6
|
3
|
3
|
21
|
NERICA-L32
|
84
|
114
|
96
|
12
|
186
|
3859
|
25.05
|
6
|
3
|
5
|
22
|
NERICA-L33
|
85
|
116
|
91
|
13
|
205
|
3991
|
25.77
|
5
|
3
|
5
|
23
|
NERICA-L34
|
86
|
116
|
93
|
12
|
203
|
3894
|
25.53
|
6
|
3
|
4
|
24
|
NERICA-L36
|
85
|
115
|
94
|
13
|
204
|
4094
|
25.18
|
6
|
3
|
4
|
|
|
|
|
|
|
|
|
|
|
|
|
Plot/No
|
Designation
|
Flwdays
|
Matdays
|
PltHght
|
NmTiller
|
Pan_m
|
Yld
|
Panlght
|
PanExt
|
Pltvigor
|
PSht
|
25
|
NERICA-L37
|
92
|
123
|
93
|
13
|
200
|
3434
|
26.14
|
6
|
3
|
3
|
26
|
NERICA-L38
|
87
|
116
|
96
|
12
|
203
|
3808
|
25.26
|
6
|
3
|
4
|
27
|
NERICA-L39
|
94
|
125
|
123
|
11
|
192
|
3161
|
29.12
|
5
|
2
|
3
|
28
|
NERICA-L40
|
89
|
118
|
100
|
13
|
204
|
3637
|
26.48
|
6
|
3
|
3
|
29
|
NERICA-L41
|
91
|
122
|
101
|
12
|
200
|
3997
|
26.00
|
5
|
3
|
4
|
30
|
NERICA-L42
|
91
|
121
|
103
|
12
|
190
|
3866
|
26.75
|
6
|
3
|
4
|
31
|
NERICA-L45
|
88
|
117
|
91
|
11
|
206
|
3620
|
25.72
|
7
|
3
|
4
|
32
|
NERICA-L46
|
90
|
119
|
97
|
12
|
204
|
3875
|
26.74
|
6
|
4
|
3
|
33
|
NERICA-L48
|
91
|
121
|
101
|
12
|
197
|
3621
|
26.60
|
6
|
3
|
4
|
34
|
NERICA-L49
|
87
|
117
|
100
|
12
|
206
|
4274
|
26.23
|
6
|
2
|
4
|
35
|
NERICA-L50
|
88
|
113
|
91
|
13
|
203
|
3557
|
24.46
|
6
|
4
|
3
|
36
|
NERICA-L53
|
91
|
121
|
92
|
13
|
206
|
3746
|
26.38
|
5
|
4
|
4
|
37
|
NERICA-L54
|
89
|
115
|
90
|
12
|
196
|
3753
|
23.68
|
5
|
4
|
4
|
38
|
NERICA-L55
|
91
|
121
|
95
|
12
|
218
|
3761
|
26.24
|
6
|
3
|
3
|
39
|
NERICA-L56
|
93
|
122
|
98
|
15
|
203
|
4158
|
26.86
|
5
|
3
|
4
|
40
|
NERICA-L60
|
92
|
121
|
93
|
12
|
172
|
3764
|
25.68
|
6
|
3
|
3
|
41
|
SUAKOKO 8
|
101
|
129
|
91
|
11
|
183
|
3618
|
26.21
|
5
|
3
|
3
|
42
|
TOX 4004-43-1-2-1
|
95
|
121
|
116
|
11
|
219
|
3766
|
27.53
|
5
|
3
|
5
|
43
|
WITA 7
|
92
|
123
|
106
|
11
|
184
|
3824
|
24.32
|
7
|
4
|
5
|
44
|
TOG 5681 (Parent)
|
85
|
114
|
108
|
12
|
181
|
2148
|
23.36
|
6
|
2
|
3
|
45
|
IR 64 (Parent)
|
84
|
116
|
93
|
13
|
189
|
3587
|
25.23
|
6
|
3
|
4
|
46
|
WITA 4 (Check)
|
94
|
124
|
112
|
12
|
206
|
4149
|
26.37
|
5
|
3
|
5
|
47
|
FKR 19 (Check)
|
81
|
112
|
102
|
11
|
196
|
3229
|
24.59
|
6
|
2
|
3
|
48
|
FKR 54 (Check)
|
83
|
116
|
108
|
10
|
202
|
4177
|
26.11
|
6
|
2
|
4
|
|
Means
|
89
|
119
|
98
|
12
|
199
|
3864
|
25.93
|
6
|
3
|
4
|
|
LSD
|
2.22
|
2.90
|
4.80
|
1.17
|
20.14
|
549.47
|
2.33
|
0.52
|
0.45
|
0.34
|
|
|
|
|
|
|
|
|
|
|
|
|
Plot/No
|
Pthres
|
Hairnes
|
Awning
|
Prybrpan
|
Secbrpan
|
Lflgth
|
Lfwdth
|
FlaglAng
|
Bastlcol
|
Grlght
|
Grwidth
|
1000grwt
|
|
1
|
3
|
2
|
0
|
10
|
25
|
32.23
|
1.07
|
1
|
1
|
8.44
|
2.35
|
23
|
|
2
|
5
|
2
|
0
|
10
|
19
|
27.61
|
1.17
|
1
|
1
|
8.98
|
2.33
|
23
|
|
3
|
4
|
2
|
0
|
10
|
16
|
27.75
|
1.20
|
4
|
2
|
7.72
|
2.66
|
23
|
|
4
|
4
|
2
|
0
|
10
|
20
|
30.81
|
1.10
|
2
|
3
|
8.88
|
2.25
|
23
|
|
5
|
3
|
4
|
5
|
10
|
21
|
30.13
|
1.08
|
3
|
3
|
8.59
|
2.17
|
24
|
|
6
|
4
|
3
|
0
|
10
|
17
|
27.90
|
1.10
|
2
|
1
|
8.98
|
2.25
|
23
|
|
7
|
3
|
3
|
0
|
10
|
21
|
28.76
|
1.10
|
2
|
1
|
8.83
|
2.51
|
23
|
|
8
|
3
|
2
|
0
|
9
|
19
|
29.29
|
1.07
|
1
|
1
|
9.18
|
2.45
|
24
|
|
9
|
5
|
2
|
0
|
9
|
17
|
27.01
|
1.10
|
1
|
3
|
8.72
|
2.29
|
23
|
|
10
|
3
|
2
|
0
|
9
|
18
|
29.43
|
1.08
|
1
|
1
|
9.14
|
2.24
|
25
|
|
11
|
3
|
4
|
0
|
10
|
19
|
26.00
|
1.03
|
1
|
1
|
8.75
|
2.33
|
24
|
|
12
|
4
|
4
|
0
|
8
|
15
|
27.25
|
1.05
|
2
|
3
|
9.43
|
2.30
|
23
|
|
13
|
3
|
2
|
0
|
10
|
20
|
29.88
|
1.04
|
1
|
1
|
9.43
|
2.30
|
23
|
|
14
|
3
|
2
|
0
|
11
|
21
|
30.81
|
1.07
|
1
|
1
|
9.55
|
2.29
|
24
|
|
15
|
4
|
2
|
0
|
11
|
19
|
27.92
|
1.06
|
1
|
1
|
9.27
|
2.24
|
24
|
|
16
|
3
|
2
|
0
|
8
|
17
|
27.94
|
1.08
|
1
|
1
|
8.72
|
2.18
|
24
|
|
17
|
4
|
2
|
0
|
10
|
21
|
32.59
|
1.03
|
2
|
1
|
9.20
|
2.30
|
23
|
|
18
|
4
|
2
|
0
|
10
|
23
|
30.25
|
1.06
|
1
|
1
|
9.30
|
2.32
|
25
|
|
19
|
5
|
2
|
0
|
10
|
25
|
28.32
|
1.00
|
1
|
1
|
8.87
|
2.55
|
24
|
|
20
|
3
|
3
|
0
|
10
|
21
|
28.01
|
1.05
|
3
|
1
|
8.65
|
2.28
|
23
|
|
21
|
5
|
2
|
0
|
8
|
17
|
28.68
|
1.02
|
1
|
1
|
8.86
|
2.25
|
24
|
|
22
|
5
|
2
|
0
|
9
|
17
|
27.11
|
1.03
|
1
|
1
|
9.25
|
2.35
|
24
|
|
23
|
4
|
2
|
0
|
10
|
19
|
29.14
|
1.01
|
1
|
1
|
9.06
|
2.25
|
23
|
|
24
|
4
|
2
|
0
|
9
|
19
|
26.65
|
1.08
|
1
|
3
|
8.54
|
2.21
|
24
|
|
25
|
3
|
3
|
0
|
10
|
21
|
29.49
|
1.08
|
1
|
1
|
8.77
|
2.27
|
21
|
|
26
|
4
|
2
|
0
|
9
|
20
|
28.67
|
1.05
|
1
|
1
|
8.54
|
2.40
|
23
|
|
27
|
3
|
2
|
0
|
10
|
23
|
33.75
|
0.93
|
3
|
3
|
8.29
|
2.14
|
24
|
|
28
|
3
|
2
|
0
|
9
|
18
|
28.21
|
1.09
|
2
|
1
|
8.96
|
2.28
|
25
|
|
29
|
4
|
2
|
0
|
10
|
22
|
30.75
|
1.11
|
1
|
1
|
8.42
|
2.28
|
25
|
|
30
|
4
|
2
|
0
|
10
|
22
|
30.81
|
1.02
|
1
|
1
|
8.93
|
2.36
|
24
|
|
31
|
4
|
2
|
0
|
9
|
19
|
27.74
|
1.09
|
1
|
1
|
8.82
|
2.39
|
23
|
|
32
|
3
|
3
|
0
|
9
|
20
|
29.12
|
1.00
|
1
|
1
|
9.02
|
2.44
|
25
|
|
33
|
4
|
2
|
0
|
9
|
19
|
29.68
|
1.03
|
1
|
1
|
8.88
|
2.24
|
24
|
|
34
|
4
|
2
|
0
|
11
|
22
|
30.08
|
1.04
|
1
|
1
|
8.80
|
2.44
|
24
|
|
35
|
3
|
2
|
0
|
9
|
17
|
26.65
|
1.01
|
1
|
1
|
9.39
|
2.34
|
23
|
|
36
|
4
|
2
|
0
|
9
|
18
|
29.64
|
1.01
|
1
|
1
|
8.71
|
2.32
|
24
|
|
37
|
4
|
3
|
0
|
9
|
17
|
27.09
|
1.04
|
1
|
3
|
8.86
|
2.25
|
24
|
|
38
|
3
|
2
|
0
|
9
|
21
|
30.07
|
1.03
|
2
|
3
|
9.74
|
2.40
|
24
|
|
39
|
4
|
1
|
0
|
10
|
21
|
30.10
|
1.06
|
1
|
1
|
8.57
|
2.29
|
24
|
|
40
|
3
|
3
|
0
|
10
|
21
|
29.82
|
1.07
|
1
|
1
|
8.68
|
2.33
|
24
|
|
41
|
3
|
2
|
0
|
11
|
21
|
33.98
|
0.95
|
2
|
3
|
8.85
|
2.31
|
23
|
|
42
|
5
|
2
|
1
|
11
|
25
|
30.48
|
1.01
|
2
|
1
|
9.07
|
2.52
|
21
|
|
43
|
5
|
2
|
0
|
11
|
20
|
28.43
|
1.00
|
2
|
1
|
8.54
|
2.45
|
22
|
|
44
|
3
|
2
|
0
|
9
|
15
|
26.59
|
1.04
|
3
|
3
|
8.00
|
2.59
|
23
|
|
45
|
4
|
3
|
0
|
10
|
21
|
26.86
|
0.93
|
1
|
1
|
8.57
|
2.36
|
22
|
|
46
|
5
|
2
|
0
|
10
|
20
|
28.87
|
0.97
|
3
|
1
|
8.73
|
2.31
|
23
|
|
47
|
3
|
2
|
0
|
9
|
19
|
26.07
|
0.93
|
2
|
1
|
8.38
|
2.32
|
24
|
|
48
|
4
|
2
|
0
|
10
|
21
|
29.74
|
1.14
|
2
|
1
|
8.65
|
2.45
|
24
|
|
Mean
|
4
|
2
|
0
|
10
|
20
|
29.05
|
1.05
|
2
|
1
|
8.84
|
2.34
|
24
|
|
Lsd
|
0.00
|
0.16
|
0.00
|
0.49
|
2.29
|
2.17
|
0.08
|
0.30
|
0.09
|
0.15
|
0.05
|
0.60
|
|
Genotype x environment interaction and stability analysis
The additive main effect and multiplicative interaction (AMMI) analysis of variance for seed yield per plot in forty-eight genotypes tested across 12 environments (6-locations by 2-seasons) (Table 6). The result showed strong evidence that environment (E), genotype (G), and genotype-by-environment (G x E) interaction were highly significant at (p < 0.01), as E and G, respectively accounted for 78.6, 3.5, and 17.9% of the total variation. The total sum of squares due to G x E interaction was mainly explained by the first two principal component axes (IPCA1 and 2), which were significant and respectively accounted for 27.3% and 23.8% of the sum squares. The IPCA1 mean square was almost four times larger than the error means square. The IPCA 3 and IPCA 4 were equally significant and accounted for 13.3% and 10.5% of the G x E interactive sum of squares, respectively. Table 7 shows the GGE analysis of variance for rice yield in forty-eight rice genotypes evaluated across twelve environments (6-location by 2-seasons). The result showed significant (P< 0.01) Environment (E), Genotype (G), and Genotype-by-Environment (G x E) interaction that accounted for 60.4%, 2.8%, and 13.8% of the total sum squares, respectively. The environmental sum of squares was about twenty-one times larger than the genotype sum of squares and four times larger than the GEI sum of squares.
The biplot of AMMI for 48 rice genotypes in 12 environments. The y-axis represents the IPCA1 scores, while the x-axis represents the seed yield per plot (main effect) of the accessions (Figure 3). NERICA-L56 was the overall best genotype combining relative stability and high yield. Genotypes NERICA-L8, NERICA-L12, NERICA-L33, NERICA-L36, NERICA-L42, and FKR 54 were highly stable and above average in yield, while NERICA-L28 was above average in yield but relatively unstable due to large interaction. IR 64 and NERICA-L60 had a subpar yield but stable. The poorest of the genotypes due to instability and lowest yield were TOG 5681 and FKR 19. Irrigated Ibadan 2008 (E1), Irrigated Ibadan 2009 (E2), Valley bottom Ibadan 2008 (E3), Valley fringe Ibadan 2008 (E5), Valley fringe Ibadan 2009 (E6), and Valley fringe Kpalime 2009 (E8) had subpar yield. The valley bottom Ouédémé 2008 (E9) and valley fringe Ouédémé 2008 (E11) were most stable whereas valley bottom Ouedeme 2009 (E10) and valley fringe Ouédémé 2009 (E12) were most unstable producing large interactions. Environment (E7) was observed to be next to E9 as far as yield and stability of performance are concerned.
Table 6: The additive main effect and multiplicative interaction (AMMI) model analysis of variance for rice yield in forty-eight genotypes tested across 12 environments (6-locations by 2-seasons).
Source
|
Df
|
Sum of
squares
|
Mean
square
|
Percentage total
Sum of squares
|
Percentage
treatment
|
Percentage
G x E
|
Total
|
1726
|
7097293236.77
|
4111989.13
|
|
|
|
Treatment
|
575
|
5471072240.27
|
9514908.24**
|
77.1
|
|
|
Genotype
|
47
|
192681506.17
|
4099606.51**
|
|
3.5
|
|
|
Environment
|
11
|
4299546982.94
|
390867907.54**
|
|
78.6
|
|
|
G x E
|
517
|
978843751.17
|
1893314.80**
|
|
17.9
|
|
|
IPCA 1
|
57
|
267371718.91
|
4690731.91**
|
|
|
27.3
|
IPCA 2
|
55
|
232488363.78
|
4227061.16**
|
|
|
23.8
|
IPCA 3
|
53
|
130469255.67
|
2461684.07**
|
|
|
13.3
|
IPCA 4
|
51
|
102507705.53
|
2009955.01*
|
|
|
10.5
|
IPCA 5
|
49
|
80847056.65
|
1649939.93
|
|
|
8.3
|
IPCA 6
|
47
|
70716162.42
|
1504599.20
|
|
|
7.2
|
IPCA 7
|
45
|
40623835.32
|
902751.90
|
|
|
4.2
|
Residual
|
160
|
53819652.89
|
336372.83
|
|
|
|
Error
|
1151
|
1626220996.50
|
1412876.63
|
22.9
|
|
|
*, **, significant at 5% and 1% probability level respectively
Table 7: GGE analysis of variance for rice yield in forty-eight rice genotypes evaluated across twelve environments (6-location by 2-seasons).
Source
|
Df
|
SS
|
MS
|
% Total SS
|
Total
|
1727
|
7107535378.46
|
|
|
Genotype
|
47
|
199353914.53
|
4241573.00**
|
2.8
|
Environment
|
11
|
4294297637.53
|
390390700.00**
|
60.4
|
G x E
|
517
|
984022532.68
|
1903332.00**
|
13.8
|
Block
|
24
|
351823964.70
|
14659330.00**
|
|
Error
|
1128
|
1278037329.02
|
1133012.00
|
|
*, **, significant at 5% and 1% probability level respectively
Correlation Among the Morphological Traits of Rice Genotypes
All 48 rice genotypes were evaluated in 12 environments (Table 8). Plant vigor was negatively and highly significantly correlated with plant height (r = -0.55), panicle number per square meter (-0.56), primary branch panicle (-0.33), secondary branch panicle (-0.30), and leaf length (-0.50). Tiller number per square meter showed a highly significant negative correlation with plant height (-0.35) and primary branch panicle number (-0.29%), and a significant negative correlation with grain length (-0.19) and grain width (-0.20). Days to flowering showed a highly significant positive correlation with maturity date (0.97), plant height (0.65), panicle number per square meter (0.27), panicle length (0.35), primary branch panicle (0.58), secondary branch panicle (0.42), and leaf length (0.75); significant positive correlation with panicle threshability (0.16) and grain width (0.17); highly significant negative correlation with panicle exertion (-0.34); and significant negative correlation with hairiness (-0.17). Days to maturity had a highly significant positive correlation with plant height
Table 8: The genotypic correlation coefficient between twenty-two characters of rice in twelve environments (6 locations by 2 seasons)
Character
|
No
|
Flw
|
Mat
|
Plt
|
Pan
|
PSht
|
Pthres
|
Yld
|
Hairnes
|
Pan/
|
Awn
|
Pan
|
Pry
|
Sec
|
Lf
|
Lf
|
Flagl
|
Bastl
|
Gr
|
Gr
|
I000
|
|
Till
|
days
|
days
|
Hght
|
Ext
|
|
|
|
|
meter
|
|
lght
|
brpan
|
brpan
|
lght
|
wdth
|
Ang
|
col
|
lght
|
width
|
gwt
|
Pltvigor
|
0.04
|
0.04
|
-0.06
|
-0.55**
|
-0.11
|
0.04
|
-0.11
|
0.14
|
0.15
|
-0.56**
|
-0.15
|
0.04
|
-0.33**
|
-0.30**
|
-0.50**
|
0.02
|
-0.18
|
-0.08
|
0.13
|
0.09
|
-0.01
|
NmTiller
|
|
0.12
|
0.12
|
-0.35**
|
-0.09
|
-0.07
|
-0.08
|
-0.14
|
0.06
|
0.02
|
-0.04
|
-0.14
|
-0.29**
|
-0.05
|
-0.02
|
0.01
|
-0.19
|
-0.04
|
-0.19*
|
-0.20*
|
0.10
|
Flwdays
|
|
|
0.97**
|
0.65**
|
-0.34**
|
-0.04
|
0.16*
|
0.03
|
-0.17*
|
0.27**
|
0.12
|
0.35**
|
0.58**
|
0.42**
|
0.75**
|
0.06
|
0.4
|
0.1
|
-0.13
|
0.17*
|
-0.12
|
Matdays
|
|
|
|
0.66**
|
-0.26**
|
-0.05
|
0.15
|
0.09
|
-0.14
|
0.56**
|
0.15
|
0.43**
|
0.63**
|
0.54**
|
0.87**
|
-0.06
|
0.37
|
0.09
|
-0.13
|
0.03
|
-0.08
|
PltHght
|
|
|
|
|
-0.11
|
-0.09
|
0.19*
|
-0.27**
|
-0.28**
|
0.67**
|
-0.01
|
0.26**
|
0.68**
|
0.45**
|
0.74**
|
-0.29
|
0.42
|
0.11
|
-0.27**
|
0.23**
|
-0.14
|
PanExt
|
|
|
|
|
|
-0.13
|
-0.12
|
0.30**
|
-0.06
|
-0.01
|
-0.04
|
-0.27**
|
0.17
|
-0.01
|
-0.31**
|
0.53
|
-0.23
|
-0.33**
|
0.09
|
0.18
|
-0.17*
|
PSht
|
|
|
|
|
|
|
0.20*
|
0.45**
|
-0.27**
|
-0.19*
|
-0.18*
|
0.28**
|
-0.05
|
0.05
|
-0.12
|
0.07
|
-0.16
|
-0.15
|
0.01
|
0.00
|
-0.22**
|
Pthres
|
|
|
|
|
|
|
|
-0.04
|
-0.18*
|
0.40**
|
0.02
|
0.15
|
0.16*
|
0.17*
|
0.27**
|
-0.31
|
0.04
|
0.07
|
-0.05
|
-0.04
|
-0.03
|
Yld
|
|
|
|
|
|
|
|
|
-0.08
|
-0.34**
|
0.01
|
0.79**
|
0.24**
|
0.26**
|
0.08
|
0.69
|
-0.05
|
-0.41**
|
0.37**
|
-0.25**
|
0.24**
|
Hairnes
|
|
|
|
|
|
|
|
|
|
-0.21**
|
0.46**
|
-0.55**
|
-0.18*
|
-0.24**
|
-0.36**
|
0.04
|
0.21
|
0.23**
|
0.00
|
-0.13
|
0.01
|
Pan_m
|
|
|
|
|
|
|
|
|
|
|
-0.45**
|
0.38**
|
0.80**
|
0.46**
|
0.87**
|
0.23
|
0.00
|
-0.08
|
-0.55**
|
0.11
|
-0.13
|
Awning
|
|
|
|
|
|
|
|
|
|
|
|
0.04
|
0.13
|
0.19*
|
0.14
|
0.12
|
0.44
|
0.24**
|
-0.09
|
-0.18*
|
0.00
|
Panlght
|
|
|
|
|
|
|
|
|
|
|
|
|
0.48**
|
0.67**
|
0.94**
|
0.56
|
-0.26
|
-0.29**
|
0.17*
|
-0.53**
|
0.13
|
Prybrpan
|
|
|
|
|
|
|
|
|
|
|
|
|
|
0.79**
|
0.65**
|
-0.16
|
0.26
|
-0.25**
|
-0.05
|
0.23**
|
-0.25**
|
Secbrpan
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
0.74**
|
-0.41
|
-0.01
|
-0.30**
|
0.1
|
0.09
|
-0.13
|
Lflgth
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
-0.34
|
0.03
|
0.08
|
0.18*
|
-0.22**
|
0.01
|
Lfwdth
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
0.14
|
0.00
|
-0.12
|
0.33**
|
0.34**
|
Lfwdth
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
0.35**
|
-0.58**
|
0.25**
|
-0.09
|
Bastlcol
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
-0.21**
|
-0.13
|
0.00
|
Grlght
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
-0.34**
|
0.07
|
Grwidth
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
-0.25**
|
(0.66), panicle number per square meter (0.56), panicle length (0.43), primary branch panicle (0.63), secondary branch panicle (0.54), and leaf length (0.87), and highly significant negative correlation with panicle exertion (-0.26). Plant height showed a highly significant positive correlation with panicle number per square meter (0.67), panicle length (0.26), primary branch panicle (0.68), secondary branch panicle (0.45), leaf length (0.74), and grain width (0.23); significant positive correlation with panicle threshability (0.19); and highly significant negative correlation with yield (-0.27) and grain length (-0.27).
Panicle exertion showed a highly significant positive correlation with yield (0.30). Meanwhile, panicle exertion showed a highly significant negative correlation with panicle length (-0.27), leaf length (-0.31), basal leaf sheath coloration (-0.33), and significant correlation with 1,000-grain weight (-0.17). Panicle shattering showed a highly significant positive correlation with yield (0.45) and panicle length (0.28); significant correlation with panicle threshability (0.20); highly significant negative correlation with hairiness (-0.27); and significant correlation with (-0.18). Panicle threshability showed a significant negative correlation with hairiness (-0.18); highly significant positive correlations were panicle number per square meter (0.40) and leaf length (0.27); and significant correlation with primary branch panicle (0.16) and secondary branch panicle (0.17). Yield showed a highly significant positive correlation with panicle length (0.79), primary branch panicle (0.24), secondary branch panicle (0.26), grain length (0.37), and 1,000-grain weight (0.24), and highly significant negative correlation with panicle number per square meter (-0.34) and basal leaf sheath coloration (-0.41).
Hairiness showed a highly significant positive correlation withawn0.46) and basal leaf sheath coloration (0.23); highly significant negative correlation with panicle number per square meter (-0.21), panicle length (-0.55), secondary branch panicle (-0.24), and leaf length (-0.36); and significant negative correlation with primary branch panicle (-0.18). Panicle number per square meter was a highly significant negative correlation with awning (-0.45) and grain length (-0.55), and highly significant positive correlation with panicle length (0.38), primary branch panicle (0.80), secondary branch panicle (0.46), and leaf length (0.87). Awning showed a highly significant positive correlation with basal leaf sheath coloration (0.24); a significant positive correlation with secondary branch panicle (0.19); and a significant negative correlation with grain width (-0.18). Panicle length showed a highly significant positive correlation with primary branch panicle number (0.48), secondary branch panicle number (0.67), and leaf length (0.94), and significant positive and negative correlation with grain length (0.17) and grain width (-0.53), respectively.
Primary branch panicle number showed a highly significant positive correlation with secondary branch panicle (0.79), leaf length (0.65), and grain width (0.23), and highly significant negative correlation with basal leaf sheath coloration (-0.25) and 1,000-grain weight (-0.25). Secondary branch panicle number showed a highly significant positive correlation with leaf length (0.74) and a highly significant negative correlation with basal leaf sheath coloration (-0.30). Leaf length showed a highly significant positive correlation with grain width (-0.22) and a significant positive correlation with grain length (0.18). Leaf width showed a highly significant positive correlation with grain width (0.33), 1,000-grain weight (0.34), basal leaf sheath coloration (0.35), and grain width (0.25), and a highly significant negative correlation with grain length (-0.58). Highly significant negative correlations were also observed between basal leaf sheath coloration and grain length (-0.21), grain length and grain width (-0.34), and grain width and 1,000-grain weight (-0.25).
Variability Among 48 Rice Genotypes Based On Morpho-agronomic Traits
PCA of the morpho-agronomic traits of 48 rice genotypes revealed eight PC axes with Eigenvalues greater than 1.0, which together accounted for 75.13% of the total variation. The relative discriminating power of the PCA, as revealed by Eigenvalues, was 4.13, 2.77, 2.36, 1.83, 1.66, 1.43, 1.27, and 1.09 for PC1, PC2, PC3, PC4, PC5, PC6, PC7, and PC8, respectively. PC1, PC2, PC3, and PC4 explained 18.79%, 12.57%, 10.71%, and 8.33% of the total variation, respectively, together accounting for 50.39% of the total variation. PC1 attributed to variation in days to flowering, days to physiological maturity, plant height, primary branch panicle, secondary branch panicle, and leaf length. PC2 was associated with yield, panicle shattering, panicle threshability, flag leaf angle, and base tiller coloration. PC3–6, and PC8 mainly attributed to variation in grain width, awning, panicle exertion, plant vigor, and panicle number per square meter, respectively, whereas PC7 was associated with tiller number at 60 days (Table 9). The plot of the relationship among all 48 genotypes showed a considerable amount of variability, although most of the genotypes from the same source did not sort out, as explained by PC1 and PC2 (Figure 4). Additionally, the results of PCA showed that rice genotypes were grouped into four distinct clusters. The ordination of rice genotypes on PC1 and PC2 accounted for 51.5% of the total variation, showing that genotypes TOG 5681, FKR 19, WITA 4, NERICA-L38, and NERICA-L28 were quite distinct from other genotypes (Figure 3).
Table 9: Phenotypic characteristics with respect to their principal component, Eigen values and variation of 48 rice genotypes.
|
PC 1
|
PC 2
|
PC 3
|
PC 4
|
PC 5
|
PC 6
|
PC 7
|
PC 8
|
Flowering date
|
0.79*
|
-0.11
|
0.08
|
0.2
|
0.07
|
-0.31
|
0.31
|
-0.18
|
Maturity date
|
0.84*
|
-0.09
|
0.15
|
0.18
|
0.05
|
-0.21
|
0.24
|
-0.18
|
Plant height (cm)
|
0.68*
|
-0.14
|
-0.32
|
-0.17
|
-0.03
|
0.25
|
-0.01
|
0.27
|
Number of Tiller at 60 days
|
-0.15
|
0.03
|
0.26
|
0.03
|
-0.12
|
-0.26
|
0.58*
|
0.39
|
Panicle number/m2
|
-0.19
|
0.1
|
0.15
|
0.42
|
0.17
|
0.16
|
0.11
|
0.64*
|
Yield (g)
|
0.12
|
0.64*
|
0.3
|
0.21
|
0.41
|
0.2
|
0.14
|
0
|
Panicle length (cm)
|
0.39
|
0.43
|
0.24
|
0.04
|
-0.18
|
0.35
|
-0.07
|
-0.15
|
Panicle exsertion
|
-0.09
|
-0.06
|
-0.13
|
-0.54
|
0.64*
|
0.11
|
-0.1
|
-0.16
|
Plant vigour
|
-0.32
|
0.15
|
0.17
|
0.38
|
0.22
|
-0.58*
|
0.08
|
-0.29
|
Panicle shattering
|
0.02
|
0.69*
|
-0.57
|
0.37
|
-0.12
|
0.02
|
-0.07
|
-0.06
|
Panicle threshability
|
0.02
|
0.69*
|
-0.57
|
0.37
|
-0.12
|
0.02
|
-0.07
|
-0.06
|
Hairnes
|
-0.26
|
-0.41
|
0.2
|
0.35
|
0.46
|
-0.1
|
-0.25
|
0.01
|
Awning
|
0.14
|
-0.31
|
0.19
|
0.52*
|
0.32
|
0.27
|
-0.23
|
0.05
|
Primary branch panicle
|
0.77*
|
0.15
|
-0.04
|
-0.09
|
0.34
|
-0.1
|
-0.22
|
-0.05
|
Secondary branch panicle
|
0.71*
|
0.24
|
0.26
|
-0.12
|
0.06
|
-0.1
|
-0.2
|
0.28
|
Leaf length (cm)
|
0.77*
|
0.01
|
0.41
|
-0.02
|
-0.24
|
0.05
|
-0.04
|
-0.01
|
Leaf width (cm)
|
-0.06
|
0.1
|
-0.1
|
0.03
|
0.47
|
0.5
|
0.59*
|
-0.2
|
Flag leaf angle
|
0.37
|
-0.60*
|
-0.39
|
0.29
|
0.03
|
0.24
|
0.02
|
0.06
|
Base tiller coloration
|
-0.02
|
-0.52*
|
-0.06
|
0.5
|
-0.25
|
0.18
|
-0.05
|
-0.2
|
Grain length (mm)
|
-0.19
|
0.41
|
0.49
|
0
|
0.15
|
-0.03
|
-0.3
|
0.08
|
Grain width (mm)
|
0.14
|
-0.05
|
-0.61*
|
-0.19
|
0.27
|
-0.25
|
0.17
|
0.18
|
1000grain weight (g)
|
-0.2
|
0.04
|
0.45
|
-0.15
|
-0.24
|
0.35
|
0.22
|
-0.2
|
Eigen value
|
4.13
|
2.77
|
2.36
|
1.83
|
1.66
|
1.43
|
1.27
|
1.09
|
% variance
|
18.8
|
12.57
|
10.71
|
8.33
|
7.55
|
6.5
|
5.76
|
4.93
|
Cumulative % variance
|
18.8
|
31.36
|
42.07
|
50.4
|
57.9
|
64.44
|
70.2
|
75.1
|
*component contributors; PC: Principal component
Furthermore, 48 rice genotypes were delineated into nine distinct clusters using the FASTCLUS clustering procedure (Table 10). Clusters I–IX contained 8, 2, 9, 2, 1, 9, 10, 6, and 1 varieties, respectively. Genotypes in cluster II (19 and 2) out yielded the checks with the highest yield (4,181 g) and longest panicle (30.06 cm), while genotypes in cluster VI (6, 27, 32, 34, 37, 39, 40, 44, and 46) showed the lowest grain yield (3,689 g). Compared with other genotypes, those in cluster IV (4 and 45) were early in flowering (by 85 days) and reaching 70% physiological maturity (by 114 days). The genotype in cluster V (26) showed the highest plant height at maturity. Genotypes in clusters I and IX (1, 18, 22, 24, 25, 30, 35, 36, and 48) showed the highest tiller number, while the accession in cluster V (26) showed the lowest tiller number and panicle exertion. Panicle number per square meter was the highest in cluster III genotypes (3, 14, 16, 21, 28, 38, 41, 43, and 47) and lowest in cluster IV genotypes (4 and 45). Genotypes in clusters IV (4 and 45) and V (26) showed the lowest plant vigor, and together with the genotype in cluster IX (3), the lowest panicle shattering. The genotype in cluster V (26) showed greater panicle threshability than those in cluster II (19 and 2). Genotypes in clusters VII and IX (7, 8, 9, 10, 11, 15, 20, 24, 29, 31, and 42) showed pronounced hairiness.
Table 10: Mean and standard of deviation of characters that separate the 48 rice genotypes into nine distinct clusters using the FASTCLUS clustering procedure.
Character (Group)
|
I
|
II
|
III
|
IV
|
V
|
VI
|
VII
|
VIII
|
IX
|
|
|
|
|
1, 18, 22
|
19, 2
|
14, 16, 21
|
4, 45
|
26
|
6, 27, 32
|
7, 8, 9, 10
|
5, 12, 13
|
24
|
Min
|
Max
|
Diff
|
|
25, 30, 35
|
|
28, 3, 38
|
|
|
34, 37, 39,
|
11, 15, 20
|
17, 23, 33
|
|
|
|
|
|
36, 48
|
|
41, 43, 47
|
|
|
40, 44, 46
|
29, 31, 42
|
|
|
|
|
|
Flowering days
|
90(2.6)
|
87(0.4)
|
90(4.4)
|
85(0.0)
|
87(8.9)
|
91(4.9)
|
89(4.9)
|
87(3.9)
|
92(2.7)
|
85
|
92
|
7
|
Maturity days
|
119(3.1)
|
117(1.3)
|
120(3.2)
|
114(0.0)
|
118(8.9)
|
120(4.4)
|
119(3.6)
|
118(2.1)
|
123(0.0)
|
114
|
123
|
9
|
Plant height (cm)
|
97(7.7)
|
94(1.9)
|
102(7.0)
|
108(0.0)
|
113(15.1)
|
101(11.1)
|
100(7.7)
|
102(4.7)
|
93(0.0)
|
93
|
113
|
20
|
Number of tiller
|
13(1.5)
|
12(0.8)
|
12(0.9)
|
12(0.0)
|
11(0.4)
|
12(0.7)
|
12(0.5)
|
12(1.0)
|
13(0.0)
|
11
|
13
|
2
|
Panicle/m2
|
198(8.8)
|
190(0.3)
|
203(4.5)
|
181(0.0)
|
194(3.1)
|
198(15.4)
|
200(9.3)
|
199(7.2)
|
200(0.0)
|
181
|
203
|
22
|
Yield (gms)
|
3881(35.9)
|
4181(23.3)
|
3772(41.2)
|
3803(0.0)
|
380889.0)
|
3689(27.7)
|
3963(50.4)
|
33965(51.5)
|
4094(0.0)
|
3689
|
4181
|
492
|
Panicle length
|
25.43(1.0)
|
30.06(5.5)
|
25.72(0.9)
|
23.36(0.0)
|
26.86(3.2)
|
26.04(0.9)
|
25.63(1.1)
|
25.96(0.5)
|
26.14(0.0)
|
23.36
|
30.06
|
6.7
|
Panicle Exertion
|
6(0.6)
|
6(0.0)
|
6(0.5)
|
6(0.0)
|
5(0.8)
|
6(0.4)
|
6(0.5)
|
6(0.5)
|
6(0.0)
|
5
|
6
|
1
|
Plant vigor
|
3(0.5)
|
3(0.2)
|
3(0.4)
|
2(0.0)
|
2(0.1)
|
3(0.3)
|
3(0.4)
|
3(0.3)
|
3(0.0)
|
2
|
3
|
1
|
Panicle Shatering
|
4(0.4)
|
4(1.0)
|
4(0.5)
|
3(0.0)
|
3(0.1)
|
4(0.6)
|
4(0.8)
|
4(0.7)
|
3(0.0)
|
3
|
4
|
1
|
Panicle Threshability
|
5(1.5)
|
4(0.5)
|
5(1.7)
|
5(0.0)
|
6(0.9)
|
5(1.0)
|
5(1.0)
|
6(1.6)
|
5(0.0)
|
4
|
6
|
2
|
Hairness
|
2(0.3)
|
2(0.7)
|
2(0.8)
|
2(0.0)
|
2(0.0)
|
2(0.4)
|
3(0.9)
|
2(0.0)
|
3(0.0)
|
2
|
3
|
1
|
Awning
|
0(0.0)
|
0(0.0)
|
0(0.0)
|
0(0.0)
|
0(0.0)
|
0(0.3)
|
1(1.6)
|
0(0.0)
|
0(0.0)
|
0
|
1
|
1
|
Primary branch panicles
|
10(0.8)
|
10(0.3)
|
10(0.6)
|
9(0.0)
|
10(0.7)
|
10(0.8)
|
9(0.9)
|
10(0.7)
|
10(0.0)
|
9
|
10
|
1
|
Secondary branch panicles
|
20(2.9)
|
20(1.3)
|
19(2.0)
|
15(0.0)
|
21(2.5)
|
20(2.4)
|
19(2.4)
|
21(1.5)
|
21(0.0)
|
15
|
21
|
6
|
Leaf length (cm)
|
28.91(1.6)
|
27.81(0.3)
|
28.68(2.1)
|
26.59(0.0)
|
29.91(5.4)
|
29.45(2.2)
|
29.08(1.2)
|
29.57(1.5)
|
29.49(0.0)
|
26.59
|
29.91
|
3.32
|
Leaf width (cm)
|
1.03(0.0)
|
1.11(0.1)
|
1.07(0.1)
|
1.04(0.0)
|
0.93(0.0)
|
1.02(0.1)
|
1.06(0.0)
|
1.07(0.0)
|
1.08(0.0)
|
0.93
|
1.11
|
0.18
|
Flag Angle
|
1(0.1)
|
2(1.4)
|
2(1.0)
|
3(0.0)
|
2(0.7)
|
2(0.2)
|
2(0.7)
|
1(0.2)
|
1(0.0)
|
1
|
3
|
2
|
Base tiller coloration
|
1(0.8)
|
1(0.0)
|
1(0.8)
|
3(0.0)
|
2(1.8)
|
1(1.0)
|
2(1.0)
|
1(0.9)
|
1(0.0)
|
1
|
3
|
2
|
Grain length (mm)
|
8.73(0.2)
|
8.82(0.2)
|
8.74(0.5)
|
8(0.0)
|
8.34(0.1)
|
9.04(0.4)
|
8.94(0.2)
|
9.05(0.4)
|
8.77(0.0)
|
8
|
9.05
|
1.05
|
Grain width (mm)
|
2.37(0.1)
|
2.31(0.0)
|
2.34(0.1)
|
2.59(0.0)
|
2.23(0.1)
|
2.36(0.1)
|
2.3(0.1)
|
2.34(0.1)
|
2.27(0.0)
|
2.23
|
2.59
|
0.36
|
1000gwth (gms)
|
23(0.6)
|
23(0.1)
|
24(0.7)
|
23(0.0)
|
24(0.2)
|
23(1.1)
|
24(0.7)
|
24(0.8)
|
21(0.0)
|
21
|
24
|
3
|
Genotypes in cluster VII (7, 8, 9, 10, 11, 15, 20, 29, 31, and 42) showed prominent awnings, which were absent in other clusters. Genotypes in clusters IV (4, 45) and VII (7, 8, 9, 10, 11, 15, 20, 29, 31, and 42) showed fewer primary branch panicles (9) than those in other clusters (10). The highest number of secondary branch panicles (21) was found in varieties in clusters V (26), VIII (5, 12, 13, 17, 23, and 33), and IX (24), whereas genotypes in other cluster produced only 15–20 secondary branch panicles. The genotype in cluster V (26) produced the longest leaf (30cm), whereas genotypes in cluster IV (4 and 45) showed the shortest leaf (25.6cm). Genotypes in clusters II (19 and 2) showed greater leaf width (1.1cm) than the genotype in cluster V (26) (0.93cm). Genotypes in cluster IV (4 and 45) showed the largest flag leaf angle and the most prominent base tiller coloration. Genotypes in nearly all nine clusters showed no significant differences in grain length (8–9 cm) and grain width (2.3–2.6 cm). However, genotype 24 in cluster IX recorded the lowest 1,000-grain weight (21.0g) compared with genotypes in other clusters (23 and 24g).
Marker performance and characterization
Of the 50 SSR markers used to genotype the 48 rice genotypes,10 were polymorphic (Table 11). The study showed that makers used generated 49 alleles with an average of 4.9 alleles per marker. Alleles per marker ranged between 3 and 8 alleles. The highest number of alleles was observed with RM125 (Na = 8 alleles) while the least number of alleles were observed with EM433, RM494, and RM514 (NA = 3 alleles). The markers’ ability to detect heterozygosity varied from marker to marker, RM433 detecting the highest heterozygosity (H = 0.93) and RM495 detecting the least heterozygosity (H = 0.02) among the samples evaluated. The polymorphic information content also varied among markers. RM154 had the highest PIC while the PIC was observed with RM162.
Genetic diversity and structure among rice samples
Structure analysis revealed a peak at ΔK = 44.22 corresponding to K=2 (Figure 5a). This implied a two-substructure level with admixtures among the studied accessions. It was observed that the two parents did not fall within the same genetic structure, likewise the checks used in the study. A total of 16 samples comprising, 8 intraspecific, 6 interspecific, and 2 checks make the first genetic structure (Q1) while a total of 17, comprising majorly the interspecific samples (16) and a parent (IR64) make up the second genetic structure (Q2). Admixture categories comprised of 2 intraspecific, 11 interspecific, 1 check (FKR54), and 1 parent (TOG5681) (Figure 5b).
The study showed more alleles observed within the interspecific varieties than the intraspecific rice genotypes. Observed heterozygosity was lesser than expected in both genotype groups, although higher diversity was observed in the interspecific genotypes than the intraspecific genotypes. However, the fixation index was lower in the interspecific genotypes when compared to the intraspecific genotypes (Table 11). Analysis of molecular variance revealed that within-group variation was higher than variation observed between groups (Table 12).
Table 11. Population diversity among sample rice varieties.
Population
|
Na
|
Ne
|
I
|
Ho
|
He
|
F
|
Intraspecific
|
|
|
|
|
|
|
|
Mean
|
3.40
|
2.22
|
0.88
|
0.46
|
0.53
|
0.19
|
|
SE
|
0.48
|
0.22
|
0.11
|
0.13
|
0.05
|
0.22
|
Interspecific
|
|
|
|
|
|
|
|
Mean
|
3.80
|
2.26
|
0.90
|
0.45
|
0.52
|
0.17
|
|
SE
|
0.47
|
0.23
|
0.10
|
0.12
|
0.05
|
0.22
|
|
|
|
|
|
|
|
|
Total
|
Mean
|
3.60
|
2.24
|
0.89
|
0.45
|
0.53
|
0.18
|
|
SE
|
0.33
|
0.16
|
0.07
|
0.09
|
0.04
|
0.15
|
Na: number of alleles; Ne: number of effective alleles; I: Shannon information’s index; Ho: Observed heterozygosity; He: Expected heterozygosity; F: Fixation index
Table 12. Analysis of Molecular Variance.
Source
|
df
|
MS
|
Est. Var.
|
%Pol
|
Among Pops
|
1
|
16.397
|
0.646
|
9%
|
Within Pops
|
41
|
6.480
|
6.480
|
91%
|
Total
|
42
|
|
7.126
|
100%
|
MS; mean square; Est Var: estimated variance explained.
Clustering of rice genotypes
The dendrogram of 43 genotypes, their two parents, and three checks resulted in five clustered groups and one of the parents as an outgroup (TOG 5681) to the clusters at a similarity index of 0.49. The first cluster comprised of two intraspecific genotypes (1,3), the second cluster encompasses a majority of the genotypes distributed into four subclusters which include cluster IIA comprising of three intraspecific genotypes (2,4,7), cluster IIB comprised of six genotypes that are both intraspecific and interspecific (5, 6, 15, 16, 17, 19), likewise cluster IIC comprised of twenty genotypes (8, 9, 10,11, 18, 24, 28, 36, 40, 35, 37, 38, 39, 27, 23, 45, 30, 33, 34, 12) while are all interspecific genotypes except genotype 45 which represents one of the parents, IR64,while the last subcluster, IID, comprised of three genotypes (20, 29, 42) that are interspecific in nature. The third cluster is composed of four interspecific genotypes (13, 14, 25, 26). The fourth cluster is comprised of six genotypes (21, 32, 22, 31,46, 48) that are both interspecific and checks. The fifth cluster is composed of the remaining three genotypes (41, 47, 43) which represent an interspecific genotype and two checks (Figure 6).