Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. DNA Extraction and Amplification
2.3. SSR Analysis
2.4. ISSR Analysis
2.5. Statistical Analysis
2.5.1. SSR Markers
2.5.2. ISSR Markers
2.5.3. Association Analysis
3. Results
3.1. Genetic Relationships Based on the SSR Markers
3.2. Genetic Relationships Based on ISSR Analysis
3.3. Association of SSR Loci with Chemical Compounds and Bulb Morphological Traits
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accessions | Collection Site | Prefecture | Latitude | Longitude | Altitude (m) |
---|---|---|---|---|---|
AS1 | Agios Petros | Lefkada | 38°40′ Ν | 20°36′ Ε | 328 |
AS2 | Nea Vyssa (market) | Evros | 41°35′ Ν | 26°32′ Ε | 31 |
AS4 | Polichni | Messinia | 37°16′ N | 21°56′ Ε | 432 |
AS5 | Κarya | Lefkada | 38°45′ Ν | 20°38′ Ε | 510 |
AS6 | Katouna | Lefkada | 38°46′ N | 20°42′ Ε | 165 |
AS7 | Tripoli | Arkadia | 37°30′ N | 22°22′ Ε | 662 |
AS8 | Manasi | Lefkada | 38°41′ Ν | 20°36′ Ε | 557 |
AS9 | Vrysoula | Ioannina | 39°40′ Ν | 20°32′ Ε | 220 |
AS10 | Trachy, Skyros Island | Evia | 38°57′ Ν | 24°30′ Ε | 10 |
AS11 | Tsoureki | Messinia | 37°19′ Ν | 21°57′ Ε | 467 |
AS12 | Κefalonia (market) | Kefalonia | 38°17′ Ν | 20°31′ Ε | 500 |
AS13 | Andania | Messinia | 37°15′ Ν | 21°59′ Ε | 85 |
AS14 | Komotini | Rodopi | 41°05′ Ν | 25°24′ Ε | 42 |
AS15 | Altomira | Messinia | 36°58′ Ν | 22°13′ Ε | 827 |
AS17 | Mavriki(i) | Arkadia | 37°23′ Ν | 22°27′ Ε | 950 |
AS19 | Lithovouni | Arkadia | 37°28′ Ν | 22°27′ Ε | 676 |
AS21 | Stadio Tripoleos | Arkadia | 37°27′ N | 22°26′ Ε | 675 |
AS23 | Kakaletri | Messinia | 37°24′ Ν | 22°55′ Ε | 607 |
AS24 | Dermatianika | Lakonia | 36°54′ Ν | 23°02′ Ε | 35 |
AS25 | Mesa Vouni, Andros Island | Cyclades | 37°47′ Ν | 24°55′ Ε | 585 |
AS28 | Kitries | Messinia | 36°55′ Ν | 22°08′ Ε | 3 |
AS30 | Agios Theodoros | Kefalonia | 38°11′ Ν | 20°28′ Ε | 2 |
AS32 | Megali Mantineia | Messinia | 36°57′ Ν | 22°09′ Ε | 207 |
AS33 | Kato Doloi | Messinia | 36°93′ Ν | 22°17′ Ε | 315 |
AS34 | Milos Island | Cyclades | 36°40′ Ν | 24°23′ Ε | 153 |
AS35 | Manthurea | Arkadia | 37°24′ Ν | 22°23′ Ε | 750 |
AS36 | Mavriki(ii) | Arkadia | 37°23′ Ν | 22°27′ Ε | 950 |
SSR | Repeat Motif | Forward Primer | Labelling | Reverse Primer | Tm (°C) |
---|---|---|---|---|---|
Asa08 1 | (GT)8 | TGATTGAAACGAATCCCACA | 5′ FAM | GGGGGTTACCTGAACCTGTTA | 54 |
Asa10 1 | (AC)7 | TTGTTGTTCTGCCATTTT | 5′ HEX | GATCTAAGCCGAGAGAAA | 48 |
Asa24 1 | (GT)4(GT)3(GT)5 | TTGTTGTGCCGAGTTCCATA | 5′ FAM | CAGCAATTTACCAAAGCCAAG | 57 |
GB-AS-076 2 | (GA)7 | CGGCGGGTTTAGTGATTT | 5′ HEX | TTCGTTGGGTTCGATTTG | 52 |
GB-AS-102 2 | (AAAT)3 | AATCATCTTCGGGCCACT | 5′ TAM | CCTAGAACGAGTGTGAAGGG | 52 |
Primer ID | Primer Sequence (5′–3′) | Tm (°C) | No of Bands Scored | Range (bp) | PIC |
---|---|---|---|---|---|
UBC-811 | (GA)8C | 51 °C | 19 | 590–1875 | 0.500 |
UBC-812 | (GA)8A | 51 °C | 16 | 400–2700 | 0.371 |
UBC-818 | (CA)8G | 51 °C | 18 | 490–1800 | 0.499 |
UBC-826 | (AC)8C | 51 °C | 14 | 650–2700 | 0.456 |
UBC-846 | (CA)8RT | 51 °C | 10 | 680–1300 | 0.500 |
UBC-880 | (GGAGA)3 | 51 °C | 7 | 550–1390 | 0.499 |
Locus | Na | Ne | Nm | I | PIC | Obs. Ho | Exp. Ho | Obs. He | Exp. He | Fst |
---|---|---|---|---|---|---|---|---|---|---|
Asa08 | 9 | 3.358 | 0.317 | 1.548 | 0.669 | 0.214 | 0.295 | 0.786 | 0.705 | 0.440 |
Asa10 | 5 | 3.609 | 0.079 | 1.436 | 0.683 | 0.630 | 0.274 | 0.370 | 0.726 | 0.759 |
Asa24 | 4 | 1.873 | 0.338 | 0.807 | 0.398 | 0.464 | 0.532 | 0.536 | 0.468 | 0.425 |
GB-AS-076 | 4 | 2.302 | 0.936 | 0.941 | 0.470 | 0.107 | 0.432 | 0.893 | 0.568 | 0.211 |
GB-AS-102 | 4 | 1.157 | 0.038 | 0.332 | 0.133 | 0.964 | 0.864 | 0.036 | 0.136 | 0.868 |
Mean | 5.2 | 2.460 | 0.251 | 1.013 | 0.471 | 0.476 | 0.480 | 0.524 | 0.520 | 0.500 |
Source | df | SS | MS | Est. Var. | % |
---|---|---|---|---|---|
Among Pops | 27 | 183.036 | 6.779 | 0.678 | 34% |
Among Indiv | 112 | 0.000 | 0.000 | 0.000 | 0% |
Within Indiv | 140 | 182.500 | 1.304 | 1.304 | 66% |
Total | 279 | 365.536 | 1.981 | 100% |
Genotype | Trait | Fisher’s Exact Test (p) | Logistic Regression (p) |
---|---|---|---|
SSR | |||
Asa08-Locus 7 | Allylprop1enyldisulfide | 0.037 | 0.037 |
Asa10-Locus 4 | Pyruvate | 0.036 | 0.05 |
Asa10-Locus 2 | Bulb position of root disc (BPRD) | <0.001 | 0.024 |
Asa10-Locus 5 | Shape of bulb base (SBB) | 0.006 | 0.045 |
Asa10-Locus 2 | 0.002 | 0.024 | |
ISSR | |||
811-Locus 8 | 4H-1,2,3-trithiine | 0.041 | 0.007 |
826-Locus 11 | Anthocyanin stripes on clove scales (ASCS) | 0.003 | 0.05 |
812-Locus 14 | Bulb compactness of cloves (BCC) | 0.004 | 0.006 |
818-Locus 9 | Bulb position of root disc (BPRD) | 0.050 | 0.05 |
846-Locus 6 | Bulb structure type (BST) | 0.010 | 0.008 |
880-Locus 2 | Carbohydrates | 0.008 | 0.032 |
811-Locus 3 | Diallyl trisulfide (DATS) | 0.025 | 0.02 |
811-Locus 2 | Number of cloves per compound bulb (NC/B) | 0.010 | 0.01 |
818-Locus 18 | 0.034 | 0.035 | |
811-Locus 6 | Total Identified Organosulfur Compounds (OS) | 0.015 | 0.039 |
826-Locus 6 | 0.009 | 0.039 | |
826-Locus 9 | Shape of bulb base (SBB) | 0.037 | 0.016 |
846-Locus 6 | 0.007 | 0.03 | |
826-Locus 9 | Shape of Mature Bulb (SMB) | 0.018 | 0.07 |
846-Locus 5 | 0.006 | 0.019 | |
812-Locus 5 | Total soluble solids (TSS) content (oBrix) | 0.008 | 0.027 |
818-Locus 11 | Anthocyanin stripes on dry external scales of bulb (ASBDES) | 0.042 | 0.036 |
846-Locus 6 | 0.050 | 0.012 |
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Papaioannou, C.; Fassou, G.; Petropoulos, S.A.; Lamari, F.N.; Bebeli, P.J.; Papasotiropoulos, V. Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation. Agriculture 2023, 13, 1408. https://doi.org/10.3390/agriculture13071408
Papaioannou C, Fassou G, Petropoulos SA, Lamari FN, Bebeli PJ, Papasotiropoulos V. Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation. Agriculture. 2023; 13(7):1408. https://doi.org/10.3390/agriculture13071408
Chicago/Turabian StylePapaioannou, Charikleia, Georgia Fassou, Spyridon A. Petropoulos, Fotini N. Lamari, Penelope J. Bebeli, and Vasileios Papasotiropoulos. 2023. "Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation" Agriculture 13, no. 7: 1408. https://doi.org/10.3390/agriculture13071408
APA StylePapaioannou, C., Fassou, G., Petropoulos, S. A., Lamari, F. N., Bebeli, P. J., & Papasotiropoulos, V. (2023). Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation. Agriculture, 13(7), 1408. https://doi.org/10.3390/agriculture13071408