DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania
Abstract
:1. Introduction
2. Material and Methods
2.1. The Material
2.2. DNA Extraction
2.3. Mitochondrial DNA Markers
2.4. Nuclear DNA Markers
2.5. Statistical Analyses
3. Results
3.1. The Mitochondrial DNA Analysis
3.2. The Nuclear DNA Analysis
4. Discussion
4.1. DNA Contamination Avoidance
4.2. Evolutionary Origin of Scots Pine
4.3. Genetic Associations with the Present-Day Gene Pools of Scots Pine
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Population | Long | Lat | Nobs | B_1 | C_2 | T_3 | P_2 | Mean4 | B_2 | E_1 | E_2 |
---|---|---|---|---|---|---|---|---|---|---|---|
Northwestern Lithuania | |||||||||||
DARB | 21.42073 | 56.01161 | 17 | 0.42 | 0.13 | 0.14 | 0.28 | 0.24 | 0 | 0.01 | 0.04 |
KAMA | 22.58897 | 56.27021 | 50 | 0.12 | 0.13 | 0.25 | 0.44 | 0.24 | 0 | 0.04 | 0.09 |
KAMA_BOG 2 | 22.58888 | 56.27031 | 50 | 0.81 | 0.47 | 0.27 | 0.19 | 0.44 | 0.02 | 0.01 | 0.04 |
KURT | 23.01582 | 55.84321 | 22 | 0.03 | 0.08 | 0.34 | 0.54 | 0.25 | 0 | 0.01 | 0.01 |
PLUN | 21.67079 | 56.01509 | 20 | 0.62 | 0.15 | 0.65 | 0.37 | 0.45 | 0.05 | 0.09 | 0.07 |
TRYS | 22.60041 | 55.99533 | 19 | 0.28 | 0.05 | 0.05 | 0.06 | 0.11 | 0 | 0.01 | 0.02 |
VARN | 22.49134 | 55.71269 | 21 | 0.39 | 0.25 | 0.43 | 0.19 | 0.31 | 0.08 | 0.02 | 0.14 |
Central Lithuania | |||||||||||
BARG | 23.45353 | 55.49002 | 47 | 0.09 | 0.04 | 0.07 | 0.15 | 0.09 | 0 | 0 | 0.13 |
BARG_BOG 2 | 23.45362 | 55.49013 | 50 | 0.31 | 0.61 | 0.50 | 0.50 | 0.49 | 0.02 | 0.02 | 0.14 |
GRAZ | 26.06653 | 55.65148 | 20 | 0.23 | 0.38 | 0.41 | 0.35 | 0.34 | 0.01 | 0 | 0 |
VAIS | 24.10089 | 54.82318 | 20 | 0.12 | 0.28 | 0.21 | 0.14 | 0.19 | 0.01 | 0.01 | 0.03 |
Eastern Lithuania | |||||||||||
AZVI | 26.03584 | 55.46754 | 20 | 0.2 | 0.08 | 0.2 | 0.18 | 0.17 | 0 | 0.01 | 0 |
GEGU | 24.51172 | 55.80243 | 20 | 0.55 | 0.23 | 0.35 | 0.24 | 0.34 | 0.07 | 0.01 | 0.05 |
LABA | 25.85967 | 55.19655 | 21 | 0.19 | 0.14 | 0.18 | 0.15 | 0.16 | 0.01 | 0 | 0.01 |
MIKE | 25.18647 | 55.67154 | 20 | 0.35 | 0.08 | 0.06 | 0.57 | 0.27 | 0 | 0.03 | 0.01 |
SALA | 26.21100 | 55.82984 | 20 | 0.25 | 0.21 | 0.34 | 0.5 | 0.33 | 0.01 | 0 | 0.02 |
TRAK | 24.83398 | 54.55192 | 19 | 0.16 | 0.2 | 0.16 | 0.05 | 0.14 | 0.01 | 0.01 | 0.01 |
ROKI | 25.63185 | 55.97338 | 20 | 0.05 | 0.28 | 0.29 | 0.37 | 0.25 | 0 | 0.01 | 0.01 |
Southern Lithuania | |||||||||||
ANCI | 23.66721 | 54.08405 | 19 | 0.53 | 0.56 | 0.5 | 0.61 | 0.55 | 0.07 | 0.04 | 0.05 |
BRAZ | 23.43601 | 54.76620 | 20 | 0.25 | 0.2 | 0.71 | 0.46 | 0.41 | 0.01 | 0.05 | 0.02 |
CIAP | 24.45519 | 54.02410 | 50 | 0.81 | 0.19 | 0.33 | 0.59 | 0.48 | 0.05 | 0.02 | 0.06 |
CIAP_BOG 2 | 24.45528 | 54.02415 | 50 | 0.01 | 0.25 | 0.27 | 0.14 | 0.16 | 0.00 | 0.00 | 0.01 |
PUNI | 24.07702 | 54.53224 | 19 | 0.13 | 0.32 | 0.63 | 0.59 | 0.42 | 0.02 | 0.02 | 0.01 |
VEIS | 23.84428 | 54.07806 | 20 | 0.24 | 0.07 | 0.41 | 0.75 | 0.37 | 0.04 | 0.03 | 0.06 |
Southwestern LT | |||||||||||
MOCI | 22.23994 | 55.10132 | 4 | 0.06 | 0.02 | 0.02 | 0.03 | 0.03 | 0.01 | 0 | 0.01 |
NORK | 21.53281 | 55.44790 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
VIES | 22.41296 | 55.08369 | 3 | 0.07 | 0.09 | 0.02 | 0 | 0.04 | 0.01 | 0 | 0.01 |
PAGE | 21.90091 | 55.14596 | 20 | 0.52 | 0.49 | 0.58 | 0.39 | 0.50 | 0.02 | 0.02 | 0.14 |
SVEK | 21.44141 | 55.51897 | 20 | 0.09 | 0.39 | 0.42 | 0.21 | 0.28 | 0.02 | 0 | 0.01 |
JUOD 1 | 21.11488 | 55.52645 | 19 | 0.42 | 0.15 | 0.58 | 0.17 | 0.33 | 0.01 | 0 | 0.05 |
Sea pines | 0 | 0 | 7 | - | - | - | - | - | - | - | - |
Total | 730 |
Tree ID (Lab. ID) | DNA Conc.Ng/Μl | Age, Years BP 1 | Mtdna Nad 7.1 PCR Quality | Mtdna (PCR Attempts) | Ndna Loci of Acceptable Quality | Ndna (PCR Attempts) |
---|---|---|---|---|---|---|
B_1 (RF-I-B) | 27.9 | 10,647–10,178 | Fine, 300 bp | 3 | 11 | 2 |
B_2 (RF-I-B-2) | 13.7 | 11,236–10,780 | Fine, 300 bp | 3 | 11 | 2 |
C_2 (RF-I-C-2) | 16.1 | 11,068–10,574 | Fine, 300 bp | 3 | 11 | 2 |
P_2 (RF-I-P-2) | 16.9 | 10,561–10,256 | NA | 6 | 11 | 2 |
T_3 (RF-I-P2(1)) | 10.9 | 11,103–10,704 | NA | 6 | 11 | 2 |
E_1 (RF-I-E-I) | 12.6 | 11,597–10,768 | NA | 6 | 11 | 3 |
E_2 (RF-I-E-2) | 16.5 | 11,226–10,808 | NA | 6 | 11 | 3 |
A_2 (RF-III-A-2) | 41.1 | 8972–8486 | NA | 6 | 6 not used | 4 |
A_3 (RF-III-A-3) | 33.1 | 9023–8652 | NA | 6 | 6 not used | 4 |
Tree ID | Sample ID | Sample DNA Present in the PCR Mix | Size Standard Quality, RFU 1 | Nad7-1 Allele Size, bp | Nad7-1 Fragment Hight in RFU 1 | mtDNA Haplotype |
---|---|---|---|---|---|---|
C_2 | 1 | Yes | 2000 | 300 | 4871 | A (universal) |
C_2 | 2 | Yes | 2000 | 300 | 4919 | A (universal) |
Control_1 | - | No | 2000 | NA | NA | - |
B_1 | 1 | Yes | 6000 | 300 | 5316 | A (universal) |
B_1 | 2 | Yes | 5500 | 300 | 5719 | A (universal) |
Control_2 | - | No | 5500 | NA | NA | - |
B_2 | 1 | Yes | 4500 | 300 | 3977 | A (universal) |
B_2 | 2 | Yes | 4500 | 300 | 250 | A (universal) |
Control_3 | - | 4500 | NA | NA | - |
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Danusevičius, D.; Buchovska, J.; Žulkus, V.; Daugnora, L.; Girininkas, A. DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania. Forests 2021, 12, 317. https://doi.org/10.3390/f12030317
Danusevičius D, Buchovska J, Žulkus V, Daugnora L, Girininkas A. DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania. Forests. 2021; 12(3):317. https://doi.org/10.3390/f12030317
Chicago/Turabian StyleDanusevičius, Darius, Jurata Buchovska, Vladas Žulkus, Linas Daugnora, and Algirdas Girininkas. 2021. "DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania" Forests 12, no. 3: 317. https://doi.org/10.3390/f12030317
APA StyleDanusevičius, D., Buchovska, J., Žulkus, V., Daugnora, L., & Girininkas, A. (2021). DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania. Forests, 12(3), 317. https://doi.org/10.3390/f12030317