Genetic Evaluation of Kazakhstani Potato Germplasm for Pathogen and Pest Resistance Using DNA Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. DNA Isolation
2.3. PCR and Restriction Analysis
3. Results
3.1. Virus Resistance Screening
3.2. Late Blight and Potato Wart Screening
3.3. PCN Resistance Screening
4. Discussion
4.1. Top Global Cultivars
4.2. Top Local Cultivars
4.3. DNA Marker Applicability
4.4. Perspectives on Potato Breeding
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Marker | Gene/QTL | Type | Forward and Reverse Primer Sequences (5′-3′) | PCR Conditions | Size (bp) | Resistance | References |
---|---|---|---|---|---|---|---|
Potato wart | |||||||
Potato virus | |||||||
GP122564 | Ry-fsto | CAPS/EcoRV | F-TATTTTAGGGGTACTTCTTTCTTATGTT; R-CTGTCAAAAAAATTCACTTGCATAACTAC | 94 °C—1 min, 40 cycles (93 °C—20 s, 53 °C—25 s, 72 °C—1 min), 72 °C—5 min | 718 bp 564 bp | PVYN, | [1] |
GP122718 | Ry-fsto | CAPS/EcoRV | F-TATTTTAGGGTACTTCTTTCTTA; R-GCACTCAATAGCCCTTCTT | 94 °C—1 min, 40 cycles (93 °C—20 s, 53 °C—25 s, 72 °C—1 min), 72 °C—5 min | 718 bp 564 bp 400 bp | PVYN, | [4] |
ADG1 | Ryadg | PCR-baced, AS | F-CACACTCTCGTATCAGTTTGA; R-ATTTAATAGCGTGACAGT CAAC | 93 °C—2 min; 35 × (93 °C—45 s, 55 °C—45 s, 72 °C—80 s), 72 °C –10 min. | 356 bp | PVYO, PVYN, PVA | [29] |
ADG2 | Ryadg | PCR-baced, AS | F-CACACTCTCGTATCAGTTTGA; R-ATTTAATAGCGTGACAGT CAAC | 93 °C—2 min; 35 × (93 °C—45 s, 55 °C—45 s, 72 °C—80 s), 72 °C –10 min. | 354 bp | PVYO, PVYN, PVA | [29] |
RysC3 | Ryadg | SCAR | F-ATACACTCATCTAAATTTGATGG; R-AGGATATACGGCATCATTTTTCCGA | 93 °C—9 min, 35 × (94 °C—45 s, 60 °C—45 s, 72 °C—60 s), 72 °C—5 min | 321 bp | PVY | [30] |
RY186 | Rychc | PCR-baced, AS | F-TGGTAGGGATATTTTCCTTAGA; R-GCAAATCCTAGGTTATCAACTCA | 95 °C—10 min, 35 × (94 °C—30 s, 55 °C—30 s, 72 °C—1.5 min), 72 °C—5 min | 587 bp | PVY | [31] |
SCARysto4 | Rysto | SCAR | F-ATTCGTTCGCCTCTCTCCT R-TCATCACCCCTAACAAATACAA | 94 °C—1 min, 35 × (94 °C—30 s; 54 °C –60 s; 72 °C—60 s), 72 °C—10 min | 100 bp | PVY | [32,33] |
SPUD237 | Nb | CAPS/AluI | F-TTCCTGCTGATACTGACTAGAAAACC R-AGCCAAGGAAAAGCTAGCATCCAAG | 94 °C—1 min, 35 × (94 °C—15 s; 55 °C—15 s; 72 °C—40 s), 72 °C—10 min | 3 resistance products | PVX | [34] |
CP60 | Rx1 | CAPS/DdeI | F-CAGCCTACCGCGAAAGTGCCTTCG R-GCCAACCCCACGAGTTTCTCACTGAC | 94 °C—3 min, 35 × (92 °C—45 s, 58 °C—45 s, 72 °C—1 min), 72 °C—10 min | 350 bp | PVX | [35] |
PVX | Rx1 | PCR-baced, AS | ATCTTGGTTTGAATACATGG CACAATATTGGAAGGATTCA | 94 °C—10 min, 35 × (94 °C—30 s, 58 °C—30, 72 °C—1 min), 72 °C—5 min | 1230 bp | PVX | [36] |
RGASC850 | Rladg | SCAR | F-GAATGCCAGGAATGGGAAAGACTACTTT R-TCACATCCAAGCAAAACCAA | 95 °C—4 min 32 × (95 °C—45 s, 53 °C—1 min, 72 °C—1 min), 72 °C—10 min | 850 bp | PLRV | [37] |
SC811 | Ns | CAPS/MboI | F-CGAACAAAATACGTAATGCATTGAATAA R-GACCT ATATCAGTCCCTTCTAATCCACTAT | 94 °C—60 s, 30 × (93 °C—15 s, 56 °C—20 s, 72 °C—60 s), 72 °C—5 min | 260 bp | PVS | [38] |
CP16 | Ns | CAPS/HindIII | F-CTTAAACGCGTCAAGTGAAACT R-TTAGGGACATACAAACAAACCTCA | 94 °C—60 s, 35 × (94 °C—15 s, 55 °C—15 s, 72 °C—60 s), 72 °C—3 min | 460 bp | PVS | [39] |
Potato late blight | |||||||
GP76 | unknown | CAPS/RsaI | F-ATGAAGCAACACTGATGCAA R-TTCTCCAATGAACGCAAACT | 93 °C—2 min, 40 × (93 °C—30 s, 55 °C—30 s, 72 °C—1 min), 72 °C—10 min | 500 bp | Phytophthora infestans | [28] |
BA47f2 | R1 | PCR-baced, AS | F-TAACCAACATTATCTTCTTTGCC R-GAATTTGGAGAGGGGTTTGCTG | 93 °C—2 min, 40 × (93 °C—45 s, 55 °C—45 s and 72 °C—90 s), 72 °C—10 min | 650 bp | Phytophthora infestans | [40] |
R11400 | R1 | PCR-baced, AS | F-CACTCGTGACATATCCTCACTA R-CAACCCTGGCATGCCACG | 93 °C—2 min, 40 × (93 °C—45 s, 55 °C—45 s and 72 °C—90 s), 72 °C—10 min | 1400 bp | Phytophthora infestans | [7] |
GP179 | R1 | PCR-baced, AS | F-GGTTTTAGTGATTGTGCTGC R-AATTTCAGACGAGTAGGCACT | 93 °C—2 min, 40 × (93 °C—45 s; 55 °C—45 s; 72 °C—1min 20 s), 72 °C—10 min | 570 bp | Phytophthora infestans | [40] |
CT214 | Rpi-ber1 | CAPS/HinfI | F-CGCGAAAGAGTGCTGATAG R-CCGCTGCCTATGGAGAGT | 94 °C—5 min, 35 × (94 °C—45s, 55 °C—45 s, 72 °C—1 min), 72 °C—8 min | 3 resistance products | Phytophthora infestans | [41] |
GP94 | Rpi-phu1 | PCR-baced, AS | F-ATGTATCACAATCACATTCTTGCTC R-TGTAAAACCAACAAGTAGTGTTGC | 2 min— 95 °C, 40 × (93 °C—1 min, 56 °C—1 min, 72 °C—1 min), 72 °C—10 min | 350 bp | Phytophthora infestans | [42] |
45/XI | Rpi-Smira1 | PCR-baced, AS | F-AGAGAGGTTGTTTCCGATAGACC R-TCGTTGTAGTTGTCATTCCACAC | 94 °C—3 min; 39 × (94 °C—15 s, 55 °C—15 s, 72 °C—60 s), 72 °C– 7 min | 900–1500 bp | Phytophthora infestans | [43] |
Potato cyst nematodes | |||||||
TG689 | H1 | PCR-baced, AS | F-TAAAACTCTTGGTTATAGCCTAT R-CAATAGAATGTGTTGTTTCACCAA | 94 °C—5 min, 35 × (94 °C—45 s, 55 °C—45 s, and 72 °C—1 min), 72 °C—8 min | 141 bp | Globodera rostochiensis, Ro 1 | [44] |
239E4left | H1 | CAPS/AluI | F-GGCCCCACAAACAAGAAAAC R-AGGTACCTCCATCTCATTTTGTAAG | 94 °C—3 min 35 × (94 °C—30 s, 51 °C—30s, 72 °C—90 s), 72 °C 5 min | 230 bp | Globodera rostochiensis | [45] |
Gro1-4 | Gro1-4 | SCAR | F-TCTTTGGAGATACTGATTCTCA R-CGACCTAAAATGAAAAGCATCT | 94 °C—3 min, 35 × (92 °C—45 s, 52 °C—45 s, 72 °C—1 min), 72 °C—10 min | 602 bp | Globodera rostochiensis, Ro 1 | [15] |
N146 | H1 | SCAR | F-AAGCTCTTGCCTAGTGCTC R-AGGCGGAACATGCCATG | 94 °C—10 min, 35 × (94 °C—30 s, 55 °C—30 s, 72 °C—1 min), 72 °C—5 min | 506 bp | Globodera rostochiensis | [36] |
N195 | H1 | SCAR | F-TGGAAATGGCACCCACTA R-CATCATGGTTTCACTTGTCAC | 94 °C—10 min, 35 × (94 °C—30 s, 55 °C—30 s, 72 °C—1 min), 72 °C—5 min | 337 bp | Globodera rostochiensis | [36] |
U14 | GroV1 | SCAR | F-GGGCTTGTATAAGACCTCCGAGAGG R-CCCTTCCTTGGGTAGTTTGAGCG | 92 °C, 7 min; 25 × (92 °C, 1 min; 57 °C, 1 min; 72 °C, 2 min); 72 °C, 5 min | 366 bp | Globodera rostochiensis | [46] |
X02 | GroV1 | PCR-baced, AS | F-CCACCAAACCCATAAAGCTGC R-TGTGAATTGGTATGAATCTGCAACC | 92 °C, 7 min; 25 × (92 °C, 1 min; 50 °C, 1 min; 72 °C, 2 min); 72 °C, 5 min | 854 bp | Globodera rostochiensis | [46] |
C237 | GpaIVSadg | CAPS/TaqI | F-GCAGTCCTAATTGCACGTAACA R-CTTACTTGGGCAACCCAGAAT | 94 °C—10 min, 35 × (at 94 °C—30 s, 60 °C—30 s, 72 °C—1 min), 72 °C—5 min | 423 bp | Globodera pallida, Pa2/3 | [47] |
GP34 | Gpa2 | CAPS/TaqI | F-CGTTGCTAGGTAAGCATGAAGAAG R-GTTATCGTTGATTTCTCGTTCCG | 94 °C—3 min, 35 × (94 °C—15 s, 62 °C—15 s, 72 °C—1 min), 72 °C, 5 min | 495 bp | Globodera pallida, Pa2 | [35] |
Nl25 | Sen1 | Pcr-baced, AS | F-TATTGTTAATCGTTACTCCCTC; R-AGAGTCGTTTTACCGACTCC | 93 °C—3 min, 35 × (93 °C—2 min, 93 °C—45s, 72 °C—1.5 min), 72 °C—10 min. | 1400 bp 1200 bp | Synchytrium endobioticum | [48] |
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Adilbayeva, K.; Moisseyev, R.; Kolchenko, M.; Kenzhebekova, R.; Khassanov, V.; Beisembina, B.; Azhimakhan, M.; Tokbergenova, Z.; Sharipova, D.; Krasavin, V.; et al. Genetic Evaluation of Kazakhstani Potato Germplasm for Pathogen and Pest Resistance Using DNA Markers. Agronomy 2024, 14, 1923. https://doi.org/10.3390/agronomy14091923
Adilbayeva K, Moisseyev R, Kolchenko M, Kenzhebekova R, Khassanov V, Beisembina B, Azhimakhan M, Tokbergenova Z, Sharipova D, Krasavin V, et al. Genetic Evaluation of Kazakhstani Potato Germplasm for Pathogen and Pest Resistance Using DNA Markers. Agronomy. 2024; 14(9):1923. https://doi.org/10.3390/agronomy14091923
Chicago/Turabian StyleAdilbayeva, Kamila, Ruslan Moisseyev, Mariya Kolchenko, Roza Kenzhebekova, Vadim Khassanov, Bibigul Beisembina, Moldir Azhimakhan, Zhursinkul Tokbergenova, Dinara Sharipova, Valeriy Krasavin, and et al. 2024. "Genetic Evaluation of Kazakhstani Potato Germplasm for Pathogen and Pest Resistance Using DNA Markers" Agronomy 14, no. 9: 1923. https://doi.org/10.3390/agronomy14091923