An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genetic Materials and DNA Isolation
2.2. PCR Amplification and Genotyping Assays
2.3. Data Analysis
3. Results
3.1. Marker Polymorphism
3.2. Genetic Diversity Analysis
3.3. Genetic Distance and Grouping of Samples
3.4. Structure and Pattern of Classification
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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No. | Species | Genbank Code | Province | No. | Species | Genbank Code | Province |
---|---|---|---|---|---|---|---|
1 | AST | IUGB-00133 | Golestan | 51 | ACY | IUGB-00373 | Chaharmahal and Bakhtiari |
2 | AST | IUGB-00134 | Qazvin | 52 | ACY | IUGB-00189 | Lorestan |
3 | AST | IUGB-00485 | Urmiyeh | 53 | ACY | IUGB-00236 | Khuzestan |
4 | AST | IUGB-00516 | Khoozestan | 54 | ACY | IUGB-00267 | Gilan |
5 | AST | IUGB-00911 | Ilam | 55 | ACY | IUGB-00188 | East Azerbaijan |
6 | AST | IUGB-01569 | Lorestan | 56 | ACY | IUGB-00359 | Kurdistan |
7 | AST | IUGB-01696 | Kermanshah | 57 | ACY | IUGB-00403 | Kohgiluyeh and Boyer-Ahmad |
8 | AST | IUGB-00615 | Unknown | 58 | ACY | IUGB-00210 | Lorestan |
9 | AST | IUGB-00597 | Unknown | 59 | ACY | IUGB-00200 | Kermanshah |
10 | AST | IUGB-00604 | Unknown | 60 | ACY | IUGB-00150 | West Azerbaijan |
11 | AST | IUGB-00576 | Unknown | 61 | ACY | IUGB-00168 | Kermanshah |
12 | AST | IUGB-00618 | Unknown | 62 | ACY | IUGB-00034 | Kermanshah |
13 | AST | IUGB-01845 | Ilam | 63 | ACY | IUGB-00090 | Kermanshah |
14 | AST | IUGB-00518 | Kermanshah | 64 | ACY | IUGB-00258 | Ardabil |
15 | AST | IUGB-00540 | Lorestan | 65 | ACY | IUGB-01592 | Lorestan |
16 | AST | IUGB-00544 | Kurdestan | 66 | ACY | IUGB-00202 | East Azerbaijan |
17 | AST | IUGB-00547 | Khoozestan | 67 | ACY | IUGB-00229 | Lorestan |
18 | AST | IUGB-00548 | Hamadan | 68 | ACY | IUGB-00090 | Kermanshah |
19 | AST | IUGB-00602 | Unknown | 69 | ACY | IUGB-00270 | Gilan |
20 | AST | IUGB-00856 | Ilam | 70 | ACY | IUGB-00059 | Lorestan |
21 | AST | IUGB-00854 | Ilam | 71 | ACY | IUGB-00132 | Kermanshah |
22 | AST | IUGB-00515 | Khoozestan | 72 | ACY | IUGB-00095 | Kermanshah |
23 | AST | IUGB-00534 | Kurdestan | 73 | ACY | IUGB-00062 | Kermanshah |
24 | AST | IUGB-00613 | Unknown | 74 | ACY | IUGB-00065 | Kurdestan |
25 | AST | IUGB-00590 | Unknown | 75 | ACY | IUGB-00391 | Lorestan |
26 | AT | NPGBI-01-0836 | Unknown | 76 | ACR | IUGB-00379 | Kermanshah |
27 | AT | IUGB-00020 | Ardabil | 77 | ACR | IUGB-01564 | Lorestan |
28 | AT | IUGB-00107 | Gilan | 78 | ACR | IUGB-00881 | Ilam |
29 | AT | IUGB-00223 | Mazandaran | 79 | ACR | IUGB-00817 | Ilam |
30 | AT | IUGB-00224 | Gilan | 80 | ACR | IUGB-00170 | Fars |
31 | AT | IUGB-00245 | Alborz | 81 | ACR | IUGB-00408 | Kermanshah |
32 | AT | IUGB-00247 | Mazandaran | 82 | ACR | IUGB-00319 | Chaharmahal and Bakhtiari |
33 | AT | IUGB-00260 | Gilan | 83 | ACR | IUGB-00280 | East Azerbaijan |
34 | AT | IUGB-00325 | Alborz | 84 | ACR | IUGB-00149 | Fars |
35 | AT | IUGB-00365 | Mazandaran | 85 | ACR | IUGB-01564 | Lorestan |
36 | AT | IUGB-00366 | Mazandaran | 86 | ACR | IUGB-00830 | Ilam |
37 | AT | IUGB-00369 | Gilan | 87 | ACR | IUGB-01267 | Kermanshah |
38 | AT | IUGB-00402 | Gilan | 88 | ACR | IUGB-00334 | Ilam |
39 | AT | IUGB-00249 | Mazandaran | 89 | ACR | IUGB-00284 | Kermanshah |
40 | AT | IUGB-00367 | East Azerbaijan | 90 | ACR | NPGBI-28940 | Kermanshah |
41 | AT | IUGB-00273 | Ardabil | 91 | ACR | NPGBI-27828 | Hamadan |
42 | AT | IUGB-00274 | Alborz | 92 | ACR | NPGBI-28954 | Kermanshah |
43 | AT | IUGB-00374 | Gilan | 93 | ACR | NPGBI-28112 | Hamadan |
44 | AT | IUGB-00383 | Mazandaran | 94 | ACR | NPGBI-29131 | Tehran |
45 | AT | IUGB-00386 | East Azerbaijan | 95 | ACR | NPGBI-28024 | Khorasan |
46 | AT | IUGB-00396 | Mazandaran | 96 | ACR | NPGBI-28126 | Zanjan |
47 | AT | IUGB-00400 | Mazandaran | 97 | ACR | NPGBI-28348 | Kermanshah |
48 | AT | IUGB-00401 | Mazandaran | 98 | ACR | NPGBI-28157 | Zanjan |
49 | AT | IUGB-00404 | Gilan | 99 | ACR | NPGBI-50067 | Khorasan |
50 | AT | IUGB-00405 | Alborz | 100 | ACR | NPGBI-28917 | West Azerbaijan |
Primer | Sequence (5–3) | Tm | NTB | NPB | PIC | Rp | MI |
---|---|---|---|---|---|---|---|
SCoT-2 | CAACAATGGCTACCACCC | 56 | 7 | 7 | 0.45 | 5.64 | 3.20 |
SCoT-3 | CAACAATGGCTACCACCG | 56 | 9 | 9 | 0.34 | 4.44 | 3.12 |
SCoT-5 | CAACAATGGCTACCACGA | 53.70 | 8 | 8 | 0.44 | 7.06 | 3.55 |
SCoT-12 | ACGACATGGCGACCAACG | 58.20 | 9 | 9 | 0.36 | 4.82 | 3.23 |
SCoT-17 | CATGGCTACCACCGGCCC | 53 | 11 | 11 | 0.42 | 7.76 | 4.60 |
SCoT-18 | ACCATGGCTACCACCGCG | 60.50 | 10 | 10 | 0.48 | 9.28 | 4.84 |
SCoT-19 | GCAACAATGGCTACCACC | 56 | 12 | 12 | 0.43 | 10.38 | 5.11 |
SCoT-21 | CACCATGGCTACCACCAT | 56 | 10 | 10 | 0.41 | 7.18 | 4.13 |
Mean | 9.50 | 9.50 | 0.42 | 7.07 | 3.97 | ||
CBDP-1 | TGAGCACGATCCAAT AGC | 56 | 10 | 10 | 0.48 | 9.98 | 4.80 |
CBDP-2 | TGAGCACGATCCAATAAT | 56 | 9 | 9 | 0.47 | 8.80 | 4.27 |
CBDP-3 | TGAGCACGATCCAAT ACC | 56 | 10 | 10 | 0.45 | 9.60 | 4.55 |
CBDP-4 | TGAGCACGATCCAAT AAG | 56 | 10 | 10 | 0.46 | 9.52 | 4.58 |
CBDP-5 | TGAGCACGATCCAAT CTA | 56 | 9 | 9 | 0.43 | 7.72 | 3.88 |
CBDP-6 | TGAGCACGATCCAAT CAG | 56 | 12 | 12 | 0.44 | 9.70 | 5.36 |
CBDP-7 | TGAGCACGATCCAAT CGA | 56 | 9 | 9 | 0.43 | 6.32 | 3.89 |
CBDP-8 | TGAGCACGATCCAAT CGG | 56 | 10 | 10 | 0.41 | 8.70 | 4.10 |
CBDP-9 | TGAGCACGATCCAAT GAT | 56 | 11 | 11 | 0.46 | 9.24 | 5.12 |
CBDP-10 | TGAGCACGATCCAAT GTT | 56 | 9 | 9 | 0.40 | 6.46 | 3.66 |
CBDP-11 | TGAGCACGATCCAAT TGC | 56 | 9 | 9 | 0.46 | 8.24 | 4.15 |
CBDP-12 | TGAGCACGATCCAATATA | 56 | 8 | 8 | 0.44 | 6.74 | 3.56 |
Mean | 9.67 | 9.67 | 0.45 | 8.42 | 4.33 |
Primer | Sequence (5–3) | Tm | NTB | NPB | PIC | Rp | MI | |
---|---|---|---|---|---|---|---|---|
Xgwm-16 | Forward | GCTTGGACTAGCTAGAGTATCATAC | 62.8 | 2 | 2 | 0.50 | 1.96 | 1.00 |
Reverse | CAATCTTCAATTCTGTCGCACGG | |||||||
Xgwm-44 | Forward | GTTGAGCTTTTCAGTTCGGC | 59.9 | 2 | 2 | 0.47 | 2.42 | 0.93 |
Reverse | ACTGGCATCCACTGAGCTG | |||||||
Xgwm-111 | Forward | TCTGTAGGCTCTCTCCGACTG | 59.5 | 2 | 2 | 0.24 | 3.32 | 0.47 |
Reverse | ACCTGATCAGATCCCACTCG | |||||||
Xgwm-121 | Forward | TCCTCTACAAACAAACACAC | 54.3 | 2 | 2 | 0.09 | 2.12 | 0.19 |
Reverse | CTCGCAACTAGAGGTGTATG | |||||||
Xgwm-271 | Forward | CAAGATCGTGGAGCCAGC | 58.5 | 2 | 2 | 0.36 | 2.74 | 0.73 |
Reverse | AGCTGCTAGCTTTTGGGACA | |||||||
Xgwm-272 | Forward | TGCTCTTTGGCGAATATATGG | 55.9 | 2 | 2 | 0.08 | 3.84 | 0.15 |
Reverse | GTTCAAAACAAATTAAAAGGCCC | |||||||
Xgwm-292 | Forward | TCACCGTGGTCACCGAC | 59.3 | 2 | 2 | 0.34 | 3.14 | 0.67 |
Reverse | CCACCGAGCCGATAATGTAC | |||||||
Xgwm-296 | Forward | AATTCAACCTACCAATCTCTG | 55.6 | 2 | 2 | 0.30 | 2.16 | 0.61 |
Reverse | GCCTAATAAACTGAAAACGAG | |||||||
Xgwm-301 | Forward | GAGGAGTAAGACACATGCCC | 59.5 | 2 | 2 | 0.40 | 1.86 | 0.79 |
Reverse | GTGGCTGGAGATTCAGGTTC | |||||||
Xgwm-325 | Forward | TTTCTTCTGTCGTTCTCTTCCC | 69.3 | 2 | 2 | 0.44 | 2.00 | 0.88 |
Reverse | TTTTTACGCGTCAACGACG | |||||||
Xgwm-349 | Forward | GGCTTCCAGAAAACAACAGG | 59.5 | 2 | 2 | 0.21 | 1.80 | 0.41 |
Reverse | ATCGGTGCGTACCATCCTAC | |||||||
Xgwm-382 | Forward | GTCAGATAACGCCGTCCAAT | 59.2 | 2 | 2 | 0.33 | 2.28 | 0.67 |
Reverse | CTACGTGCACCACCATTTTG | |||||||
Xgwm-455 | Forward | ATTCGGTTCGCTAGCTACCA | 56 | 2 | 2 | 0.36 | 2.46 | 0.73 |
Reverse | ACGGAGAGCAACCTGCC | |||||||
Xgwm-469 | Forward | CAACTCAGTGCTCACACAACG | 63.5 | 2 | 2 | 0.23 | 2.00 | 0.45 |
Reverse | CGATAACCACTCATCCACACC | |||||||
Xgwm-515 | Forward | AACACAATGGCAAATGCAGA | 60 | 2 | 2 | 0.32 | 3.06 | 0.64 |
Reverse | CCTTCCTAGTAAGTGTGCCTCA | |||||||
Xgwm-565 | Forward | GCGTCAGATATGCCTACCTAGG | 62.1 | 2 | 2 | 0.46 | 2.40 | 0.92 |
Reverse | AGTGAGTTAGCCCTGAGCCA | |||||||
Xgwm-583 | Forward | TTCACACCCAACCAATAGCA | 59.3 | 2 | 2 | 0.43 | 2.52 | 0.86 |
Reverse | TCTAGGCAGACACATGCCTG | |||||||
Xgwm-608 | Forward | ACATTGTGTGTGCGGCC | 60.4 | 2 | 2 | 0.18 | 2.46 | 0.35 |
Reverse | GATCCCTCTCCGCTAGAAGC | |||||||
Xgwm-624 | Forward | TTGATATTAAATCTCTCTATGTG | 51.3 | 2 | 2 | 0.48 | 2.36 | 0.97 |
Reverse | AATTTTATTTGAGCTATGCG | |||||||
Xgwm-157 | Forward | GTCGTCGCGGTAAGCTTG | 60 | 2 | 2 | 0.46 | 1.98 | 0.93 |
Reverse | GAGTGAACACACGAGGCTTG | |||||||
Xgwm-212 | Forward | AAGCAACATTTGCTGCAATG | 60 | 2 | 2 | 0.30 | 2.96 | 0.59 |
Reverse | TGCAGTTAACTTGTTGAAAGGA | |||||||
Xgwm-232 | Forward | ATCTCAACGGCAAGCCG | 55 | 2 | 2 | 0.21 | 3.50 | 0.43 |
Reverse | CTGATGCAAGCAATCCACC | |||||||
Xgwm-311 | Forward | TCACGTGGAAGACGCTCC | 60 | 2 | 2 | 0.21 | 2.52 | 0.41 |
Reverse | CTACGTGCACCACCATTTTG | |||||||
Xgwm-484 | Forward | ACATCGCTCTTCACAAACCC | 55 | 2 | 2 | 0.39 | 1.96 | 0.79 |
Reverse | AGTTCCGGTCATGGCTAGG | |||||||
Mean | 1.96 | 1.96 | 0.32 | 2.52 | 0.64 |
Marker | Species | Na | Ne | I | He | PPL (%) | Variation within Species | Variation among Species |
---|---|---|---|---|---|---|---|---|
SCoT | T. aestivum | 1.868 | 1.398 | 0.399 | 0.253 | 93.42 | 81% | 19% |
Ae. tauschii | 1.789 | 1.471 | 0.433 | 0.285 | 89.47 | |||
Ae. cylindrica | 1.882 | 1.514 | 0.480 | 0.306 | 96.05 | |||
Ae. crassa | 1.921 | 1.502 | 0.467 | 0.305 | 93.42 | |||
Mean | 1.865 | 1.471 | 0.441 | 0.287 | 93.09 | |||
CBDP | T. aestivum | 1.879 | 1.495 | 0.451 | 0.296 | 93.97 | 80% | 20% |
Ae. tauschii | 1.957 | 1.581 | 0.511 | 0.340 | 96.55 | |||
Ae. cylindrica | 1.948 | 1.656 | 0.555 | 0.377 | 97.41 | |||
Ae. crassa | 1.948 | 1.458 | 0.438 | 0.283 | 97.41 | |||
Mean | 1.933 | 1.547 | 0.489 | 0.324 | 96.34 | |||
SSR | T. aestivum | 1.510 | 1.382 | 0.320 | 0.217 | 61.22 | 58% | 42% |
Ae. tauschii | 1.735 | 1.524 | 0.448 | 0.303 | 79.59 | |||
Ae. cylindrica | 1.143 | 1.160 | 0.152 | 0.099 | 32.65 | |||
Ae. crassa | 1.388 | 1.306 | 0.267 | 0.179 | 51.02 | |||
Mean | 1.444 | 1.343 | 0.297 | 0.199 | 56.12 | |||
Combined data | T. aestivum | 1.801 | 1.441 | 0.408 | 0.266 | 87.14 | 58% | 42% |
Ae. tauschii | 1.859 | 1.534 | 0.473 | 0.315 | 90.87 | |||
Ae. cylindrica | 1.763 | 1.511 | 0.444 | 0.298 | 82.99 | |||
Ae. crassa | 1.826 | 1.441 | 0.412 | 0.269 | 87.55 | |||
Mean | 1.812 | 1.482 | 0.435 | 0.287 | 87.14 |
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Pour-Aboughadareh, A.; Poczai, P.; Etminan, A.; Jadidi, O.; Kianersi, F.; Shooshtari, L. An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers. Plants 2022, 11, 1205. https://doi.org/10.3390/plants11091205
Pour-Aboughadareh A, Poczai P, Etminan A, Jadidi O, Kianersi F, Shooshtari L. An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers. Plants. 2022; 11(9):1205. https://doi.org/10.3390/plants11091205
Chicago/Turabian StylePour-Aboughadareh, Alireza, Peter Poczai, Alireza Etminan, Omid Jadidi, Farzad Kianersi, and Lia Shooshtari. 2022. "An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers" Plants 11, no. 9: 1205. https://doi.org/10.3390/plants11091205