Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microsatellite Primer Development
2.2. Microsatellite Characterization and Preliminary Population Genetics Analyses
3. Results and Discussion
3.1. Microsatellite Primer Development
3.2. Population Genetics in Prioria balsamifera
3.3. Population Genetics in Prioria oxyphylla
3.4. Microsatellite Cross-Species Amplification in African Prioria
4. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Locus | Primer Sequences (5′-3′) 1 | Labelled Primer | Repeat Motif 2 | Allele Size Range (bp) | GenBank Accession No. |
---|---|---|---|---|---|
Prioria balsamifera | |||||
Multiplex 1 | |||||
PriB07 | F: CACTGCTTAGAGCGATGCTCAGGGCAAGATGAATAATG | Q3-VIC | (TC)8 | 144–147 | MN648900 |
R: AAAGGAACCACCGATGAATA | |||||
PriB19 | F: CACTGCTTAGAGCGATGCTCTGAATTATTATCAGCCACTTC | Q3-VIC | (TC)8 | 198–207 | MN648909 |
R: GGCGTTTCTTAATTTGGTTT | |||||
PriB23 | F: CACTGCTTAGAGCGATGCTAATATGGAGTCATCGCTTCC | Q3-VIC | (GA)9 | 243–254 | MN648912 |
R: GCATTCGGACAGAGGGAG | |||||
PriB10 | F: TAGGAGTGCAGCAAGCATTTTGCATCTAAAGTTTGAGGG | Q2-NED | (AG)9 | 146–149 | MN648902 |
R: TAATGGAGCTTATGCTTTGG | |||||
PriB22 | F: TAGGAGTGCAGCAAGCATAACGGACCGGTACTTACAGA | Q2-NED | (TG)9 | 203–211 | MN648911 |
R: GCTTAGACAAATGTTAGAATCACC | |||||
PriB04 | F: CTAGTTATTGCTCAGCGGTAATATGCTTGGAATGGATGG | Q4-PET | (GA)8 | 113–142 | MN648899 |
R: ATTACTCCTTGGCGCAGTC | |||||
Multiplex 2 | |||||
PriB13 | F: TGTAAAACGACGGCCAGTTGTTTACTAACTTGCAGAATCCA | Q1-6-FAM | (CT)12 | 139–159 | MN648905 |
R: CAGTAAGGATGGCTCTCCC | |||||
PriB15 | F: CACTGCTTAGAGCGATGCCAAGTCTACGCCAAATGGTC | Q3-VIC | (TC)12 | 147–167 | MN648907 |
R: GCGTTTAAACATCAATTGGAC | |||||
PriB02 | F: TAGGAGTGCAGCAAGCATTGCGTGTACATGTGTATCTCC | Q2-NED | (GA)10 | 95–116 | MN648897 |
R: AGACACCCAACTTTCAATGAT | |||||
PriB14 | F: TAGGAGTGCAGCAAGCATGGGAAGACAAACAAGAGTCAG | Q2-NED | (CT)9 | 153–157 | MN648906 |
R: TGACCTAAAGAATAAGACATCCC | |||||
PriB12 | F: CTAGTTATTGCTCAGCGGTAAATTTGCCCTCCCTTACAT | Q4-PET | (GT)12 | 136–159 | MN648904 |
R: TGACTACAAAGCATATGAATAGAAA | |||||
Multiplex 3 | |||||
PriB03 | F: CACTGCTTAGAGCGATGCATCGGTGAGTACATCGAACC | Q3-VIC | (AC)8 | 106–112 | MN648898 |
R: GCAGTTCAAGTTAGTTTGTGC | |||||
PriB11 | F: CACTGCTTAGAGCGATGCCAATAGAATGATGGTCAAGAGC | Q3-VIC | (CT)8 | 144–160 | MN648903 |
R: CTTCCAGAGAAACCCACCT | |||||
PriB18 | F: TAGGAGTGCAGCAAGCATAGAGTCGTTGTGAGCTGTGA | Q2-NED | (AG)14 | 168–202 | MN648908 |
R: AGTGACACGCGTTCAAATAC | |||||
PriB08 | F: CTAGTTATTGCTCAGCGGTATATTGCAGCAGAGACACCA | Q4-PET | (AG)8 | 147–167 | MN648901 |
R: AGTTTCGCTCTTCTTACCGA | |||||
PriB20 | F: CTAGTTATTGCTCAGCGGTTGTGTTGCAAGAACGATAGTC | Q4-PET | (GA)10 | 196–223 | MN648910 |
R: ACAAGACTCTAAATTCCAAGACA | |||||
Prioria oxyphylla | |||||
Multiplex 1 | |||||
PriO03 | F: CACTGCTTAGAGCGATGCGAGAAGTGGTCTCCAACCAT | Q3-VIC | (TC)8 | 103–117 | MN648914 |
R: CCTGAAGTCGAGAGGAGTGT | |||||
PriO23 | F: CACTGCTTAGAGCGATGCTTACGCTATTTACTTTGCCGT | Q3-VIC | (AG)9 | 196–213 | MN648926 |
R: GCGTTTATGTGAAGCATTTG | |||||
PriO18 | F: TAGGAGTGCAGCAAGCATAGGAGGTCCCGGATAATCTA | Q2-NED | (TTG)8 | 168–185 | MN648922 |
R: TAGGGACATGAGCAGTAGCA | |||||
PriO04 | F: CTAGTTATTGCTCAGCGGTTACATGCACCGTTTGAGTGT | Q4-PET | (CT)11 | 115–120 | MN648915 |
R: CTGCGTTTGAAGTGGAAAT | |||||
Multiplex 2 | |||||
PriO13 | F: TGTAAAACGACGGCCAGTTGGAAATCATTCAATCTCCC | Q1-6-FAM | (GCA)8 | 151–162 | MN648919 |
R: ATCCATCCCTCCTCGTTG | |||||
PriO19 | F: CACTGCTTAGAGCGATGCGAAATTCTGTGGTAGTGGTGG | Q3-VIC | (TTC)8 | 182–227 | MN648923 |
R: GAGCTATCAATATCACCAAACG | |||||
PriO10 | F: TAGGAGTGCAGCAAGCATAACCCTCTCACTTCCATCTTT | Q2-NED | (TC)12 | 128–151 | MN648918 |
R: GAAGGCCTAAGTAATTATCAACC | |||||
PriO22 | F: TAGGAGTGCAGCAAGCATGTGAGCTGGAACGCAAGT | Q2-NED | (TC)11 | 165–203 | MN648925 |
R: TACGTCCAATCCTTCTAGTCA | |||||
PriO16 | F: CTAGTTATTGCTCAGCGGTTGTCGGAGCCAATCTATTCT | Q4-PET | (AG)11 | 169–189 | MN648921 |
R: CAGCAAATTTCACCACTTCA | |||||
PriO24 | F: CTAGTTATTGCTCAGCGGTGTTGCACGGAGGAAATACAT | Q4-PET | (AG)10 | 250–259 | MN648927 |
R: TGTAGAATAAGATAAGGTTGCCA | |||||
Multiplex 3 | |||||
PriO01 | F: TGTAAAACGACGGCCAGTTGCATAGTGCTACTCCTCACA | Q1-6-FAM | (AG)8 | 94–115 | MN648913 |
R: GGGATGGTCACTACCATAGTT | |||||
PriO07 | F: CACTGCTTAGAGCGATGCTCATCTATCAAGTAAGAGGTGGA | Q3-VIC | (AC)11 | 128–144 | MN648917 |
R: TCTCCACTTGAATGTAAATGCT | |||||
PriO15 | F: CACTGCTTAGAGCGATGCTTTGATAGAGATCAATGGCG | Q3-VIC | (TTG)9 | 155–182 | MN648920 |
R: CAAACTGATACCAAATTAAGTGAA | |||||
PriO06 | F: TAGGAGTGCAGCAAGCATGCACAAGAGGCTATGGAGTT | Q2-NED | (AG)9 | 111–135 | MN648916 |
R: AACCGTTGGAATTCTCGTTA | |||||
PriO20 | F: CTAGTTATTGCTCAGCGGTTCACCAGGATGTATAACATTGC | Q4-PET | (TC)10 | 193–213 | MN648924 |
R: GTATATTGCGTGAACATACCCA |
PIC | Na | Na | Ho | He | FIS | Null | Na | Ho | He | FIS | Null | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Prioria balsamifera | Luki (n = 34) | Yangambi (n = 31) | ||||||||||
PriB07 | 0.292 | 2 | 2 | 0.412 | 0.500 | 0.179 | 0.055 | 1 | 0.000 | 0.000 | na | na |
PriB19 | 0.044 | 2 | 2 | 0.088 | 0.086 | −0.031 | 0.000 | 1 | 0.000 | 0.000 | na | na |
PriB23 | 0.372 | 4 | 2 | 0.559 | 0.507 | −0.104 | 0.000 | 4 | 0.258 | 0.237 | −0.088 | 0.000 |
PriB10 | 0.336 | 2 | 2 | 0.382 | 0.314 | −0.222 | 0.000 | 2 | 0.483 | 0.503 | 0.042 | 0.013 |
PriB22 | 0.197 | 3 | 3 | 0.382 | 0.372 | −0.029 | 0.000 | 1 | 0.000 | 0.000 | na | na |
PriB04 | 0.000 | 1 | 1 | 0.000 | 0.000 | na | na | 1 | 0.000 | 0.000 | na | na |
PriB13 | 0.705 | 7 | 6 | 0.706 | 0.684 | −0.032 | 0.000 | 5 | 0.548 | 0.535 | −0.025 | 0.000 |
PriB15 | 0.584 | 6 | 5 | 0.735 | 0.613 | −0.204 | 0.000 | 3 | 0.613 | 0.524 | −0.173 | 0.000 |
PriB02 | 0.651 | 9 | 5 | 0.441 | 0.446 | 0.010 | 0.002 | 6 | 0.516 | 0.749 | 0.314 * | 0.125 |
PriB14 | 0.000 | 1 | 1 | 0.000 | 0.000 | na | na | 1 | 0.000 | 0.000 | na | na |
PriB12 | 0.737 | 7 | 4 | 0.500 | 0.741 | 0.328 * | 0.141 | 4 | 0.655 | 0.649 | −0.009 | 0.018 |
PriB03 | 0.404 | 3 | 3 | 0.529 | 0.551 | 0.040 | 0.045 | 2 | 0.419 | 0.455 | 0.080 | 0.021 |
PriB11 | 0.529 | 6 | 5 | 0.647 | 0.544 | −0.194 | 0.000 | 3 | 0.516 | 0.539 | 0.044 | 0.007 |
PriB18 | 0.316 | 7 | 3 | 0.147 | 0.140 | −0.051 | 0.000 | 7 | 0.226 | 0.507 | 0.558 * | 0.209 |
PriB08 | 0.146 | 3 | 3 | 0.324 | 0.280 | −0.160 | 0.000 | 1 | 0.000 | 0.000 | na | na |
PriB20 | 0.518 | 6 | 5 | 0.735 | 0.608 | −0.213 | 0.000 | 4 | 0.138 | 0.134 | −0.032 | 0.000 |
Multilocus average | 0.364 | 4.313 | 3.250 | 0.412 | 0.399 | −0.032 | 0.017 | 2.880 | 0.273 | 0.302 | 0.097 | 0.037 |
Prioria oxyphylla | Luki (n = 21) | Yangambi (n = 32) | ||||||||||
PriO03 | 0.504 | 6 | 5 | 0.714 | 0.688 | −0.040 | 0.000 | 4 | 0.250 | 0.308 | 0.191 | 0.048 |
PriO23 | 0.597 | 4 | 1 | 0.000 | 0.000 | na | na | 3 | 0.071 | 0.505 | 0.863 * | 0.748 |
PriO18 | 0.309 | 3 | 3 | 0.154 | 0.465 | 0.678 * | 0.486 | 1 | 0.000 | 0.000 | na | na |
PriO04 | 0.367 | 2 | 1 | 0.000 | 0.000 | na | na | 1 | 0.000 | 0.000 | na | na |
PriO13 | 0.593 | 4 | 4 | 0.524 | 0.515 | −0.019 | 0.000 | 3 | 0.625 | 0.659 | 0.052 | 0.010 |
PriO19 | 0.720 | 10 | 4 | 0.429 | 0.484 | 0.118 | 0.015 | 8 | 0.563 | 0.640 | 0.123 | 0.058 |
PriO10 | 0.679 | 6 | 3 | 0.158 | 0.457 | 0.660* | 0.348 | 5 | 0.130 | 0.621 | 0.794 * | 0.550 |
PriO22 | 0.606 | 5 | 3 | 0.111 | 0.307 | 0.652 | 0.451 | 3 | 0.438 | 0.538 | 0.189 | 0.092 |
PriO16 | 0.136 | 2 | 1 | 0.000 | 0.000 | na | na | 2 | 0.000 | 0.239 | 1.000 * | 0.000 |
PriO24 | 0.416 | 4 | 4 | 0.421 | 0.467 | 0.100 | 0.065 | 3 | 0.000 | 0.420 | 1.000 * | 0.000 |
PriO01 | 0.706 | 6 | 5 | 0.476 | 0.621 | 0.238 | 0.091 | 4 | 0.625 | 0.646 | 0.033 | 0.000 |
PriO07 | 0.754 | 8 | 4 | 0.167 | 0.557 | 0.707 * | 0.415 | 8 | 0.615 | 0.810 | 0.244 * | 0.133 |
Prio15 | 0.589 | 5 | 4 | 0.000 | 0.788 | 1.000 * | 0.000 | 2 | 0.000 | 0.515 | 1.000 * | 0.000 |
PriO06 | 0.782 | 10 | 6 | 0.762 | 0.731 | −0.044 | 0.013 | 8 | 0.750 | 0.750 | 0.000 | 0.000 |
PriO20 | 0.706 | 7 | 2 | 0.000 | 0.356 | 1.000 | 0.000 | 6 | 0.261 | 0.667 | 0.614 * | 0.424 |
Multilocus average | 0.564 | 5.467 | 3.330 | 0.261 | 0.429 | 0.407 | 0.157 | 4.070 | 0.289 | 0.488 | 0.416 | 0.159 |
Species | PriB07 | PriB19 | PriB23 | PriB10 | PriB22 | PriB04 | PriB13 | PriB15 | PriB02 | PriB14 | PriB12 | PriB03 | PriB11 | PriB18 | PriB08 | PriB20 | 16 SSRs |
Prioria balsamifera | X | X | X | X | X | X | X | X | X | X | X | X | X | X | X | X | 16 |
Prioria oxyphylla | X | X | X | X | X | X | 6 | ||||||||||
Prioria buchholzii | X | X | X | X | X | X | X | X | 8 | ||||||||
Prioria msoo | X | X | X | 3 | |||||||||||||
Prioria gilbertii | X | X | X | X | 4 | ||||||||||||
Prioria mannii | X | X | 2 | ||||||||||||||
Prioria joveri | 0 | ||||||||||||||||
Overall | 1 | 1 | 1 | 1 | 1 | 5 | 1 | 4 | 2 | 2 | 2 | 3 | 4 | 1 | 6 | 4 | |
PriO03 | PriO23 | PriO18 | PriO04 | PriO13 | PriO19 | PriO10 | PriO22 | PriO16 | PriO24 | PriO01 | PriO07 | PriO15 | PriO06 | PriO20 | 15 SSRs | ||
Prioria balsamifera | X | 1 | |||||||||||||||
Prioria oxyphylla | X | X | X | X | X | X | X | X | X | X | X | X | X | X | X | 15 | |
Prioria buchholzii | X | X | X | X | X | X | X | X | X | X | X | X | X | 13 | |||
Prioria msoo | X | X | X | X | X | X | 6 | ||||||||||
Prioria gilbertii | X | X | X | X | X | 5 | |||||||||||
Prioria mannii | X | X | X | 3 | |||||||||||||
Prioria joveri | X | X | 2 | ||||||||||||||
Overall | 3 | 4 | 2 | 1 | 5 | 6 | 2 | 2 | 3 | 2 | 4 | 2 | 3 | 5 | 1 |
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Vanden Abeele, S.; Hardy, O.J.; Beeckman, H.; Ilondea, B.A.; Janssens, S.B. Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla. Forests 2019, 10, 1037. https://doi.org/10.3390/f10111037
Vanden Abeele S, Hardy OJ, Beeckman H, Ilondea BA, Janssens SB. Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla. Forests. 2019; 10(11):1037. https://doi.org/10.3390/f10111037
Chicago/Turabian StyleVanden Abeele, Samuel, Olivier J. Hardy, Hans Beeckman, Bhély Angoboy Ilondea, and Steven B. Janssens. 2019. "Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla" Forests 10, no. 11: 1037. https://doi.org/10.3390/f10111037