Chin J Plant Ecol ›› 2006, Vol. 30 ›› Issue (1): 147-156.DOI: 10.17521/cjpe.2006.0021
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WANG Ying, KANG Ming, HUANG Hong-Wen*()
Received:
2005-01-06
Accepted:
2005-04-10
Online:
2006-01-06
Published:
2006-01-30
Contact:
HUANG Hong-Wen
WANG Ying, KANG Ming, HUANG Hong-Wen. SUBPOPULATION GENETIC STRUCTURE IN A PANMICTIC POPULATION AS REVEALED BY MOLECULAR MARKERS: A CASE STUDY OF CASTANEA SEQUINII USING SSR MARKERS[J]. Chin J Plant Ecol, 2006, 30(1): 147-156.
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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2006.0021
引物编号 Locus code | 片段大小范围 Size range (bp) | 等位基因数 No.of alleles | 预期杂合度 He | 观察杂合度 Ho | 近交系数 FIS | 居群分化系数 FST | 哈迪-温格平衡检验 Hardy-weinberg equilibrium test |
---|---|---|---|---|---|---|---|
CsCAT1 | 160~201 | 19 | 0.879 | 0.538 | 0.359 | 0.094 | NS |
CsCAT2 | 180~226 | 13 | 0.864 | 0.774 | 0.034 | 0.078 | NS |
CsCAT3 | 197~215 | 6 | 0.637 | 0.594 | -0.023 | 0.089 | NS |
CsCAT4 | 217~261 | 13 | 0.818 | 0.817 | -0.047 | 0.054 | NS |
CsCAT5 | 217~242 | 7 | 0.753 | 0.607 | 0.181 | 0.031 | NS |
CsCAT7 | 190~217 | 6 | 0.761 | 0.538 | 0.256 | 0.038 | NS |
CsCAT8 | 190~210 | 6 | 0.729 | 0.658 | 0.117 | 0.018 | NS |
CsCAT14 | 150~160 | 6 | 0.754 | 0.770 | -0.151 | 0.049 | NS |
CsCAT15 | 127~142 | 12 | 0.790 | 0.355 | 0.436 | 0.119 | NS |
平均值Mean | 9.78 | 0.778 | 0.625 | 0.129 | 0.063 | NS |
Table 1 List of 9 primers used and size range, genetic diversity and genetic differentiation parameters, and Hardy-weinberg equilibrium test
引物编号 Locus code | 片段大小范围 Size range (bp) | 等位基因数 No.of alleles | 预期杂合度 He | 观察杂合度 Ho | 近交系数 FIS | 居群分化系数 FST | 哈迪-温格平衡检验 Hardy-weinberg equilibrium test |
---|---|---|---|---|---|---|---|
CsCAT1 | 160~201 | 19 | 0.879 | 0.538 | 0.359 | 0.094 | NS |
CsCAT2 | 180~226 | 13 | 0.864 | 0.774 | 0.034 | 0.078 | NS |
CsCAT3 | 197~215 | 6 | 0.637 | 0.594 | -0.023 | 0.089 | NS |
CsCAT4 | 217~261 | 13 | 0.818 | 0.817 | -0.047 | 0.054 | NS |
CsCAT5 | 217~242 | 7 | 0.753 | 0.607 | 0.181 | 0.031 | NS |
CsCAT7 | 190~217 | 6 | 0.761 | 0.538 | 0.256 | 0.038 | NS |
CsCAT8 | 190~210 | 6 | 0.729 | 0.658 | 0.117 | 0.018 | NS |
CsCAT14 | 150~160 | 6 | 0.754 | 0.770 | -0.151 | 0.049 | NS |
CsCAT15 | 127~142 | 12 | 0.790 | 0.355 | 0.436 | 0.119 | NS |
平均值Mean | 9.78 | 0.778 | 0.625 | 0.129 | 0.063 | NS |
居群 Population | 平均等位 基因数A | 平均有效等位 基因数Ae | 预期杂合度 He | 观察杂合度 Ho | 特有等位 基因数Ape | 近交系数 FIS | 取样个体数 Sampling size | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
随机大居群 Panmictric population | 9.778(1.561 5) | 4.954(0.595 8) | 0.776(0.024 4) | 0.625 | 0.190 | 197 | |||||||||||||||||
广水 Guangshui | 6.111(0.696 1) | 3.578(0.332 9) | 0.705(0.021 4) | 0.634 | 3 | 0.109 | 43 | ||||||||||||||||
麻城 Macheng | 8.444(1.168 0) | 4.537(0.556 7) | 0.750(0.033 9) | 0.620 | 20 | 0.169 | 118 | ||||||||||||||||
岳西 Yuexi | 6.000(0.500 0) | 3.638(0.330 7) | 0.704(0.030 2) | 0.622 | 6 | 0.104 | 36 |
Table 2 The genetic diversity parameters of large panmictic population and three subpopulations of Castanea sequnii sampled
居群 Population | 平均等位 基因数A | 平均有效等位 基因数Ae | 预期杂合度 He | 观察杂合度 Ho | 特有等位 基因数Ape | 近交系数 FIS | 取样个体数 Sampling size | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
随机大居群 Panmictric population | 9.778(1.561 5) | 4.954(0.595 8) | 0.776(0.024 4) | 0.625 | 0.190 | 197 | |||||||||||||||||
广水 Guangshui | 6.111(0.696 1) | 3.578(0.332 9) | 0.705(0.021 4) | 0.634 | 3 | 0.109 | 43 | ||||||||||||||||
麻城 Macheng | 8.444(1.168 0) | 4.537(0.556 7) | 0.750(0.033 9) | 0.620 | 20 | 0.169 | 118 | ||||||||||||||||
岳西 Yuexi | 6.000(0.500 0) | 3.638(0.330 7) | 0.704(0.030 2) | 0.622 | 6 | 0.104 | 36 |
位点 Locus | 10个距离等级(km)的Moran's I值 Moran's I for 10 distance classes (km) | 累积机率 Cum. Prob | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | ||
CsCAT1-180 | 0.32** | 0.26** | 0.31** | 0.16** | -0.03 | -0.13** | -0.15** | -0.55** | -0.57** | 0.15** | 0.000* |
CsCAT1-188 | 0.01 | 0.02 | -0.02 | -0.07 | 0.02 | -0.02 | -0.00 | -0.00 | -0.01 | 0.01 | 0.045* |
CsCAT1-190 | 0.07** | -0.09** | 0.04* | -0.06** | -0.04* | 0.01 | 0.00 | -0.02 | 0.03 | -0.02 | 0.001* |
CsCAT2-209 | 0.15** | 0.05** | 0.06** | -0.01 | -0.23** | -0.13** | 0.02 | -0.01 | 0.17** | -0.11** | 0.000* |
CsCAT3-201 | 0.09** | -0.02 | 0.03 | -0.04 | -0.17** | 0.04* | -0.00 | 0.01 | 0.05* | -0.04 | 0.000* |
CsCAT3-207 | 0.04** | 0.01 | -0.01 | 0.01 | 0.07** | -0.00 | 0.05** | -0.04* | -0.08** | -0.13** | 0.000* |
CsCAT4-230 | 0.06** | 0.04* | -0.02 | 0.02 | -0.00 | -0.03 | -0.12** | -0.02 | -0.03 | 0.04** | 0.000* |
CsCAT4-238 | 0.10** | 0.05** | -0.07** | -0.03 | 0.02 | 0.04** | 0.04* | -0.11** | -0.03 | -0.08** | 0.000* |
CsCAT4-242 | 0.07** | 0.08** | 0.01 | 0.15** | 0.00 | -0.11** | -0.20** | -0.07** | -0.11** | 0.11** | 0.000* |
CsCAT4-253 | 0.05** | -0.05* | -0.01 | -0.05* | -0.01 | 0.01 | 0.01 | -0.02 | -0.00 | -0.00 | 0.056 |
CsCAT5-227 | 0.04** | -0.03 | 0.02 | -0.01 | 0.01 | -0.03 | -0.06** | -0.01 | -0.04 | 0.04* | 0.037* |
CsCAT5-232 | 0.12** | 0.07** | 0.07** | 0.04* | 0.07** | -0.01 | -0.05* | -0.20** | -0.13** | -0.11** | 0.000* |
CsCAT7-205 | 0.16** | 0.08** | -0.08** | 0.00 | -0.06** | 0.01 | -0.08** | -0.18** | 0.00 | 0.09** | 0.000* |
CsCAT7-209 | 0.05** | 0.05* | -0.04* | -0.01 | -0.08** | 0.02 | 0.00 | -0.08** | -0.01 | 0.05** | 0.000* |
CsCAT7-215 | 0.02 | -0.03 | -0.03 | 0.02 | -0.02 | 0.02 | -0.03 | 0.01 | -0.01 | 0.00 | 1.000 |
CsCAT7-217 | -0.00 | -0.02 | 0.02 | 0.00 | 0.02 | -0.00 | 0.03 | -0.01 | -0.03 | -0.07* | 0.176 |
CsCAT8-190 | 0.02 | -0.02 | 0.01 | -0.01 | -0.03 | -0.05 | 0.02 | -0.01 | -0.02 | 0.02 | 0.780 |
CsCAT8-201 | 0.02 | 0.04* | 0.04* | 0.02 | -0.05 | -0.03 | 0.05* | -0.05 | -0.11** | -0.00 | 0.001* |
CsCAT8-204 | -0.04 | 0.03 | -0.02 | -0.01 | 0.01 | -0.03 | 0.01 | -0.01 | 0.00 | -0.01 | 0.798 |
CsCAT8-207 | 0.04* | 0.01 | -0.00 | 0.05** | -0.04* | -0.02 | 0.04** | -0.07** | -0.09** | 0.01 | 0.000* |
CsCAT14-150 | -0.02 | 0.00 | -0.01 | -0.03 | 0.03* | -0.03 | 0.02 | -0.01 | 0.00 | -0.00 | 0.400 |
CsCAT14-153 | 0.03* | 0.01 | -0.01 | 0.05** | 0.03* | -0.04 | -0.05* | -0.01 | 0.02 | -0.10** | 0.000* |
CsCAT14-155 | 0.14** | -0.01 | 0.05** | 0.19** | 0.07** | -0.12** | -0.11** | -0.02 | 0.09** | -0.41** | 0.000* |
CsCAT14-157 | 0.10** | 0.08** | 0.14** | 0.11** | -0.13** | -0.26** | -0.08** | -0.02 | -0.02 | 0.02 | 0.000* |
CsCAT15-133 | 0.19** | 0.16** | -0.01 | -0.04 | -0.16** | -0.15** | -0.04 | 0.09** | 0.01 | -0.09** | 0.000* |
CsCAT15-134 | 0.16** | 0.11** | 0.09** | 0.12** | 0.04* | -0.00 | -0.12** | -0.28** | -0.06** | -0.08** | 0.000* |
CsCAT15-135 | 0.02 | 0.02 | 0.05* | -0.00 | -0.06** | -0.06** | -0.02 | -0.02 | -0.05* | 0.06** | 0.022* |
平均Average | 0.08 | 0.03 | 0.02 | 0.02 | -0.03 | -0.04 | -0.03 | -0.06 | -0.04 | -0.03 | - |
最大值Maximum | 0.32 | 0.26 | 0.31 | 0.19 | 0.07 | 0.04 | 0.05 | 0.09 | 0.17 | 0.15 | - |
最小值Minimum | -0.04 | -0.09 | -0.08 | -0.07 | -0.23 | -0.26 | -0.20 | -0.55 | -0.57 | -0.41 | - |
Table 3 Spatial autocorrelation coefficients (Moran's I) for 10 distance classes in panmictic population of Castanea squinii
位点 Locus | 10个距离等级(km)的Moran's I值 Moran's I for 10 distance classes (km) | 累积机率 Cum. Prob | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | ||
CsCAT1-180 | 0.32** | 0.26** | 0.31** | 0.16** | -0.03 | -0.13** | -0.15** | -0.55** | -0.57** | 0.15** | 0.000* |
CsCAT1-188 | 0.01 | 0.02 | -0.02 | -0.07 | 0.02 | -0.02 | -0.00 | -0.00 | -0.01 | 0.01 | 0.045* |
CsCAT1-190 | 0.07** | -0.09** | 0.04* | -0.06** | -0.04* | 0.01 | 0.00 | -0.02 | 0.03 | -0.02 | 0.001* |
CsCAT2-209 | 0.15** | 0.05** | 0.06** | -0.01 | -0.23** | -0.13** | 0.02 | -0.01 | 0.17** | -0.11** | 0.000* |
CsCAT3-201 | 0.09** | -0.02 | 0.03 | -0.04 | -0.17** | 0.04* | -0.00 | 0.01 | 0.05* | -0.04 | 0.000* |
CsCAT3-207 | 0.04** | 0.01 | -0.01 | 0.01 | 0.07** | -0.00 | 0.05** | -0.04* | -0.08** | -0.13** | 0.000* |
CsCAT4-230 | 0.06** | 0.04* | -0.02 | 0.02 | -0.00 | -0.03 | -0.12** | -0.02 | -0.03 | 0.04** | 0.000* |
CsCAT4-238 | 0.10** | 0.05** | -0.07** | -0.03 | 0.02 | 0.04** | 0.04* | -0.11** | -0.03 | -0.08** | 0.000* |
CsCAT4-242 | 0.07** | 0.08** | 0.01 | 0.15** | 0.00 | -0.11** | -0.20** | -0.07** | -0.11** | 0.11** | 0.000* |
CsCAT4-253 | 0.05** | -0.05* | -0.01 | -0.05* | -0.01 | 0.01 | 0.01 | -0.02 | -0.00 | -0.00 | 0.056 |
CsCAT5-227 | 0.04** | -0.03 | 0.02 | -0.01 | 0.01 | -0.03 | -0.06** | -0.01 | -0.04 | 0.04* | 0.037* |
CsCAT5-232 | 0.12** | 0.07** | 0.07** | 0.04* | 0.07** | -0.01 | -0.05* | -0.20** | -0.13** | -0.11** | 0.000* |
CsCAT7-205 | 0.16** | 0.08** | -0.08** | 0.00 | -0.06** | 0.01 | -0.08** | -0.18** | 0.00 | 0.09** | 0.000* |
CsCAT7-209 | 0.05** | 0.05* | -0.04* | -0.01 | -0.08** | 0.02 | 0.00 | -0.08** | -0.01 | 0.05** | 0.000* |
CsCAT7-215 | 0.02 | -0.03 | -0.03 | 0.02 | -0.02 | 0.02 | -0.03 | 0.01 | -0.01 | 0.00 | 1.000 |
CsCAT7-217 | -0.00 | -0.02 | 0.02 | 0.00 | 0.02 | -0.00 | 0.03 | -0.01 | -0.03 | -0.07* | 0.176 |
CsCAT8-190 | 0.02 | -0.02 | 0.01 | -0.01 | -0.03 | -0.05 | 0.02 | -0.01 | -0.02 | 0.02 | 0.780 |
CsCAT8-201 | 0.02 | 0.04* | 0.04* | 0.02 | -0.05 | -0.03 | 0.05* | -0.05 | -0.11** | -0.00 | 0.001* |
CsCAT8-204 | -0.04 | 0.03 | -0.02 | -0.01 | 0.01 | -0.03 | 0.01 | -0.01 | 0.00 | -0.01 | 0.798 |
CsCAT8-207 | 0.04* | 0.01 | -0.00 | 0.05** | -0.04* | -0.02 | 0.04** | -0.07** | -0.09** | 0.01 | 0.000* |
CsCAT14-150 | -0.02 | 0.00 | -0.01 | -0.03 | 0.03* | -0.03 | 0.02 | -0.01 | 0.00 | -0.00 | 0.400 |
CsCAT14-153 | 0.03* | 0.01 | -0.01 | 0.05** | 0.03* | -0.04 | -0.05* | -0.01 | 0.02 | -0.10** | 0.000* |
CsCAT14-155 | 0.14** | -0.01 | 0.05** | 0.19** | 0.07** | -0.12** | -0.11** | -0.02 | 0.09** | -0.41** | 0.000* |
CsCAT14-157 | 0.10** | 0.08** | 0.14** | 0.11** | -0.13** | -0.26** | -0.08** | -0.02 | -0.02 | 0.02 | 0.000* |
CsCAT15-133 | 0.19** | 0.16** | -0.01 | -0.04 | -0.16** | -0.15** | -0.04 | 0.09** | 0.01 | -0.09** | 0.000* |
CsCAT15-134 | 0.16** | 0.11** | 0.09** | 0.12** | 0.04* | -0.00 | -0.12** | -0.28** | -0.06** | -0.08** | 0.000* |
CsCAT15-135 | 0.02 | 0.02 | 0.05* | -0.00 | -0.06** | -0.06** | -0.02 | -0.02 | -0.05* | 0.06** | 0.022* |
平均Average | 0.08 | 0.03 | 0.02 | 0.02 | -0.03 | -0.04 | -0.03 | -0.06 | -0.04 | -0.03 | - |
最大值Maximum | 0.32 | 0.26 | 0.31 | 0.19 | 0.07 | 0.04 | 0.05 | 0.09 | 0.17 | 0.15 | - |
最小值Minimum | -0.04 | -0.09 | -0.08 | -0.07 | -0.23 | -0.26 | -0.20 | -0.55 | -0.57 | -0.41 | - |
Fig.3 Correlogram using mean value of Moran's I at 9 Microsatellite loci and 10 distance intervals in panmictic population (95%CI: 95% confidence interval)
Fig.4 The correlogram of 3 subpopulations using mean value of Moran's I at 9 Microsatellite loci: 9 distance intervals in Guangshui(a) and Macheng(b) subpopulation, 10 distance intervals in Yuexi(c) subpopulation (95%CI: 95% confidence interval)
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