Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling and Fungal Isolation
2.2. DNA Extraction
2.3. PCR Amplification
2.4. Data Analysis
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Type of Locality and Host Genotype | Number of Localities (Number of Strains), Sprayed/Non-Sprayed/Total | ||
---|---|---|---|
Zemgale | Kurzeme | Total | |
Commercial orchards | 3/0/3 (26/0/26) | 5/0/5 (44/0/44) | 8/0/8 (70/0/70) |
‘Lobo’ | 2/0/2 (19/0/19) | 2/0/2 (6/0/6) | 4/0/4 (25/0/25) |
‘Auksis’ | 1/0/1 (7/0/7) | 1/0//1 (2/0//2) | 2/0/1 (9/0/9) |
‘Kovalenkovskoje’ | - | 1/0/1 (7/0/7) | 1/0/1 (7/0/7) |
‘Belorusskoje Malinovoje’ | - | 2/0/2 (14/0/14) | 2/0/2 (14/0/14) |
‘Rubin’ | - | 1/0/1 (6/0/6) | 1/0/1 (6/0/6) |
Malus domestica, unknown | - | 2/0/2 (9/0/9) | 2/0/2 (9/0/9) |
Home gardens | 0/4/4 (0/23/23) | 0/1/1 (0/3/3) | 0/5/5 (0/26/26) |
‘Huvitus’ | 0/1/1 (0/11/11) | - | 0/1/1 (0/11/11) |
‘Sister of Liberty’ | 0/1/1 (0/1/1) | - | 0/1/1 (0/1/1) |
‘Antonovka’ | 0/1/1 (0/2/2) | - | 0/1/1 (0/2/2) |
‘Auksis’ | 0/1/1 (0/1/1) | - | 0/1/1 (0/1/1) |
‘Vista Bella’ | 0/1/1 (0/1/1) | - | 0/1/1 (0/1/1) |
‘Rudens Svītrainais’ | 0/1/1 (0/5/5) | - | 01/1 (0/5/5) |
Malus domestica, unknown | 0/1/1 (0/2/2) | 0/1/1 (0/3/3) | 0/1/1 (0/3/3) |
Germplasm collections | 1/1/2 (12/17/29) | - | 1/1/2 (12/17/29) |
‘Rāja’ | 0/1/1 (0/7/7) | - | 0/1/1 (0/7/7) |
Nr.16-97-109 | 0/1/1 (0/5/5) | - | 0/1/1 (0/5/5) |
‘Belorusskoje Malinovoje’ | 0/1/1 (0/5/5) | - | 0/1/1 (0/5/5) |
Nr.29-97-1 | 1/0/1 (6/0/6) | - | 1/0/1 (6/0/6) |
‘Stars’ | 1/0/1 (5/0/5) | - | 1/0/1 (5/0/5) |
‘Popes ābele’ | 1/0/1 (1/0/1) | - | 1/0/1 (1/0/1) |
Greenery | 0/1/1 (0/18/18) | - | 0/1/1 (0/18/18) |
Columnar apple, unknown | 0/1/1 (0/10/10) | - | 0/1/1 (0/10/10) |
‘Carnikava’ | 0/1/1 (0/4/4) | - | 0/1/1 (0/4/4) |
Malus toringo | 0/1/1 (0/4/4) | - | 0/1/1 (0/4/4) |
Total | 4/6/10 (38/58/96) | 5/1/6 (44/3/47) | 9/7/16 (82/61/143) |
Locus | Primer Sequences, 5′–3′ | Allele Size Range, bp | Annealing Temperature, °C | Reference |
---|---|---|---|---|
Vicacg8/42 | F:(FAM-)TGTCAGCCACGCTAGAAG R:CACCGGACGAATCATGC | 196–232 | 60 | [21] |
Vitg11/70 | F:(HEX-)GAAGAGGTTGGAGTGGTTG R:GAACCGAATCTGTACAGGAC | 184–196 | 60 | |
Vigtg10/95 | F:(ROX-)AGGTGTTGCTGTCTTGGAG R:CGATAGTGTCATTTCCAATCC | 134–169 | 58 | |
Vica9/152 | F:(FAM-)GCACCTGCTCTGTCTATCTC R:AAGGTTCAGGCACTGGAG | 167–191 | 58 | |
Vitc2/D | F:(TAMRA-)GCTCCTTCTGGGTAAGA R:CTCTACATCTCATCCCATC | 184–278 | 58 | |
Viga7/116 | F:(ROX-)GCCTGGTTGTGGATCTGTC R:ATCCTGCTACATCGACCTTC | 159–173 | 60 | |
Vigt10/ε | F:(ROX-)GCAGTGCAGGAATAGTAAGG R:GCTGTGATACCAGAGAACGA | 171–173 | 60 | |
Vict1/130 | F:(NED-)GATTGGTGACGCATGTGT R:GCTGGAGATTGCGTAGAC | 132–152 | 58 | |
EMVi029 | F:(TAMRA-)ACGAGTCCCAGGTCTCACAG R:TGTTGACGGTCACGGTGTAT | 164–248 | 58 * | [32] |
1tc1g | F:(NED-)TCACTCAACAATACAGTTTCTTAG R:TTTCACGGTAGCGATAGGAG | 111–185 | 58 | [13] |
1tc1b | F:(HEX-)CGATTGGGGATATGAAGACTT R:TTAGTAATCAAATCGCACCCA | 149–210 | 58 | |
1tc1a | F:(FAM-)TCGAGATCCTCAAACTTCCTT R:TTTTAACTGTGCGGCCTG | 109–187 | 58 |
Locus | Allele Size Range, bp | Na | Pa | Ne | I | h | PIC |
---|---|---|---|---|---|---|---|
Vicacg8/42 | 192–226 | 13 | 8 | 2.75 | 1.42 | 0.64 | 0.627 |
Vitg11/70 | 186–210 | 11 | 6 | 5.79 | 1.96 | 0.83 | 0.823 |
Vigtg10/95 | 128–157 | 9 | 4 | 2.30 | 1.14 | 0.57 | 0.549 |
Vica9/152 | 152–185 | 9 | 4 | 2.65 | 1.42 | 0.62 | 0.602 |
Vitc2D | 188–252 | 29 | 10 | 14.31 | 2.88 | 0.93 | 0.934 |
Viga7/116 | 139–174 | 9 | 3 | 3.55 | 1.53 | 0.72 | 0.710 |
Vigt10/ε | 174–176 | 2 | 1 | 1.01 | 0.04 | 0.01 | 0.013 |
Vict1/130 | 149–157 | 5 | 1 | 1.68 | 0.87 | 0.40 | 0.405 |
EMVi029 | 163–218 | 15 | 8 | 4.20 | 1.91 | 0.76 | 0.746 |
1tc1g | 112–188 | 27 | 15 | 9.27 | 2.63 | 0.89 | 0.884 |
1tc1b | 151–191 | 10 | 6 | 2.44 | 1.31 | 0.59 | 0.604 |
1tc1a | 109–160 | 19 | 8 | 13.62 | 2.73 | 0.93 | 0.925 |
Group | N | Na | Pa | Ne | k | I | h |
---|---|---|---|---|---|---|---|
K1 | 54 | 7.33 | 1.67 | 3.60 | 14 | 1.33 | 0.59 |
K2 | 40 | 6.08 | 0.92 | 3.71 | 11 | 1.18 | 0.53 |
K3 | 49 | 9.00 | 2.75 | 4.57 | 14 | 1.51 | 0.64 |
Source of Variation | Degrees of Freedom | Sum of Squares | Variance Components | Percentage Variation | PhiPT | Probability |
---|---|---|---|---|---|---|
Among populations (Zemgale and Kurzeme) | 2 | 17.33 | 0.21 | 5 | 0.052 | 0.001 |
Within population | 141 | 546.74 | 3.88 | 95 | ||
Total | 143 | 564.03 | 4.10 | 100 | ||
Among populations (STRUCTURE K = 3) * | 3 | 57.41 | 0.53 | 13 | 0.128 | 0.001 |
Within population | 140 | 507.65 | 3.63 | 87 | ||
Total | 143 | 565.06 | 4.16 | 100 | ||
Among populations (STRUCTURE K = 4) ** | 4 | 76.10 | 0.61 | 15 | 0.147 | 0.001 |
Within Pops | 145 | 511.69 | 3.53 | 85 | ||
Total | 149 | 587.79 | 4.14 | 100 |
Group (K) | Parameter | Vicacg8/42 | Vitg11/70 | Vigtg10/95 | Vica9/152 | Vitc2/D | Viga7/116 | Vigt10/ε | Vict1/130 | EMVi029 | 1tc1g | 1tc1b | 1tc1a |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
K1 | N | 54 | 54 | 54 | 54 | 54 | 54 | 54 | 54 | 54 | 54 | 54 | 54 |
Na | 5 | 5 | 6 | 7 | 13 | 6 | 1 | 4 | 8 | 13 | 7 | 13 | |
Ne | 1.42 | 2.62 | 2.12 | 3.65 | 8.84 | 3.88 | 1.00 | 1.42 | 3.70 | 3.58 | 3.04 | 7.92 | |
I | 0.65 | 1.18 | 1.05 | 1.53 | 2.33 | 1.50 | 0.00 | 0.63 | 1.65 | 1.85 | 1.35 | 2.25 | |
h | 0.30 | 0.62 | 0.53 | 0.73 | 0.89 | 0.74 | 0.00 | 0.30 | 0.73 | 0.72 | 0.67 | 0.87 | |
K2 | N | 40 | 40 | 40 | 40 | 40 | 40 | 40 | 40 | 40 | 40 | 40 | 40 |
Na | 5 | 6 | 4 | 5 | 13 | 3 | 1 | 2 | 8 | 13 | 3 | 10 | |
Ne | 1.71 | 3.32 | 2.43 | 1.53 | 8.51 | 2.89 | 1.00 | 1.05 | 5.63 | 7.69 | 1.23 | 7.55 | |
I | 0.85 | 1.43 | 1.01 | 0.74 | 2.32 | 1.08 | 0.00 | 0.12 | 1.84 | 2.25 | 0.38 | 2.14 | |
h | 0,42 | 0.70 | 0.59 | 0.35 | 0.88 | 0.65 | 0.00 | 0.05 | 0.82 | 0.87 | 0.18 | 0.87 | |
K3 | N | 49 | 49 | 49 | 49 | 49 | 49 | 49 | 49 | 49 | 49 | 49 | 49 |
Na | 9 | 9 | 6 | 7 | 19 | 5 | 2 | 5 | 6 | 20 | 6 | 14 | |
Ne | 2.65 | 4.95 | 2.04 | 2.72 | 12.84 | 2.27 | 1.04 | 2.99 | 2.26 | 9.49 | 2.57 | 9.06 | |
I | 1.46 | 1.81 | 0.99 | 1.38 | 2.72 | 0.99 | 0.10 | 1.31 | 1.09 | 2.60 | 1.24 | 2.39 | |
h | 0.62 | 0.80 | 0.51 | 0.63 | 0.92 | 0.56 | 0.04 | 0.67 | 0.56 | 0.89 | 0.61 | 0.89 |
Group (K) | N | Na | Pa | Ne | k | I | h |
---|---|---|---|---|---|---|---|
K1 | 23 | 4.67 | 0.42 | 2.94 | 7 | 1.03 | 0.50 |
K2 | 36 | 8.00 | 2.00 | 4.13 | 14 | 1.42 | 0.62 |
K3 | 58 | 7.67 | 1.83 | 3.92 | 14 | 1.32 | 0.58 |
K4 | 32 | 5.42 | 0.75 | 3.10 | 9 | 1.17 | 0.56 |
Group (K) | Parameter | Vicacg8/42 | Vitg11/70 | Vigtg10/95 | Vica9/152 | Vitc2/D | Viga7/116 | Vigt10/ε | Vict1/130 | EMVi029 | 1tc1g | 1tc1b | 1tc1a |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
K1 | N | 23 | 23 | 23 | 23 | 23 | 23 | 23 | 23 | 23 | 23 | 23 | 23 |
Na | 4 | 5 | 3 | 3 | 9 | 4 | 1 | 2 | 8 | 8 | 3 | 6 | |
Ne | 1.44 | 3.33 | 1.71 | 1.43 | 7.05 | 2.33 | 1.00 | 1.19 | 5.45 | 4.52 | 1.43 | 4.45 | |
I | 0.64 | 1.35 | 0.74 | 0.56 | 2.05 | 0.98 | 0.00 | 0.30 | 1.84 | 1.74 | 0.56 | 1.62 | |
h | 0.31 | 0.70 | 0.42 | 0.30 | 0.86 | 0.57 | 0.00 | 0.16 | 0.82 | 0.78 | 0.30 | 0.78 | |
K2 | N | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 |
Na | 10 | 9 | 3 | 6 | 16 | 4 | 1 | 4 | 7 | 17 | 6 | 13 | |
Ne | 2.75 | 3.70 | 1.66 | 2.27 | 9.00 | 2.20 | 1.00 | 2.81 | 2.72 | 11.17 | 2.87 | 7.36 | |
I | 1.55 | 1.70 | 0.69 | 1.20 | 2.47 | 0.90 | 0.00 | 1.20 | 1.27 | 2.61 | 1.26 | 2.25 | |
h | 0.64 | 0.73 | 0.40 | 0.56 | 0.89 | 0.55 | 0.00 | 0.64 | 0.63 | 0.91 | 0.65 | 0.86 | |
K3 | N | 58 | 58 | 58 | 58 | 58 | 58 | 58 | 58 | 58 | 58 | 58 | 58 |
Na | 6 | 9 | 4 | 6 | 19 | 3 | 2 | 3 | 8 | 15 | 5 | 12 | |
Ne | 2.96 | 4.38 | 1.57 | 2.25 | 10.32 | 2.15 | 1.04 | 1.41 | 2.91 | 8.09 | 1.72 | 8.25 | |
I | 1.30 | 1.72 | 0.65 | 1.15 | 2.64 | 0.85 | 0.09 | 0.52 | 1.43 | 2.35 | 0.83 | 2.27 | |
h | 0.66 | 0.77 | 0.36 | 0.56 | 0.90 | 0.54 | 0.03 | 0.29 | 0.66 | 0.88 | 0.42 | 0.88 | |
K4 | N | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 |
Na | 3 | 5 | 5 | 6 | 10 | 5 | 1 | 4 | 5 | 7 | 4 | 10 | |
Ne | 1.14 | 2.28 | 2.81 | 3.58 | 7.21 | 3.35 | 1.00 | 1.71 | 3.68 | 1.88 | 2.99 | 5.63 | |
I | 0.28 | 1.11 | 1.21 | 1.45 | 2.12 | 1.39 | 0.00 | 0.83 | 1.41 | 1.07 | 1.20 | 2.00 | |
h | 0.12 | 0.56 | 0.64 | 0.72 | 0.86 | 0.70 | 0.00 | 0.42 | 0.73 | 0.47 | 0.67 | 0.82 |
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Sokolova, O.; Moročko-Bičevska, I.; Lācis, G. Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers. Pathogens 2022, 11, 1165. https://doi.org/10.3390/pathogens11101165
Sokolova O, Moročko-Bičevska I, Lācis G. Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers. Pathogens. 2022; 11(10):1165. https://doi.org/10.3390/pathogens11101165
Chicago/Turabian StyleSokolova, Olga, Inga Moročko-Bičevska, and Gunārs Lācis. 2022. "Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers" Pathogens 11, no. 10: 1165. https://doi.org/10.3390/pathogens11101165