Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. DNA Extraction
2.3. Primer Screening and PCR Amplification
2.4. Analysis of Genetic Diversity and Population Genetic Structure
3. Results and Analysis
3.1. Genetic Diversity of M. crassipes Populations
3.2. Genetic Differentiation and Gene Flow
3.3. Population Clustering and Genetic Structure
4. Discussion
4.1. Genetic Diversity of Michelia crassipes
4.2. Genetic Differentiation and Genetic Structure
4.3. Conservation Proposal
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Primer Pair | Primer Sequence (5′-3′) | Repeat Motif | Annealing Temperature (°C) | Product Size/bp |
---|---|---|---|---|
M17 | F:GCTGCAGAGGCATTATGGTT | (ATC)6 | 60 | 239 |
R:ATGTCTGGTGGGCAGATGAT | ||||
M19 | F:AGCTTCCGGGACTTCAAACT | (CAG)5 | 60 | 237 |
R:CGTAGGCAAGAACGGATGAT | ||||
M20 | F:CCCTACTTCGACCATTGCAT | (TTG)6 | 60 | 275 |
R:CGAACCAAGAGTCCGTCAAT | ||||
M25 | F:TGCTCCATAAGGTAGGGCAT | (TC)6 | 60 | 251 |
R:TCACTCCCTCTGAAGCCATT | ||||
M27 | F:GAAGACGCTTTCCTGCAGAT | (AT)6 | 60 | 218 |
R:CACATCAAGCTTGCACGAGT | ||||
M28 | F:GCCTAAGGCGCTTCTTTTCT | (GT)8 | 60 | 237 |
R:ATGGCTAAACGAAGGGAGGT | ||||
M29 | F:AGGGGCAGAAGATGTCCTTT | (GT)6 | 60 | 267 |
R:TGCCTTGGCTTAGAAGCTGT | ||||
M30 | F:GTGGTATTGTTGGGTTCGCT | (CA)6 | 60 | 276 |
R:CCTCCAAAACCCTCCTCTTT | ||||
M31 | F:CCATGGGCAAGAGAATCAGT | (CA)6 | 60 | 246 |
R:GAAGTTCAGCCAACCACCAT | ||||
M32 | F:TCGTCCCTGGAATGAGAAGT | (CA)6 | 60 | 240 |
R:CTTAACCGATGGTGGCTTGT | ||||
N2 | F:GCGTAATTTCGTCACCCACT | (AT)6 | 60 | 231 |
R:CCTGACCGTTGGTTTGAGTT | ||||
N8 | F:CCCACCCTCAAACATCACTT | (GC)6 | 60 | 230 |
R:AATACCTTGGTTGAGGGGGT | ||||
N10 | F:TGCAAGAGTCATCCATTTCAG | (AAG)5 | 60 | 260 |
R:GCTGGGGACGTAATGTTGTT | ||||
N13 | F:CCTCACACTCACAGCAGCAT | (CAG)6 | 62 | 218 |
R:GTGGAGCTGTTACCGTTGGT |
Locus | Na | Ne | PPB (%) | I | Ho | He | PIC | Fis | Fit | Fst | Nm | Fn | HWE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
M17 | 14 | 3.594 | 85.71% | 1.457 | 0.821 | 0.697 | 0.755 | −0.178 | −0.036 | 0.121 | 1.818 | −0.037 | *** |
M19 | 7 | 1.457 | 85.71% | 0.526 | 0.291 | 0.273 | 0.458 | −0.065 | 0.340 | 0.380 | 0.408 | 0.221 | * |
M20 | 19 | 2.722 | 88.89% | 1.289 | 0.459 | 0.600 | 0.708 | 0.234 | 0.354 | 0.156 | 1.349 | 0.144 | NS |
M25 | 22 | 6.601 | 90.48% | 2.016 | 0.791 | 0.831 | 0.879 | 0.048 | 0.112 | 0.067 | 3.457 | 0.014 | NS |
M27 | 31 | 4.428 | 93.33% | 1.828 | 0.260 | 0.769 | 0.806 | 0.662 | 0.675 | 0.039 | 6.115 | 0.577 | *** |
M28 | 20 | 3.956 | 94.74% | 1.628 | 0.747 | 0.739 | 0.765 | −0.012 | 0.047 | 0.058 | 4.064 | −0.011 | NS |
M29 | 18 | 2.669 | 94.44% | 1.094 | 0.217 | 0.580 | 0.610 | 0.625 | 0.677 | 0.137 | 1.573 | 0.567 | *** |
M30 | 12 | 1.804 | 100.00% | 0.783 | 0.226 | 0.407 | 0.570 | 0.444 | 0.632 | 0.339 | 0.487 | 0.510 | *** |
M31 | 8 | 1.703 | 87.50% | 0.617 | 0.420 | 0.351 | 0.426 | −0.199 | 0.101 | 0.250 | 0.752 | 0.012 | NS |
M32 | 14 | 2.469 | 100.00% | 1.006 | 0.292 | 0.511 | 0.639 | 0.430 | 0.591 | 0.282 | 0.635 | 0.334 | *** |
N2 | 14 | 1.815 | 92.31% | 0.785 | 0.199 | 0.395 | 0.498 | 0.496 | 0.638 | 0.281 | 0.640 | 0.540 | *** |
N8 | 15 | 2.238 | 100.00% | 0.907 | 0.476 | 0.451 | 0.519 | −0.056 | 0.227 | 0.268 | 0.684 | 0.144 | * |
N10 | 14 | 1.471 | 92.86% | 0.519 | 0.247 | 0.236 | 0.242 | −0.046 | 0.080 | 0.121 | 1.823 | 0.093 | ND |
N13 | 10 | 3.183 | 70.00% | 1.240 | 0.777 | 0.663 | 0.667 | −0.173 | −0.075 | 0.083 | 2.750 | −0.042 | *** |
Mean | 15.571 | 2.865 | 91.14% | 1.121 | 0.445 | 0.536 | 0.610 | 0.158 | 0.312 | 0.185 | 1.897 | 0.219 |
Populations | Na | Ne | I | Ho | He | HWE |
---|---|---|---|---|---|---|
P1 | 4.929 | 2.590 | 1.063 | 0.505 | 0.528 | M17 **, M20 *, M27 ***, M29 *, N2 *** |
P2 | 4.571 | 2.624 | 0.920 | 0.348 | 0.439 | M17 *, M20 *, M27 ***, M28 ***, M29 **, M30 **, M32 ***, N13 *** |
P3 | 6.214 | 3.225 | 1.213 | 0.540 | 0.583 | M19 ***, M25 *, M27 ***, M29 ***, M30 ***, N2 *** |
P4 | 5.571 | 2.395 | 0.990 | 0.398 | 0.478 | M17 ***, M20 *, M25 *, M27 ***, M29 ***, M30 ***, M32 ***, N2 ***, N10 ***, N13 ** |
P5 | 5.429 | 2.673 | 1.046 | 0.433 | 0.501 | M17 ***, M25 *, M27 ***, M28 *, M29 ***, M30 **, M32 ***, N13 ** |
P6 | 8.500 | 3.723 | 1.494 | 0.488 | 0.666 | M17 ***, M19 **, M20 **, M27 ***, M28 **, M29 ***, M30 ***, M32 ***, N2 ***, N13 ** |
P7 | 4.643 | 2.825 | 1.120 | 0.401 | 0.557 | M17 *, M20 **, M25 ***, M29 **, M32 **, N8 *, N13 ** |
Mean | 5.694 | 2.865 | 1.121 | 0.445 | 0.536 |
Source of Variation | d.f. | SSD | MSD | Variance Component | Variance Ratio | p Value |
---|---|---|---|---|---|---|
Among populations | 6 | 333.849 | 55.642 | 2.564 | 21.09% | 0.001 |
Within populations | 121 | 1161.221 | 9.597 | 9.597 | 78.91% | 0.001 |
Populations | P1 | P2 | P3 | P4 | P5 | P6 | P7 |
---|---|---|---|---|---|---|---|
P1 | 2.220 | 2.708 | 3.099 | 4.877 | 2.680 | 1.459 | |
P2 | 0.101 | 2.182 | 1.854 | 2.919 | 1.573 | 0.883 | |
P3 | 0.085 | 0.103 | 5.934 | 3.062 | 2.357 | 1.478 | |
P4 | 0.075 | 0.119 | 0.040 | 3.611 | 2.093 | 1.415 | |
P5 | 0.049 | 0.079 | 0.075 | 0.065 | 2.136 | 1.172 | |
P6 | 0.085 | 0.137 | 0.096 | 0.107 | 0.105 | 1.827 | |
P7 | 0.146 | 0.221 | 0.145 | 0.150 | 0.176 | 0.120 |
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Xiao, Y.; Jiang, X.; Lu, C.; Liu, J.; Diao, S.; Jiang, J. Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers. Forests 2023, 14, 508. https://doi.org/10.3390/f14030508
Xiao Y, Jiang X, Lu C, Liu J, Diao S, Jiang J. Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers. Forests. 2023; 14(3):508. https://doi.org/10.3390/f14030508
Chicago/Turabian StyleXiao, Yuguang, Xiaolong Jiang, Chengcheng Lu, Jun Liu, Shu Diao, and Jingmin Jiang. 2023. "Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers" Forests 14, no. 3: 508. https://doi.org/10.3390/f14030508