Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice
Abstract
:1. Introduction
2. Material and Methods
2.1. Seed Material
2.2. Phenotyping of Germination Rate and Early Seedling Growth Parameters in the Germplasm Lines
2.3. Genomic DNA Isolation, PCR Analysis and Marker Selection
2.4. Molecular Data Analysis
3. Results
3.1. Phenotyping for Germination Rate and Early Seedling Growth Parameters in the Target Population
3.2. Principal Component and Association Analyses
3.3. Genetic Diversity Parameters’ Analysis
3.4. Population Genetic Structure Analysis
3.5. Analysis of Molecular Variance (AMOVA) and LD Decay Plot
3.6. Relatedness among the Germplasm Lines through Principal Coordinates and Cluster Analyses
3.7. Association of Marker Alleles with Germination Rate and Early Seedling Growth Parameters in Rice
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sl. No. | Accession No./ Vernacular Name of the Germplasm Line | Rate of Shoot Growth (RSG) | Relative Growth Rate (RGR) | Absolute Growth Rate (AGR) | Mean Germination Rate (MGR) | Inferred Ancestry Value at K = 4 | Germplasm Lines with High Seedling Growth Parameters | ||||
---|---|---|---|---|---|---|---|---|---|---|---|
Q1 | Q2 | Q3 | Q4 | Group | |||||||
1 | AC. 5993 | 0.317 | 0.347 | 0.577 | 0.182 | 0.007 | 0.004 | 0.985 | 0.004 | SP3 | RGR |
2 | AC. 6221 | 0.667 | 0.105 | 1.283 | 0.209 | 0.004 | 0.009 | 0.984 | 0.003 | SP3 | RGR |
3 | AC. 6183 | 0.520 | 0.186 | 2.137 | 0.210 | 0.003 | 0.081 | 0.913 | 0.003 | SP3 | RGR, AGR |
4 | AC. 6170 | 0.577 | 0.108 | 1.023 | 0.202 | 0.002 | 0.002 | 0.993 | 0.002 | SP3 | |
5 | AC. 6023 | 0.947 | 0.126 | 2.017 | 0.182 | 0.009 | 0.015 | 0.973 | 0.002 | SP3 | AGR |
6 | AC. 6172 | 0.440 | 0.261 | 1.040 | 0.213 | 0.007 | 0.042 | 0.949 | 0.002 | SP3 | |
7 | AC. 6027 | 1.017 | 0.241 | 1.570 | 0.224 | 0.002 | 0.002 | 0.013 | 0.982 | SP4 | RSG, MGR |
8 | AC. 6007 | 0.880 | 0.034 | 2.053 | 0.195 | 0.002 | 0.003 | 0.993 | 0.002 | SP3 | AGR |
9 | AC. 9006 | 1.227 | 0.120 | 2.063 | 0.284 | 0.005 | 0.018 | 0.964 | 0.012 | SP3 | RSG, AGR, MGR |
10 | AC. 9021 | 1.099 | 0.146 | 1.339 | 0.279 | 0.059 | 0.021 | 0.914 | 0.006 | SP3 | RSG, MGR |
11 | AC. 9028 | 1.373 | 0.114 | 2.297 | 0.305 | 0.008 | 0.105 | 0.884 | 0.004 | SP3 | RSG, AGR, MGR |
12 | AC. 9030 | 1.767 | 0.239 | 2.293 | 0.267 | 0.006 | 0.006 | 0.987 | 0.001 | SP3 | RSG, RGR, AGR, MGR |
13 | AC. 9035 | 1.800 | 0.113 | 2.717 | 0.283 | 0.01 | 0.004 | 0.968 | 0.019 | SP3 | RSG, AGR, MGR |
14 | AC. 9038 | 1.623 | 0.276 | 2.527 | 0.273 | 0.013 | 0.002 | 0.983 | 0.002 | SP3 | RSG, RGR, AGR, MGR |
15 | AC. 9043 | 1.363 | 0.221 | 1.643 | 0.309 | 0.012 | 0.002 | 0.984 | 0.002 | SP3 | RSG, RGR, MGR |
16 | AC. 9044 | 1.103 | 0.272 | 2.350 | 0.320 | 0.003 | 0.003 | 0.988 | 0.006 | SP3 | RSG, RGR, AGR, MGR |
17 | AC. 20920 | 1.120 | 0.039 | 2.073 | 0.219 | 0.037 | 0.004 | 0.954 | 0.006 | SP3 | RSG, AGR |
18 | AC. 20907 | 0.523 | 0.066 | 0.790 | 0.225 | 0.013 | 0.002 | 0.984 | 0.001 | SP3 | |
19 | AC. 20845 | 1.030 | 0.101 | 1.540 | 0.227 | 0.487 | 0.023 | 0.489 | 0.001 | Admix | RSG |
20 | AC. 20770 | 1.207 | 0.049 | 1.493 | 0.243 | 0.015 | 0.004 | 0.973 | 0.008 | SP3 | RSG |
21 | AC. 20627 | 0.700 | 0.013 | 0.927 | 0.241 | 0.402 | 0.002 | 0.595 | 0.001 | Admix | |
22 | AC. 20686 | 0.203 | 0.159 | 0.350 | 0.250 | 0.282 | 0.003 | 0.714 | 0.002 | Admix | |
23 | AC. 20664 | 0.290 | 0.080 | 0.510 | 0.232 | 0.616 | 0.01 | 0.372 | 0.002 | Admix | |
24 | AC. 20614 | 0.193 | 0.148 | 0.513 | 0.237 | 0.558 | 0.001 | 0.437 | 0.004 | Admix | |
25 | Jhagrikartik | 0.337 | 0.096 | 1.307 | 0.232 | 0.012 | 0.009 | 0.977 | 0.002 | SP3 | |
26 | Dadghani | 0.340 | 0.096 | 0.450 | 0.259 | 0.021 | 0.006 | 0.969 | 0.004 | SP3 | MGR |
27 | Shayam | 0.473 | 0.070 | 1.283 | 0.277 | 0.003 | 0.002 | 0.004 | 0.991 | SP4 | MGR |
28 | Basumati | 0.663 | 0.066 | 0.953 | 0.277 | 0.006 | 0.005 | 0.116 | 0.873 | SP4 | MGR |
29 | Bharati | 1.047 | 0.183 | 0.873 | 0.230 | 0.253 | 0.001 | 0.742 | 0.004 | Admix | RSG, RGR |
30 | Joha | 0.280 | 0.183 | 0.500 | 0.209 | 0.033 | 0.002 | 0.962 | 0.002 | SP3 | RGR |
31 | Adira-1 | 0.887 | 0.069 | 1.117 | 0.232 | 0.026 | 0.03 | 0.57 | 0.374 | Admix | |
32 | Adira-2 | 0.890 | 0.065 | 1.643 | 0.242 | 0.005 | 0.002 | 0.991 | 0.002 | SP3 | |
33 | Adira-3 | 0.840 | 0.109 | 1.373 | 0.227 | 0.173 | 0.005 | 0.413 | 0.409 | Admix | |
34 | PK6 | 0.620 | 0.157 | 1.083 | 0.204 | 0.002 | 0.004 | 0.977 | 0.017 | SP3 | RGR |
35 | Vachaw | 0.413 | 0.038 | 0.877 | 0.221 | 0.099 | 0.002 | 0.855 | 0.044 | SP3 | |
36 | Kozhivalan | 0.527 | 0.184 | 0.620 | 0.224 | 0.005 | 0.003 | 0.992 | 0.001 | Admix | RGR |
37 | Marathondi | 1.067 | 0.057 | 1.427 | 0.210 | 0.441 | 0.056 | 0.014 | 0.489 | Admix | RSG, AGR |
38 | Ezhoml-2 | 0.677 | 0.257 | 0.920 | 0.252 | 0.073 | 0.001 | 0.924 | 0.002 | SP3 | RGR, MGR |
39 | Jyothi | 0.737 | 0.251 | 1.160 | 0.269 | 0.009 | 0.001 | 0.989 | 0.002 | SP3 | RGR, MGR |
40 | Kantakopura | 0.980 | 0.121 | 1.427 | 0.227 | 0.312 | 0.002 | 0.684 | 0.002 | Admix | |
41 | Kantakaamala | 0.370 | 0.082 | 1.010 | 0.206 | 0.478 | 0.178 | 0.114 | 0.23 | Admix | |
42 | Kapanthi | 1.513 | 0.066 | 2.190 | 0.224 | 0.234 | 0.35 | 0.055 | 0.361 | Admix | AGR |
43 | Karpurkanti | 0.707 | 0.068 | 1.110 | 0.208 | 0.093 | 0.001 | 0.001 | 0.905 | SP4 | |
44 | Kathidhan | 0.447 | 0.089 | 0.867 | 0.204 | 0.423 | 0.112 | 0.461 | 0.005 | Admix | |
45 | Kundadhan | 0.777 | 0.246 | 0.933 | 0.173 | 0.897 | 0.013 | 0.088 | 0.003 | SP1 | RGR |
46 | Champaeisiali | 0.947 | 0.104 | 2.060 | 0.224 | 0.996 | 0.001 | 0.002 | 0.001 | SP2 | AGR |
47 | Latamahu | 0.323 | 0.221 | 1.153 | 0.191 | 0.779 | 0.009 | 0.208 | 0.003 | SP1 | RGR |
48 | Latachaunri | 0.237 | 0.197 | 0.653 | 0.212 | 0.705 | 0.011 | 0.281 | 0.003 | Admix | |
49 | AC. 10608 | 0.850 | 0.121 | 1.290 | 0.200 | 0.014 | 0.006 | 0.979 | 0.001 | SP3 | AGR |
50 | AC. 10187 | 0.667 | 0.157 | 2.583 | 0.206 | 0.005 | 0.079 | 0.912 | 0.003 | SP3 | RGR, AGR |
51 | AC. 10162 | 0.890 | 0.073 | 1.957 | 0.182 | 0.04 | 0.043 | 0.893 | 0.023 | SP3 | |
52 | AC. 7282 | 0.990 | 0.075 | 1.917 | 0.212 | 0.002 | 0.001 | 0.002 | 0.995 | SP4 | MGR |
53 | AC. 7269 | 0.640 | 0.244 | 1.210 | 0.184 | 0.004 | 0.003 | 0.993 | 0.001 | SP3 | RGR |
54 | AC. 7134 | 0.690 | 0.233 | 1.377 | 0.182 | 0.058 | 0.01 | 0.727 | 0.205 | Admix | RGR |
55 | AC. 7008 | 0.700 | 0.191 | 1.360 | 0.182 | 0.042 | 0.002 | 0.955 | 0.001 | SP3 | RGR |
56 | AC. 9093 | 0.573 | 0.150 | 1.030 | 0.306 | 0.003 | 0.002 | 0.99 | 0.005 | SP3 | RGR, MGR |
57 | AC. 9090 | 0.797 | 0.147 | 1.273 | 0.288 | 0.032 | 0.006 | 0.945 | 0.018 | SP3 | MGR |
58 | AC. 9076A | 0.133 | 0.195 | 0.677 | 0.252 | 0.102 | 0.011 | 0.886 | 0.002 | SP3 | MGR |
59 | AC. 9065 | 0.883 | 0.121 | 1.153 | 0.302 | 0.012 | 0.005 | 0.921 | 0.062 | SP3 | RGR, MGR |
60 | AC. 9063 | 1.190 | 0.126 | 1.557 | 0.264 | 0.202 | 0.014 | 0.783 | 0.001 | Admix | RSG, MGR |
61 | AC. 9058 | 1.170 | 0.115 | 1.407 | 0.275 | 0.007 | 0.001 | 0.991 | 0.001 | SP3 | RSG, MGR |
62 | AC. 9053A | 1.057 | 0.013 | 1.197 | 0.255 | 0.009 | 0.155 | 0.823 | 0.013 | SP3 | RSG, MGR |
63 | AC. 9050 | 0.257 | 0.151 | 0.473 | 0.261 | 0.079 | 0.003 | 0.909 | 0.009 | SP3 | RGR |
64 | AC. 9005 | 1.109 | 0.077 | 1.912 | 0.293 | 0.01 | 0.005 | 0.981 | 0.003 | SP3 | RSG, MGR |
65 | AC. 20389 | 0.707 | 0.109 | 1.220 | 0.280 | 0.003 | 0.034 | 0.951 | 0.011 | SP3 | MGR |
66 | AC. 20371 | 1.193 | 0.100 | 1.540 | 0.307 | 0.041 | 0.006 | 0.952 | 0.001 | SP3 | RSG, AGR, MGR |
67 | AC. 20423 | 0.590 | 0.142 | 1.680 | 0.213 | 0.018 | 0.005 | 0.976 | 0.001 | SP3 | AGR |
68 | AC. 20362 | 1.130 | 0.100 | 1.187 | 0.286 | 0.008 | 0.017 | 0.968 | 0.007 | SP3 | RSG, AGR, MGR |
69 | AC. 20328 | 1.120 | 0.100 | 1.660 | 0.281 | 0.155 | 0.012 | 0.816 | 0.018 | SP3 | RSG, AGR, MGR |
70 | AC.20317 | 0.150 | 0.146 | 0.497 | 0.288 | 0.078 | 0.004 | 0.884 | 0.035 | SP3 | MGR |
71 | AC. 20282 | 1.150 | 0.094 | 2.033 | 0.251 | 0.172 | 0.12 | 0.695 | 0.013 | Admix | RSG, AGR, MGR |
72 | AC. 20246 | 0.893 | 0.123 | 1.297 | 0.266 | 0.084 | 0.047 | 0.775 | 0.094 | Admix | MGR |
73 | AC. 20347 | 0.693 | 0.130 | 1.257 | 0.224 | 0.008 | 0.048 | 0.942 | 0.002 | SP3 | |
74 | Palinadhan-1 | 0.660 | 0.075 | 0.927 | 0.236 | 0.039 | 0.267 | 0.284 | 0.411 | Admix | |
75 | Chatuimuchi | 0.527 | 0.142 | 1.190 | 0.266 | 0.001 | 0.001 | 0.001 | 0.996 | SP4 | MGR |
76 | Uttarbangalocal-9 | 0.107 | 0.159 | 0.307 | 0.236 | 0.114 | 0.124 | 0.76 | 0.002 | Admix | RGR |
77 | Gochi | 0.447 | 0.159 | 0.697 | 0.246 | 0.006 | 0.048 | 0.937 | 0.009 | SP3 | RGR |
78 | Sugandha-2 | 0.433 | 0.029 | 0.890 | 0.273 | 0.002 | 0.001 | 0.003 | 0.993 | SP4 | MGR |
79 | Jhingesal | 0.937 | 0.182 | 1.547 | 0.243 | 0.458 | 0.002 | 0.539 | 0.001 | Admix | RGR |
80 | Cheruvirippu | 0.503 | 0.084 | 0.803 | 0.228 | 0.088 | 0.004 | 0.906 | 0.002 | SP3 | |
81 | Mahamaga | 0.617 | 0.100 | 1.060 | 0.218 | 0.37 | 0.071 | 0.557 | 0.002 | Admix | |
82 | Jaya | 0.507 | 0.273 | 1.033 | 0.223 | 0.057 | 0.009 | 0.933 | 0.002 | SP3 | RGR |
83 | D1 | 0.483 | 0.241 | 0.840 | 0.198 | 0.028 | 0.057 | 0.887 | 0.028 | SP3 | RGR |
84 | PK21 | 1.613 | 0.059 | 2.400 | 0.231 | 0.152 | 0.031 | 0.814 | 0.002 | Admix | RSG, AGR |
85 | Gandhakasala | 0.670 | 0.091 | 1.390 | 0.227 | 0.106 | 0.004 | 0.002 | 0.888 | SP4 | |
86 | Sreyas | 0.707 | 0.064 | 1.373 | 0.220 | 0.071 | 0.003 | 0.923 | 0.004 | SP3 | |
87 | Gondiachampeisiali | 0.910 | 0.084 | 1.423 | 0.222 | 0.995 | 0.001 | 0.002 | 0.001 | SP1 | |
88 | Chinamal | 0.533 | 0.199 | 1.117 | 0.212 | 0.578 | 0.002 | 0.409 | 0.011 | Admix | RGR |
89 | Magra | 1.060 | 0.180 | 2.073 | 0.211 | 0.451 | 0.003 | 0.541 | 0.005 | Admix | RSG |
90 | Landi | 0.843 | 0.030 | 1.590 | 0.229 | 0.847 | 0.003 | 0.148 | 0.002 | SP1 | |
91 | Lalgundi | 0.600 | 0.143 | 1.443 | 0.224 | 0.956 | 0.017 | 0.022 | 0.005 | SP1 | RGR |
92 | Balisaralaktimachi | 0.977 | 0.141 | 2.170 | 0.227 | 0.976 | 0.007 | 0.014 | 0.003 | SP1 | |
93 | Laxmibilash | 0.377 | 0.259 | 0.650 | 0.256 | 0.416 | 0.006 | 0.013 | 0.565 | Admix | MGR |
94 | Kaniar | 0.843 | 0.051 | 1.250 | 0.225 | 0.579 | 0.014 | 0.394 | 0.012 | Admix | MGR |
95 | Kanakchampa | 0.457 | 0.308 | 1.190 | 0.179 | 0.756 | 0.008 | 0.223 | 0.014 | Admix | RGR |
96 | Magura-S | 1.350 | 0.246 | 2.097 | 0.189 | 0.862 | 0.003 | 0.043 | 0.092 | SP1 | RGR, AGR |
97 | AC. 44603 | 2.050 | 0.044 | 1.100 | 0.333 | 0.036 | 0.945 | 0.018 | 0.002 | SP2 | RSG, MGR |
98 | AC. 44585 | 0.750 | 0.064 | 0.611 | 0.333 | 0.004 | 0.978 | 0.006 | 0.013 | SP2 | MGR |
99 | AC. 44598 | 0.200 | 0.056 | 0.500 | 0.333 | 0.003 | 0.968 | 0.019 | 0.01 | SP2 | MGR |
100 | AC. 44592 | 1.517 | 0.047 | 0.883 | 0.333 | 0.002 | 0.982 | 0.002 | 0.015 | SP2 | RSG, MGR |
101 | AC. 44646 | 2.033 | 0.033 | 1.200 | 0.333 | 0.002 | 0.994 | 0.002 | 0.002 | SP2 | RSG, MGR |
102 | AC. 44604 | 1.717 | 0.037 | 0.622 | 0.333 | 0.003 | 0.951 | 0.029 | 0.017 | SP2 | RSG, MGR |
103 | AC. 44597 | 3.583 | 0.023 | 1.594 | 0.333 | 0.004 | 0.993 | 0.002 | 0.001 | SP2 | RSG, MGR |
104 | AC. 44638 | 3.433 | 0.030 | 2.006 | 0.333 | 0.001 | 0.284 | 0.001 | 0.714 | Admix | RSG, AGR, MGR |
105 | AC. 44595 | 2.283 | 0.023 | 0.856 | 0.333 | 0.003 | 0.977 | 0.008 | 0.012 | SP2 | RSG, MGR |
106 | AC. 44588 | 1.900 | 0.023 | 0.717 | 0.333 | 0.002 | 0.994 | 0.003 | 0.002 | SP2 | RSG, MGR |
107 | AC. 44591 | 3.100 | 0.025 | 1.144 | 0.333 | 0.002 | 0.995 | 0.003 | 0.001 | SP2 | RSG, MGR |
108 | AC. 44594 | 5.100 | 0.045 | 2.150 | 0.333 | 0.006 | 0.979 | 0.013 | 0.002 | SP2 | RSG, MGR |
109 | AC. 43737 | 4.850 | 0.027 | 2.617 | 0.293 | 0.002 | 0.991 | 0.003 | 0.003 | SP2 | RSG, AGR, MGR |
110 | AC. 43660 | 8.983 | 0.101 | 4.450 | 0.310 | 0.003 | 0.993 | 0.003 | 0.002 | SP2 | RSG, AGR, MGR |
111 | AC. 43732 | 3.683 | 0.051 | 2.089 | 0.323 | 0.002 | 0.995 | 0.002 | 0.001 | SP2 | RSG, AGR, MGR |
112 | AC. 43661 | 4.433 | 0.034 | 2.356 | 0.327 | 0.003 | 0.988 | 0.007 | 0.002 | SP2 | RSG, AGR, MGR |
113 | AC. 43738 | 3.467 | 0.032 | 1.556 | 0.301 | 0.004 | 0.991 | 0.002 | 0.003 | SP2 | RSG, AGR, MGR |
114 | AC. 43669 | 6.533 | 0.038 | 3.722 | 0.325 | 0.004 | 0.987 | 0.006 | 0.003 | SP2 | RSG, AGR, MGR |
115 | AC. 43663 | 2.483 | 0.075 | 1.689 | 0.417 | 0.002 | 0.994 | 0.002 | 0.003 | SP2 | RSG, AGR, MGR |
116 | AC. 43658 | 2.517 | 0.050 | 1.633 | 0.293 | 0.001 | 0.996 | 0.001 | 0.001 | SP2 | RSG, AGR, MGR |
117 | AC. 43662 | 4.567 | 0.034 | 2.250 | 0.290 | 0.002 | 0.96 | 0.004 | 0.034 | SP2 | RSG, AGR, MGR |
118 | AC. 43670 | 4.333 | 0.091 | 2.294 | 0.296 | 0.004 | 0.816 | 0.003 | 0.178 | SP2 | RSG, AGR, MGR |
119 | AC. 43675 | 6.650 | 0.054 | 3.828 | 0.310 | 0.002 | 0.98 | 0.003 | 0.014 | SP2 | RSG, AGR, MGR |
120 | AC. 43676 | 0.067 | 0.047 | 0.756 | 0.286 | 0.014 | 0.935 | 0.007 | 0.044 | SP2 | MGR |
121 | CR4034-77-56-1 | 0.692 | 0.173 | 0.825 | 0.189 | 0.996 | 0.001 | 0.002 | 0.001 | SP1 | RGR, MGR |
122 | CR4034-77-25-4 | 0.725 | 0.181 | 0.912 | 0.178 | 0.995 | 0.001 | 0.002 | 0.001 | SP1 | RGR, MGR |
123 | Jalamagna | 0.930 | 0.114 | 2.320 | 0.220 | 0.996 | 0.001 | 0.002 | 0.001 | SP1 | AGR, MGR |
124 | Panidhan | 0.900 | 0.081 | 1.390 | 0.201 | 0.996 | 0.001 | 0.002 | 0.001 | SP1 | |
CV % | 10.56 | 11.71 | 12.74 | 4.17 | |||||||
LSD5% | 0.145 | 0.051 | 0.232 | 0.089 |
Sl. No | Marker | No. of Alleles | Major Allele Frequency | Gene Diversity | Heterozygosity | PIC | Inbreeding Coefficient (f) |
---|---|---|---|---|---|---|---|
1 | RM5310 | 4 | 0.790 | 0.357 | 0.032 | 0.335 | 0.910 |
2 | RM582 | 4 | 0.718 | 0.454 | 0.032 | 0.422 | 0.930 |
3 | RM13335 | 4 | 0.577 | 0.525 | 0.008 | 0.430 | 0.985 |
4 | RM6275 | 4 | 0.730 | 0.436 | 0.056 | 0.402 | 0.871 |
5 | RM50 | 4 | 0.403 | 0.685 | 0.024 | 0.626 | 0.965 |
6 | RM85 | 4 | 0.431 | 0.669 | 0.121 | 0.608 | 0.821 |
7 | RM222 | 4 | 0.625 | 0.562 | 0.024 | 0.524 | 0.957 |
8 | RM247 | 5 | 0.500 | 0.594 | 0.065 | 0.515 | 0.892 |
9 | RM328 | 3 | 0.581 | 0.570 | 0.000 | 0.504 | 1.000 |
10 | RM337 | 6 | 0.431 | 0.667 | 0.113 | 0.609 | 0.832 |
11 | RM340 | 5 | 0.722 | 0.443 | 0.097 | 0.405 | 0.783 |
12 | RM470 | 5 | 0.464 | 0.689 | 0.839 | 0.643 | −0.213 |
13 | RM472 | 3 | 0.528 | 0.506 | 0.089 | 0.386 | 0.826 |
14 | RM506 | 3 | 0.694 | 0.450 | 0.129 | 0.383 | 0.715 |
15 | RM1812 | 3 | 0.444 | 0.604 | 0.000 | 0.519 | 1.000 |
16 | RM3701 | 4 | 0.677 | 0.481 | 0.492 | 0.425 | −0.019 |
17 | RM6947 | 3 | 0.871 | 0.231 | 0.000 | 0.215 | 1.000 |
18 | RM14978 | 3 | 0.419 | 0.637 | 0.000 | 0.560 | 1.000 |
19 | RM18776 | 3 | 0.851 | 0.260 | 0.024 | 0.236 | 0.908 |
20 | RM22034 | 3 | 0.919 | 0.150 | 0.000 | 0.143 | 1.000 |
21 | RM24161 | 4 | 0.540 | 0.613 | 0.129 | 0.552 | 0.791 |
22 | RM223 | 5 | 0.649 | 0.541 | 0.056 | 0.509 | 0.897 |
23 | RM440 | 5 | 0.403 | 0.695 | 0.266 | 0.641 | 0.620 |
24 | RM201 | 3 | 0.496 | 0.574 | 0.024 | 0.482 | 0.958 |
25 | RM216 | 4 | 0.528 | 0.629 | 0.121 | 0.574 | 0.809 |
26 | RM258 | 3 | 0.387 | 0.654 | 0.000 | 0.579 | 1.000 |
27 | RM286 | 4 | 0.464 | 0.631 | 0.113 | 0.560 | 0.823 |
28 | RM3735 | 4 | 0.339 | 0.722 | 0.960 | 0.670 | −0.325 |
29 | RM1347 | 3 | 0.516 | 0.565 | 0.000 | 0.472 | 1.000 |
30 | RM7571 | 3 | 0.706 | 0.445 | 0.008 | 0.388 | 0.982 |
31 | RM14723 | 4 | 0.508 | 0.634 | 0.194 | 0.573 | 0.697 |
32 | RM103 | 3 | 0.492 | 0.557 | 0.774 | 0.458 | −0.386 |
33 | RM315 | 3 | 0.871 | 0.228 | 0.000 | 0.209 | 1.000 |
34 | RM225 | 3 | 0.508 | 0.549 | 0.177 | 0.448 | 0.679 |
35 | RM486 | 3 | 0.649 | 0.481 | 0.105 | 0.398 | 0.783 |
36 | RM256 | 3 | 0.730 | 0.403 | 0.056 | 0.333 | 0.861 |
37 | RM1113 | 3 | 0.665 | 0.460 | 0.056 | 0.374 | 0.878 |
38 | RM3423 | 3 | 0.484 | 0.575 | 0.000 | 0.483 | 1.000 |
39 | RM6100 | 3 | 0.427 | 0.644 | 0.032 | 0.569 | 0.950 |
40 | RM590 | 3 | 0.718 | 0.441 | 0.065 | 0.395 | 0.855 |
41 | RM5793 | 3 | 0.629 | 0.531 | 0.016 | 0.471 | 0.970 |
42 | RM405 | 3 | 0.685 | 0.480 | 0.000 | 0.432 | 1.000 |
43 | RM547 | 5 | 0.488 | 0.570 | 0.161 | 0.477 | 0.719 |
44 | RM7364 | 5 | 0.633 | 0.561 | 0.161 | 0.529 | 0.714 |
45 | RM205 | 3 | 0.633 | 0.522 | 0.024 | 0.458 | 0.954 |
46 | RM167 | 4 | 0.714 | 0.452 | 0.097 | 0.412 | 0.787 |
47 | RM229 | 4 | 0.363 | 0.707 | 0.129 | 0.652 | 0.819 |
48 | RM20A | 3 | 0.637 | 0.523 | 0.016 | 0.463 | 0.969 |
49 | RM235 | 5 | 0.399 | 0.715 | 0.169 | 0.667 | 0.765 |
50 | RM7003 | 4 | 0.677 | 0.491 | 0.081 | 0.443 | 0.837 |
51 | RM5436 | 4 | 0.444 | 0.618 | 0.056 | 0.540 | 0.909 |
52 | RM25181 | 5 | 0.399 | 0.704 | 0.161 | 0.653 | 0.772 |
53 | RM469 | 3 | 0.633 | 0.514 | 0.040 | 0.444 | 0.922 |
54 | RM6547 | 3 | 0.871 | 0.233 | 0.016 | 0.220 | 0.931 |
55 | RM152 | 4 | 0.492 | 0.632 | 0.016 | 0.566 | 0.975 |
56 | RM148 | 2 | 0.669 | 0.443 | 0.081 | 0.345 | 0.819 |
57 | RM421 | 3 | 0.476 | 0.624 | 0.000 | 0.549 | 1.000 |
58 | RM2634 | 3 | 0.399 | 0.655 | 0.024 | 0.581 | 0.963 |
59 | RM248 | 4 | 0.335 | 0.734 | 0.113 | 0.685 | 0.847 |
60 | RM7179 | 5 | 0.331 | 0.763 | 0.347 | 0.724 | 0.548 |
61 | RM215 | 3 | 0.597 | 0.500 | 0.016 | 0.397 | 0.968 |
62 | RM324 | 4 | 0.556 | 0.624 | 0.153 | 0.579 | 0.756 |
63 | RM317 | 3 | 0.734 | 0.395 | 0.000 | 0.323 | 1.000 |
64 | RM174 | 3 | 0.524 | 0.612 | 0.065 | 0.543 | 0.895 |
65 | RM556 | 3 | 0.847 | 0.271 | 0.032 | 0.254 | 0.882 |
66 | RM257 | 4 | 0.395 | 0.662 | 0.226 | 0.592 | 0.661 |
67 | RM502 | 3 | 0.815 | 0.310 | 0.000 | 0.275 | 1.000 |
68 | RM331 | 4 | 0.468 | 0.672 | 0.056 | 0.619 | 0.917 |
69 | RM403 | 4 | 0.577 | 0.581 | 0.081 | 0.522 | 0.862 |
70 | RM309 | 3 | 0.698 | 0.458 | 0.040 | 0.403 | 0.913 |
71 | RM6641 | 3 | 0.565 | 0.585 | 0.000 | 0.520 | 1.000 |
72 | RM3 | 3 | 0.371 | 0.664 | 0.032 | 0.590 | 0.952 |
73 | RM594 | 3 | 0.585 | 0.558 | 0.008 | 0.487 | 0.986 |
74 | RM3392 | 4 | 0.488 | 0.617 | 0.105 | 0.545 | 0.831 |
75 | RM1278 | 3 | 0.774 | 0.372 | 0.065 | 0.337 | 0.828 |
76 | RM168 | 3 | 0.629 | 0.506 | 0.161 | 0.428 | 0.684 |
77 | RM3375 | 3 | 0.581 | 0.567 | 0.032 | 0.499 | 0.944 |
78 | RM282 | 3 | 0.734 | 0.426 | 0.000 | 0.387 | 1.000 |
79 | RM26632 | 4 | 0.367 | 0.701 | 0.153 | 0.645 | 0.783 |
80 | RM1341 | 3 | 0.593 | 0.546 | 0.024 | 0.472 | 0.956 |
81 | RM4112 | 3 | 0.504 | 0.615 | 0.153 | 0.542 | 0.753 |
82 | RM20377 | 4 | 0.762 | 0.382 | 0.081 | 0.338 | 0.790 |
83 | RM210 | 5 | 0.367 | 0.733 | 0.710 | 0.685 | 0.035 |
84 | RM218 | 4 | 0.597 | 0.574 | 0.032 | 0.522 | 0.944 |
85 | RM494 | 5 | 0.387 | 0.712 | 0.024 | 0.664 | 0.966 |
86 | RM336 | 5 | 0.387 | 0.706 | 0.089 | 0.655 | 0.875 |
87 | RM3475 | 4 | 0.452 | 0.662 | 0.040 | 0.600 | 0.940 |
88 | RM480 | 4 | 0.552 | 0.607 | 0.024 | 0.551 | 0.960 |
89 | RM566 | 4 | 0.452 | 0.650 | 0.016 | 0.585 | 0.975 |
90 | RM11701 | 3 | 0.653 | 0.464 | 0.000 | 0.370 | 1.000 |
91 | RM220 | 6 | 0.355 | 0.747 | 0.194 | 0.706 | 0.743 |
92 | RM488 | 6 | 0.310 | 0.753 | 0.202 | 0.711 | 0.734 |
93 | RM6374 | 6 | 0.327 | 0.772 | 0.073 | 0.737 | 0.907 |
94 | RM233 | 5 | 0.347 | 0.728 | 0.258 | 0.681 | 0.648 |
95 | RM112 | 3 | 0.879 | 0.216 | 0.000 | 0.199 | 1.000 |
96 | RM13600 | 4 | 0.480 | 0.663 | 0.097 | 0.608 | 0.855 |
97 | RM495 | 3 | 0.613 | 0.549 | 0.032 | 0.490 | 0.942 |
98 | RM493 | 7 | 0.274 | 0.817 | 0.573 | 0.792 | 0.303 |
99 | RM444 | 5 | 0.310 | 0.776 | 0.153 | 0.740 | 0.804 |
100 | RM468 | 3 | 0.778 | 0.369 | 0.024 | 0.338 | 0.935 |
101 | RM6054 | 3 | 0.927 | 0.137 | 0.016 | 0.133 | 0.883 |
102 | RM509 | 3 | 0.766 | 0.385 | 0.000 | 0.351 | 1.000 |
103 | RM5638 | 6 | 0.625 | 0.574 | 0.129 | 0.545 | 0.777 |
104 | RM8044 | 6 | 0.286 | 0.759 | 0.226 | 0.718 | 0.704 |
105 | RM8271 | 5 | 0.415 | 0.717 | 0.145 | 0.673 | 0.799 |
106 | RM171 | 4 | 0.500 | 0.640 | 0.056 | 0.580 | 0.912 |
107 | RM16686 | 3 | 0.403 | 0.656 | 0.000 | 0.582 | 1.000 |
108 | RM434 | 4 | 0.565 | 0.596 | 0.024 | 0.538 | 0.960 |
109 | RM6091 | 4 | 0.823 | 0.310 | 0.000 | 0.291 | 1.000 |
110 | RM209 | 4 | 0.540 | 0.613 | 0.000 | 0.552 | 1.000 |
111 | RM245 | 4 | 0.565 | 0.593 | 0.000 | 0.532 | 1.000 |
112 | RM1089 | 4 | 0.419 | 0.633 | 0.065 | 0.561 | 0.899 |
113 | RM228 | 4 | 0.637 | 0.533 | 0.185 | 0.481 | 0.654 |
114 | RM401 | 3 | 0.762 | 0.388 | 0.056 | 0.351 | 0.856 |
115 | RM11 | 3 | 0.464 | 0.588 | 0.008 | 0.499 | 0.986 |
116 | RM3351 | 3 | 0.597 | 0.511 | 0.000 | 0.415 | 1.000 |
117 | RM5749 | 3 | 0.585 | 0.505 | 0.024 | 0.399 | 0.952 |
118 | RM335 | 2 | 0.730 | 0.394 | 0.073 | 0.317 | 0.817 |
119 | RM144 | 3 | 0.593 | 0.512 | 0.169 | 0.416 | 0.672 |
120 | RM300 | 3 | 0.855 | 0.258 | 0.016 | 0.240 | 0.938 |
121 | RM1132 | 4 | 0.379 | 0.719 | 0.032 | 0.668 | 0.955 |
122 | RM400 | 4 | 0.363 | 0.717 | 0.468 | 0.665 | 0.352 |
123 | RM471 | 3 | 0.790 | 0.350 | 0.000 | 0.318 | 1.000 |
124 | RM243 | 3 | 0.573 | 0.553 | 0.016 | 0.474 | 0.971 |
125 | RM467 | 3 | 0.573 | 0.566 | 0.000 | 0.494 | 1.000 |
126 | RM564 | 4 | 0.452 | 0.610 | 0.097 | 0.530 | 0.842 |
127 | RM8007 | 3 | 0.774 | 0.375 | 0.000 | 0.344 | 1.000 |
128 | RM441 | 4 | 0.476 | 0.624 | 0.581 | 0.553 | 0.073 |
129 | RM518 | 3 | 0.540 | 0.537 | 0.000 | 0.436 | 1.000 |
130 | RM253 | 4 | 0.536 | 0.602 | 0.081 | 0.534 | 0.867 |
131 | RM274 | 3 | 0.677 | 0.467 | 0.000 | 0.399 | 1.000 |
132 | RM242 | 4 | 0.573 | 0.591 | 0.016 | 0.535 | 0.973 |
133 | RM3231 | 4 | 0.343 | 0.702 | 0.661 | 0.643 | 0.063 |
134 | RM5687 | 4 | 0.411 | 0.693 | 0.645 | 0.637 | 0.073 |
135 | RM5626 | 3 | 0.581 | 0.512 | 0.742 | 0.410 | −0.446 |
136 | RM452 | 3 | 0.460 | 0.626 | 0.000 | 0.548 | 1.000 |
137 | RM14960 | 2 | 0.976 | 0.047 | 0.000 | 0.046 | 1.000 |
138 | RM558 | 2 | 0.968 | 0.062 | 0.000 | 0.060 | 1.000 |
139 | RM406 | 2 | 0.968 | 0.062 | 0.000 | 0.060 | 1.000 |
140 | RM522 | 2 | 0.976 | 0.047 | 0.000 | 0.046 | 1.000 |
141 | RM10124 | 2 | 0.968 | 0.062 | 0.000 | 0.060 | 1.000 |
142 | RM181 | 3 | 0.919 | 0.151 | 0.000 | 0.146 | 1.000 |
143 | RM175 | 3 | 0.887 | 0.207 | 0.000 | 0.197 | 1.000 |
Mean | 3.65 | 0.582 | 0.530 | 0.109 | 0.474 | 0.796 |
Sources of Variation | AMOVA for the Four Subpopulations at K = 4 | |||
---|---|---|---|---|
df. | Mean Sum of Squares | Estimated Variance | Percentage Variation | |
Among populations | 4 | 305.33 | 5.46 | 14 |
Among individuals (accessions) within population | 119 | 60.61 | 26.42 | 67 |
Within individuals (accessions) | 124 | 7.77 | 7.77 | 20 |
Total | 247 | 39.65 | 100 | |
F-Statistics | Value | p-value | ||
FST | 0.138 | |||
FIS | 0.773 | |||
FIT | 0.804 | |||
FST max. | 0.522 | |||
F’ST | 0.264 |
Traits | Marker | Chr # | Position | GLM | MLM | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Marker_F | Marker_p | q Value | Marker_R2 | F | p | q Value | Marker_R2 | ||||
RSG | RM337 | 8 | 27 | 27.20863 | 7.73E−07 | 7.34E−06 | 0.0892 | 16.54241 | 8.55E−05 | 0.001159 | 0.11592 |
RSG | RM22034 | 7 | 56 | 15.24579 | 1.56E−04 | 0.000573 | 0.05441 | 7.72005 | 0.00634 | 0.007529 | 0.0541 |
RSG | RM494 | 6 | 221 | 14.93372 | 1.81E−04 | 0.000573 | 0.05341 | 14.91786 | 1.83E−04 | 0.001159 | 0.10454 |
RGR | RM1812 | 11 | 44 | 10.65642 | 0.00143 | 0.002236 | 0.05988 | 9.21126 | 0.00295 | 0.005605 | 0.07091 |
AGR | RM337 | 8 | 27 | 16.07491 | 1.06E−04 | 0.000504 | 0.1088 | 9.56844 | 0.00246 | 0.005193 | 0.07805 |
AGR | RM7179 | 6 | 159 | 10.79532 | 0.00133 | 0.002236 | 0.07601 | 10.27457 | 0.00173 | 0.005178 | 0.08381 |
AGR | RM494 | 6 | 221 | 7.88757 | 0.00581 | 0.006494 | 0.0568 | 9.96554 | 0.00202 | 0.005178 | 0.08129 |
AGR | RM16686 | 4 | 300 | 10.75337 | 0.00136 | 0.002236 | 0.07574 | 11.68419 | 8.62E−04 | 0.003276 | 0.09531 |
MGR | RM3735 | 4 | 80 | 31.13489 | 1.52E−07 | 2.89E−06 | 0.10146 | 15.01011 | 1.75E−04 | 0.001159 | 0.1052 |
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Share and Cite
Mohanty, S.P.; Nayak, D.K.; Sanghamitra, P.; Barik, S.R.; Pandit, E.; Behera, A.; Pani, D.R.; Mohapatra, S.; Raj K. R., R.; Pradhan, K.C.; et al. Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice. Genes 2023, 14, 902. https://doi.org/10.3390/genes14040902
Mohanty SP, Nayak DK, Sanghamitra P, Barik SR, Pandit E, Behera A, Pani DR, Mohapatra S, Raj K. R. R, Pradhan KC, et al. Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice. Genes. 2023; 14(4):902. https://doi.org/10.3390/genes14040902
Chicago/Turabian StyleMohanty, Shakti Prakash, Deepak Kumar Nayak, Priyadarsini Sanghamitra, Saumya Ranjan Barik, Elssa Pandit, Abhisarika Behera, Dipti Ranjan Pani, Shibani Mohapatra, Reshmi Raj K. R., Kartik Chandra Pradhan, and et al. 2023. "Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice" Genes 14, no. 4: 902. https://doi.org/10.3390/genes14040902