| Literature DB >> 31993259 |
Alejandro Terrones1, Ana Juan1.
Abstract
PREMISE: Microsatellite markers were developed for the western Mediterranean tree Tamarix gallica (Tamaricaceae) as part of a study of its genetic diversity and structure. METHODS ANDEntities:
Keywords: Tamaricaceae; Tamarix gallica; genetic diversity; saltcedar; simple sequence repeat (SSR) markers; species delimitation
Year: 2020 PMID: 31993259 PMCID: PMC6976893 DOI: 10.1002/aps3.11317
Source DB: PubMed Journal: Appl Plant Sci ISSN: 2168-0450 Impact factor: 1.936
Characteristics of the 17 microsatellite loci developed in Tamarix gallica that successfully amplified.
| Locus | Primer sequences (5′–3′) | Repeat motif | Allele size range (bp) |
| Mix | Fluorescent dye | Concentration (F/R) (μM) | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|
| T125‐4 |
| (TGTA)7 | 121–145 | 7 | 1 | FAM | 0.04/0.16 | MN497849 |
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| T133‐2 |
| (TC)10 | 129–151 | 7 | 1 | HEX | 0.04/0.16 | MN497850 |
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| T129‐2 |
| (CA)7 | 115–151 | 16 | 1 | TAMRA | 0.06/0.24 | MN497851 |
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| T163‐3 |
| (CTC)7 | 186–198 | 5 | 1 | TAMRA | 0.04/0.16 | MN497852 |
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| T140‐31 |
| (TTC)8 | 137–152 | 7 | 2 | FAM | 0.04/0.16 | MN497853 |
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| T113‐3 |
| (GAT)7 | 93–99 | 3 | 2 | HEX | 0.04/0.16 | MN497854 |
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| T190‐32 |
| (CGA)8 | 128–135 | 4 | 2 | HEX | 0.04/0.16 | MN497855 |
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| T190‐3 |
| (GAG)7 | 168–189 | 6 | 2 | TAMRA | 0.04/0.16 | MN497856 |
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| T214‐3 |
| (ATT)5 | 104–107 | 2 | 2 | TAMRA | 0.04/0.16 | MN497857 |
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| T145‐3 |
| (TCT)13 | 90–117 | 10 | 3 | FAM | 0.04/0.16 | MN497858 |
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| T134‐31 |
| (TCT)12 | 141–168 | 7 | 3 | HEX | 0.04/0.16 | MN497859 |
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| T190‐33 |
| (CTT)6 | 107–113 | 3 | 3 | HEX | 0.04/0.16 | MN497860 |
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| T140‐32 |
| (CTT)7 | 123–132 | 4 | 3 | TAMRA | 0.04/0.16 | MN497861 |
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| T230‐2 |
| (TC)12 | 232–265 | 14 | 3 | TAMRA | 0.06/0.24 | MN497862 |
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| T168‐2 |
| (GA)7 | 169 | M | — | — | — | MN560186 |
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| T193‐3 |
| (TTC)14 | 188 | M | — | — | — | MN560187 |
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| T300‐2 |
| (AC)6 | 299 | M | — | — | — | MN560185 |
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|
A = number of alleles; M = monomorphic.
The annealing temperature was 56°C for all loci.
PCR primer concentration.
Genetic properties of the 14 polymorphic microsatellites developed in Tamarix gallica.
| Locus | Antas ( | Cagliari ( | Elche ( | Tablas de Daimiel ( | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Null alleles |
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| Null alleles |
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| Null alleles |
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| Null alleles | |
| T125‐4 | 6 | 2.663 | 0.833 | 0.624 | — | 5 | 2.875 | 0.567 | 0.652 | — | 6 | 4.327 | 0.767 | 0.769 | — | 5 | 1.928 | 0.500 | 0.481 | — |
| T133‐2 | 4 | 1.515 | 0.133 | 0.340 | 0.227 | 6 | 2.459 | 0.433 | 0.593 | 0.117 | 5 | 2.217 | 0.233 | 0.549 | 0.254 | 4 | 2.557 | 0.281 | 0.609 | 0.244 |
| T129‐2 | 13 | 5.941 | 0.900 | 0.832 | — | 9 | 7.317 | 0.833 | 0.863 | — | 8 | 2.965 | 0.733 | 0.663 | — | 5 | 3.131 | 0.813 | 0.681 | — |
| T163‐3 | 3 | 1.268 | 0.233 | 0.212 | — | 4 | 2.002 | 0.433 | 0.501 | — | 3 | 1.412 | 0.267 | 0.292 | — | 2 | 1.064 | 0.063 | 0.061 | — |
| T140‐31 | 6 | 3.114 | 0.633 | 0.679 | — | 3 | 2.456 | 0.533 | 0.593 | — | 4 | 2.308 | 0.500 | 0.567 | — | 4 | 2.114 | 0.500 | 0.527 | — |
| T113‐3 | 3 | 2.335 | 0.300 | 0.572 | 0.221 | 3 | 1.802 | 0.500 | 0.445 | — | 3 | 2.299 | 0.500 | 0.565 | — | 3 | 1.575 | 0.375 | 0.365 | — |
| T190‐32 | 4 | 2.002 | 0.533 | 0.501 | — | 2 | 1.342 | 0.300 | 0.255 | — | 2 | 1.763 | 0.500 | 0.433 | — | 2 | 1.882 | 0.313 | 0.469 | 0.152 |
| T190‐3 | 2 | 1.220 | 0.200 | 0.180 | — | 5 | 1.950 | 0.500 | 0.487 | — | 4 | 1.367 | 0.300 | 0.268 | — | 2 | 1.398 | 0.281 | 0.285 | — |
| T214‐3 | 1 | 1.000 | 0.000 | 0.000 | — | 2 | 1.763 | 0.500 | 0.433 | — | 1 | 1.000 | 0.000 | 0.000 | — | 1 | 1.000 | 0.000 | 0.000 | — |
| T145‐3 | 8 | 4.094 | 0.357 | 0.756 | 0.256 | 8 | 6.081 | 0.400 | 0.836 | 0.252 | 5 | 3.147 | 0.333 | 0.682 | 0.246 | 7 | 4.830 | 0.469 | 0.793 | 0.202 |
| T134‐31 | 4 | 1.410 | 0.267 | 0.291 | — | 4 | 2.462 | 0.633 | 0.594 | — | 4 | 1.468 | 0.333 | 0.319 | — | 4 | 2.190 | 0.531 | 0.543 | — |
| T190‐33 | 1 | 1.000 | 0.000 | 0.000 | — | 3 | 1.350 | 0.300 | 0.259 | — | 1 | 1.000 | 0.000 | 0.000 | — | 1 | 1.000 | 0.000 | 0.000 | — |
| T140‐32 | 4 | 2.799 | 0.400 | 0.643 | 0.183 | 2 | 1.471 | 0.200 | 0.320 | 0.153 | 4 | 1.978 | 0.533 | 0.494 | — | 3 | 2.118 | 0.344 | 0.528 | 0.165 |
| T230‐2 | 8 | 3.711 | 0.467 | 0.731 | 0.177 | 6 | 3.396 | 0.700 | 0.706 | — | 10 | 3.273 | 0.533 | 0.694 | 0.116 | 4 | 1.653 | 0.313 | 0.395 | — |
A = number of alleles; A e = effective number of alleles; H e = expected heterozygosity; H o = observed heterozygosity; n = number of individuals sampled.
For locus T145‐3 in Antas population, n = 28.
Significant deviation from Hardy–Weinberg equilibrium (P < 0.05).
Size ranges (in base pairs) of the 14 polymorphic microsatellite loci developed in Tamarix gallica cross‐amplified in 19 Tamarix species.
| Species | T125‐4 | T133‐2 | T129‐2 | T163‐3 | T140‐31 | T113‐3 | T190‐32 | T190‐3 | T214‐3 | T145‐3 | T134‐31 | T190‐33 | T140‐32 | T230‐2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| — | 131–159 | 116–137 | 184–187 | 134–163 | 87–99 | 129 | 165–171 | 104 | 93–111 | 150–165 | 208–209 | — | 229–247 |
|
| — | 129–133 | 118 | 186 | 160–172 | 96 | 129 | — | 122–137 | 96–102 | 144 | 208 | 129 | 236–240 |
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| — | 128 | — | 192 | 131–134 | 93 (1) | — | — | 104 | — | 156 | 209–210 | 132 | — |
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| — | 131 | 115 | 183–189 | 128–161 | 93 | 129–135 | 171–183 | 104 | 96–105 | 156–165 | 110 | 126 | 234–239 |
|
| 113–129 | 131–133 | 119–129 | 184–195 | 137–157 | 96–99 | 129–132 | 171–195 | 104 | 96–114 | 150–162 | 110 | 114–129 | 232–247 |
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| 117–141 | 131–159 | 115–133 | 187–189 | 128–157 | 93–96 | 129 | 165–177 | 104–107 | 93–117 | 150–162 | 110–209 | 126–132 (5) | 229–261 |
|
| — | 131–135 | 101 | 180 | 128 | 96 | 126 | 168 | 104 | 99 | 156 | 183 | 123 | 238 |
|
| — | 131–139 | 123 (1) | 181–186 | 137–157 | 96 (1) | 129 (1) | 165 (1) | 104 | 96 (2) | 150–159 (2) | 198–208 | 126–189 | 229–243 (3) |
|
| — | 131–139 | 104–125 | 180–195 | 128–135 | 93–96 | 129–135 | 174–192 (2) | 104 | 93–99 | — | 110–209 | 123 | — |
|
| — | 131–135 | 109 | 189 | 143–146 | 96 | 129–132 | 167 | 104 | 96 | 150 | 107 | 123 | 239 |
|
| 117–129 (1) | 131 | 117–134 | 183–195 | 126–129 | — | 129–132 | 171–180 | 104 | 99–126 | 150 (1) | 110–113 | 123 | 232–241 |
|
| — | 131 | 123–127 | 186 | 135–142 | — | 129 | 168–174 | 104 | 90–99 | 150 | — | 123 | 234–245 |
|
| — | 131–139 | 119–127 | 186–189 | 137–157 | 93–96 | 129–132 | 192–195 | 104 | — | 150–153 | 110–208 | 123–126 | 235–260 |
|
| — | 131 | 115 | 189 | 128 | 93 | 129 | 171 | 104 | 109 | 153–159 | 110 | 126–129 | 240–267 |
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| 160 (2) | 131–149 | 123–133 | 189 | 128–144 | 93 | 129 | 177 | 104 | 96 | 153–165 | 110–208 | 123 | 232–236 |
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| — | 131 | 124 | 180 | 128 | — | 126 | 168 | 104 | 90 | — | 208 | 123 | 238 |
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| — | 131–149 | 113–123 | 180–189 | 129 | — | 129–132 | 171–183 | 104 | 99 (1) | 150 (1) | 208 | 123 (1) | 234–236 |
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| — | 129–133 | 113–127 | 183–195 | 137 | 96 | 129–132 | 174–177 (2) | 104 | 91–99 (2) | 150–162 | 110 | 126 | 235–243 |
|
| — | 135–137 | — | 183–189 | 137–140 | 93 | — | 153–165 (2) | 104 | — | 162–168 | 208 | 141 | — |
Numbers in parentheses indicate the number of samples that successfully amplified. No number in parentheses indicates that all samples were successfully amplified. A dash indicates no successful amplification for any sample.
| Species | Voucher specimen accession no. | Collection locality | Geographic coordinates (WGS84) |
|
|---|---|---|---|---|
|
| ABH 73511 | Portugal, Baixo Alentejo, Melides, Lagoa de Melides | 38.129, −8.789 | 2 |
| ABH 70789 | Spain, Castellón, Burriana, Clot de la Mare de Déu | 39.879, −0.055 | 12 | |
| ABH 70742 | Spain, Murcia, Águilas, Rambla de Minglano de Cañarete | 37.433, −1.629 | 2 | |
|
| ABH 70685 | Algeria, Biskra, N3 crossing with Oumache, Km 336 | 34.719, 5.739 | 4 |
|
| ABH 70064 | Italy, Sardinia, Oristano, Cabras, Is Aruttas | 39.954, 8.403 | 1 |
| ABH 71909 | Morocco, Nador, Berkane, Oued Moulouya | 35.103, −2.360 | 1 | |
| ABH 54208 | Morocco, Nador, Driouch | 34.972, −3.360 | 1 | |
|
| MO 5568719 | Iran, Esfahan, Road from Tehran to Nain, south of junction to Esfahan | 33.0152, 52.5238 | 1 |
| MO 5568891 | Iran, Qom, old rd. from Tehran to Qom | 35.1705, 50.9777 | 1 | |
|
| ABH 70782 | Spain, Alicante, Santa Pola, Salinas de Santa Pola | 38.184, −0.602 | 6 |
| ABH 68315 | Spain, Almería, Cabo de Gata | 36.773, −2.238 | 12 | |
|
| ABH 69606 | Spain, Canary Islands, Gran Canaria, beach of La Aldea de San Nicolás | 27.996, −15.824 | 12 |
|
| Gaskin 202 | South Korea | — | 1 |
|
| ABH 57833 | Albania, Shkoder, next to rd. at south of Shkoder | 41.968, 19.547 | 1 |
| ABH 57829 | Albania, Vlore, Sarande, Borsh | 40.047, 19.846 | 1 | |
| ABH 57830 | Albania, Vlore, Sarande, Vrion, rd. from Greece to Sarande | 39.904, 20.084 | 1 | |
| ABH 57843 | Montenegro, Bar, south of Bar | 42.093, 19.104 | 1 | |
|
| ABH 70037 | Italy, Sardinia, Cagliari, Stani Simbirizzi | 39.2631, 9.2086 | 30 |
| ABH 69543 | Spain, Alicante, Elche, Pantano de Elche | 38.3174, −0.718 | 30 | |
| ABH 67467 | Spain, Almería, Vera, río Antas | 37.2054, −1.8291 | 30 | |
| ABH 73456 | Spain, Ciudad Real, Daimiel, Tablas de Daimiel | 39.1521, −3.7106 | 32 | |
|
| ABH 59877 | Greece, Central Greece, Molos‐Agios Konstantinos, Neo Thronio | 38.834, 22.703 | 1 |
| ABH 59025 | Greece, Epirus, Igoumenitsa, Marshes at NW of Igoumenitsa | 39.525, 20.198 | 1 | |
| ABH 57891 | Montenegro, Ulcinj, Sveti Nikola, Bojana river | 41.870, 19.352 | 1 | |
|
| Gaskin 10164 | China | — | 1 |
|
| MO 5568893 | Iran, Gilan, rd. from Rasht to Tehran, near Gangeh, south of Rasht | 36.8641, 49.4811 | 1 |
| MO 5568696 | Iran, Semnan, NE of Sharud toward Gorgon | 36.7252, 55.2975 | 1 | |
|
| Gaskin 10177 | China | — | 1 |
|
| ABH 54194 | Greece, Crete, Chania, Georgioupoli | 35.365, 24.248 | 1 |
| ABH 54195 | Greece, Crete, Chania, near Platanias | 35.356, 24.260 | 1 | |
| MO 6207620 | Greece, Crete, Nomos Chanion, Eparchia Apokoronou Georgioupoli beach | 35.359, 24.266 | 1 | |
|
| ABH 54320 | Greece, Crete, Chania, Paleochora beach | 35.223, 23.670 | 1 |
| ABH 54314 | Greece, Crete, Heraklion, Aposelemis | 35.330, 25.327 | 1 | |
| ABH 54317 | Greece, Crete, Heraklion, Kalo Nero | 35.014, 26.046 | 1 | |
| ABH 54326 | Greece, Crete, Heraklion, near Dermatos | 34.979, 25.335 | 1 | |
| ABH 54323 | Greece, Crete, Heraklion, near Dermatos | 34.979, 25.324 | 1 | |
| ABH 54316 | Greece, Crete, Lassithi, Xerokambos | 35.051, 26.232 | 1 | |
|
| ABH 54197 | Greece, Crete, Heraklion, near Aposelemis | 35.321, 25.327 | 1 |
| ABH 54321 | Greece, Crete, Heraklion, near Dermatos | 34.979, 25.324 | 1 | |
| ABH 55398 | Spain, Alicante, Biar, Santuario Mare de Déu de Gràcia | 38.629, −0.760 | 1 | |
|
| W 2009‐19143 | Argentina, San Juan, Ullum, at Termas de Talacasto | −31.03, −68.75 | 1 |
|
| W 2003‐14043 | Armenia, Vayots'Dzor, Yeghegnadzor | 39.68, 45.22 | 1 |
| Gaskin 4690‐06 | Turkey | — | 1 | |
|
| W 2007‐14048 | Egypt, New Valley, Western Desert Dakhleh Oasis | 25.667, 28.870 | 1 |
| W 2007‐25728 | Egypt, South Sinai, Dahab, Wadi Qnai, Oase, salzreicher Feuchtstandort | 28.4532, 34.4492 | 1 | |
| W 2007‐07364 | Jordan, Al Asimah, 11.5 km NE end of Dead Sea, 2 km N v. Tell Iktanu | 31.833, 35.676 | 1 | |
|
| ABH 58684 | Namibia, Erongo, Swerkobmund | −22.708, 14.961 | 2 |
| ABH 58683 | South Africa, Western Cape, Prince Albert, betw. Lainsburg and Beaufort West | −33.085, 21.579 | 1 |
N = number of individuals.
Vouchers were deposited at the herbaria of Universidad de Alicante, Spain (ABH); research collection of John F. Gaskin, Sidney, Montana, USA (Gaskin); Missouri Botanical Garden, St. Louis, Missouri, USA (MO); and Naturhistorisches Museum Wien, Vienna, Austria (W).