Identification of Apple Varieties Resistant to Fire Blight (Erwinia amylovora) Using Molecular Markers
Abstract
:1. Introduction
2. Material and Methods
2.1. Sample Collection
2.2. DNA Isolation
2.3. SNP Genotyping
2.4. SCAR Markers
3. Results
3.1. Monitoring
3.2. SNP Genotyping
3.3. Molecular Screening Using SCAR Markers
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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# | Genotype | Origin | Location * | Reference |
---|---|---|---|---|
1 | Idared | Cross between Jonathan and Wagener varieties, first raised in Idaho, USA. It was first released to the public in 1942 after a ten-year breeding program. Included in the State Register of the Republic of Kazakhstan since 1998. | 1; 4; 6 | [24] |
2 | Starkrimson | Pollination: Starkrimson is self-sterile and requires a pollinator to produce a crop. Origin: USA, 1870. Included in the State Register of the Republic of Kazakhstan since 1988. | 6; 8 | [25] |
3 | Gala | Developed in New Zealand, it is the result of breeding among some of the most historically important varieties such as Cox’s Orange Pippin, Golden Delicious, and Kidd’s Orange Red. Included in the State Register of the Republic of Kazakhstan since 2011. | 4; 6 | [26] |
4 | Aport | An ancient variety from Russia. The originator is not registered. Crossing them with the local wild Sievers apple tree made the new variety famous. Included in the State Register of the Republic of Kazakhstan since 1965. | 4; 7 | [27] |
5 | Fuji | Bred by crossing Red Delicious × Rale Jennet. Originator: Tohoku Science Station, Marioka, Japan. Included in the State Register of the Republic of Kazakhstan since 2011. | 1; 6 | [28] |
6 | Golden Delicious | Bred by crossing Grimes Golden × Golden Reinette. The originator is not registered. One of the symbols of West Virginia, USA. Included in the State Register of the Republic of Kazakhstan since 1965. | 1; 6 | [29] |
7 | Granny Smith | Bred by crossing a French wild apple tree with a local Australian apple tree. Originator: Maria Ann Smith, Australia. Included in the State Register of the Republic of Kazakhstan since 2011. | 6 | [30] |
8 | Suislepper | From Baltic countries, it is an old variety of folk selection. Included in the State Register of the Republic of Kazakhstan since 1965. | 7 | [31] |
9 | Renet Burhardta | A variety of Crimean origin. Originator: State Nikitsky Botanical Garden, Ukraine. Included in the State Register of the Republic of Kazakhstan since 1965. | 4; 7 | [32] |
10 | Pestrushka | An ancient South Kazakhstan variety. The originator is not registered. Included in the State Register of the Republic of Kazakhstan since 1965. | 4 | [33] |
11 | Red Delicious (5) | Red-fruited clone of the variety Delicious. Originator: private nursery in Wilsburg, USA. Included in the State Register of the Republic of Kazakhstan since 2011. | 5 | [34] |
12 | Tulpan (8) | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Autumn maturity. Passes the State variety test. | 8 | [35] |
13 | Ainur | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Winter maturity. Included in the State Register of the Republic of Kazakhstan since 2011. | 1; 7 | [35] |
14 | Aigul | Bred by crossing Aport × Golden Delicious. Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. | 7 | [35] |
15 | Saltanat | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Bred by selection of seedlings Renette Burchardt from free pollination. Included in the State Register of the Republic of Kazakhstan since 1980. | 7 | [36] |
16 | Voskhod | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Winter maturity. Included in the State Register of the Republic of Kazakhstan since 2011. | 1 | [35] |
17 | Egemen | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Winter maturity. Included in the State Register of the Republic of Kazakhstan since 2019. | 1 | [35] |
18 | Zarya Alatau | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Obtained from seedlings of the variety Renet Orleans from free pollination. Included in the State Register of the Republic of Kazakhstan since 1974. | 1 | [37] |
19 | Maksat | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Autumn maturity. Included in the State Register of the Republic of Kazakhstan since 2011. | 1 | [35] |
20 | Esen | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Bred by crossing varieties Zailiyskoye and Aport. Passes the State variety test. | 1 | [35] |
21 | Sarkyt | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Bred by crossing varieties Zarya Alatau and Aport. Passes the State variety test. | 1 | [35] |
22 | Talgarskoe | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Winter maturity. Included in the State Register of the Republic of Kazakhstan since 2004. | 1 | [35] |
23 | Zharkyn | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Passes the State variety test. | 1 | [35] |
24 | Danalyk | Variety of selection of the Kazakh Research Institute of Fruit Growing and Viticulture. Winter maturity. Included in the State Register of the Republic of Kazakhstan since 2020. | 1 | [35] |
25 | Modi | Created at the Consorzio Italiano Vivaisti in Italy by researchers in the 2000s and then introduced to the USA in 2014. Bred by crossing varieties Gala and Liberty. | 8 | [38] |
26 | Braeburn | The New Zealand variety was obtained via free pollination of Lady Hamilton in 1952. | 1; 3; 8 | [39] |
27 | Jeromini | French variety. Derived from varieties Erovan and Early Red. | 4 | [40] |
28 | Quinti | Created in Canada as a result of crossing Crimson Beauty × Red Melba in 1964, summer ripening. | 5; 8 | [41] |
29 | Kandil Sinap | An old Crimean variety of autumn ripening. Obtained by random mutation when sowing seeds of the related variety “Sary-sinap”. | 8 | [42] |
30 | Mutsu | Created in Japan in 1948. Obtained as a result of crossing Golden Delicious and Indo-Japanese varieties of apples. | 8 | [43] |
31 | Kandil Kirghiz | An ancient variety in Kyrgyzstan with a winter ripening period. | 8 | [44] |
32 | Pink Lady | An Austrian variety, bred by the English gardener John Cripps by crossing the Australian variety Lady Williams and Golden Delicious. | 4; 6 | [45] |
33 | Starks Earliest | Developed in Idaho, USA, in 1938 by the Stark brothers of Missouri. | 8 | [46] |
34 | Scarlet Spur | American winter variety. Mutant Oregonspur® Trumdor. | 6 | [47] |
35 | Summer red | Summer variety of apples of Canadian selection. The maximum height of the tree is 2.5–3.5 m, belonging to the medium height group. | 6 | [48] |
36 | Nicole Grain | No data. | - | - |
37 | Redfree | Created by the Purdue, Rutgers, and University of Illinois Agricultural Experimental Station in the 1980s, the Redfree apple was designed to be a disease-resistant summer apple. Obtained as a result of crossing a domestic apple tree and a clone of Malus floribunda 821. | 3 | [49] |
38 | Williams Pride | Was developed by the well-respected “co-op” breeding program of Purdue, Rutgers, and Illinois (PRI) universities in the 1970s, and originally known as Co-op 23. Its ancestry is similar to that of many of the PRI varieties, including Rome Beauty and Malus floribunda, but its early-season character probably comes from Mollie’s Delicious and Julyred. | 3 | [50] |
39 | Diana | Variety of Ukrainian selection, winter ripening. | 3 | [51] |
40 | Gold spur | Obtained from the variety Golden Delicious, winter term maturation. | 4 | [52] |
41 | Honeycrisp | Originates from Excelsior, Minnesota in 1974. Crossed between Mekaun and Honeygold. | 4 | [53] |
42 | Camspur | A Starkimson mutant discovered in 1967 in Washington, DC. Maturing time—Winter. Derevo: average, crown Compact. Power Supporters: Idared, Granny Smith, Everest, Professor Sprenger. | 4 | [54] |
43 | Korea | Japanese selection at the Aomori experimental station, obtained by hybridization of Golden Delicious and Indus apple trees. | 4 | [55] |
44 | Gala Anna | Produced in Italy as a Gala clone. | 5 | [56] |
45 | July Chernenko | An ancient variety of Russian selection. Obtained from crossing varieties Anis velvet and Papirovka. | 1 | [57] |
46 | Elstar | Received in 1954–1955 in the Netherlands. Created by crossing varieties Ingrid Maria and Golden Delicious. | 1 | [58] |
47 | Jonagold | Bred in the USA at the Geneva Experimental Station by crossing varieties Golden Delicious and Jonathan. | 1 | [59] |
48 | Elrosa | Wilfred and Annet Zweeren, Netherlands, 1999. | 1 | [60] |
49 | Prima | Early autumn variety of American selection. Created by crossing varieties: M. floribunda 821 and the varieties Welsey, Melba, Rum Beauty, Golden Delicious, and their derivatives. | 1 | [61] |
50 | Red Elstar | Dutch selection, winter ripening. | 1 | [62] |
51 | Maria Red | Dutch selection, winter ripening. | 1 | [63] |
52 | Red JonaPrince (1) | It is one of the clones of Jonagold, isolated in Belgium, winter ripening. | 1 | [64] |
53 | Synap Almatinsky | An ancient variety, comes from the Crimean Sinap known since the 19th century. Winter maturity. | 1 | [65] |
54 | Wilton Star | The Netherlands. The Wilton’s Star Red Jonaprince Select is a new mutation from Red Jonaprince, which colors darker red. | 2 | [66] |
55 | Deljonca | The Deljonca varieties in the German growing areas. Formed by crossing varieties Delbard Florina × Stark Jongrimes. | 2 | [67] |
56 | Santana (2) | Bred by the International Plant Research Institute Wageningen (P.R.I. Wageningen), the Netherlands. | 2 | [68] |
57 | Pinova | Winter variety of German selection is obtained by crossing varieties Golden Delicious and Clivia. | 2; 7 | [69] |
58 | Red Topaz (2) | Winter variety of Czech selection by crossing varieties Vanda and Rubín in 1984. | 2 | [70] |
59 | SQ159 | A variety of apples for long storage, suitable for organic production. Developed by PRI Wageningen (Netherlands). | 2 | [71] |
SNP Marker | Linkage Group | Gene/Locus Name | SNP ID | Taqman Assay ID | SNP Type | Reference |
---|---|---|---|---|---|---|
FBE-1_Y320 | 12 | FBE | FBE-1_Y320 | AH704YY | C/T | [73] |
FBE-2_Y192 | 12 | FBE | FBE-2_Y192 | AH89246 | C/T | [73] |
FBE-2_Y495 | 12 | FBE | FBE-2_Y495 | AHABIAZ | C/T | [73] |
FBE-2_Y551 | 12 | FBE | FBE-2_Y551 | AHBKGG7 | C/T | [73] |
FB-MR5-K35 | 3 | MR5 | FB-MR5-NZsnEH034548_K35 | AH0JFXM | G/T | [73] |
FB-MR5-R240 | 3 | MR5 | FB-MR5-NZsnEH034548_R240 | AH1SD3U | A/G | [73] |
FB-MR5-R249 | 3 | MR5 | FB-MR5-NZsnEH034548_R249 | AH21B92 | A/G | [73] |
FB-MR5-rp16k15_M106 | 3 | MR5 | FB-MR5-rp16k15_M106 | AH4AAGA | A/C | [73] |
RLP1a | 3 | RLP1 | RLP1a | AH5I8MI | C/A | [74] |
RLP1b | 3 | RLP1 | RLP1b | AH6R6SQ | A/T | [74] |
Gene, Locus | Marker | Primer Sequence (5′–3′) | PCR Cycling Program |
---|---|---|---|
F7 QTL | AE10-375 | CTGAAGCGCACGTTCTCC-F CTGAAGCGCATCATTTCTGATAG-R | 1 cycle95 °C—3 min, 35 cycles (95 °C—40 s; 60 °C—40 s; 72 °C—60 s), 1 cycle 72 °C—10 min. |
F7 QTL | GE-8019 | TTGAGACCGATTTTCGTGTG-F TCTCTCCCAGAGCTTCATTGT-R | 1 cycle 95 °C—3 min, 35 cycles (95 °C—40 s; 60 °C—40 s; 72 °C—60 s), 1 cycle 72 °C—10 min. |
Genotypes | SNP ID | SCAR Markers | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
FBE-1_Y320 | FBE-2_Y192 | FBE-2_Y495 | FBE-2_Y551 | FB-MR5-K35 | FB-MRS-R240 | FB-MR5-R249 | FB-MR5-rp16k15_M106 | RLP1a | RLP1b | AE-375 | GE-8019 | |
Idared (1, 4, 6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Starkrimson (6, 8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Gala (4, 6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Aport (4, 7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Fuji (1, 6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Golden Delicious (1, 6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Granny Smith (6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Suislepper (7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Renet Burhardta (4, 7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Pestrushka (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Red Delicious (5) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Tulpan (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Ainur (1, 7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Aigul (7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Saltanat (7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Voskhod (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Egemen (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Zarya Alatau (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Maksat (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Esen (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Sarkyt (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Talgarskoe (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Zharkyn (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Danalyk (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Modi (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Braeburn (1, 3, 8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Jeromini (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Quinti (5, 8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 1 |
Kandil Sinap (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Mutsu (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Kandil Kirghiz (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Pink Lady (4, 6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Starks Earliest (8) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Scarlet Spur (6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Summer red (6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 1 |
Nicole Grain (6) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Redfree (3) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Williams Pride (3) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 1 |
Diana (3) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Gold spur (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Honeycrisp (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 1 |
Camspur (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Korea (4) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Gala Anna (5) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
July Chernenko (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Elstar (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 1 |
Jonagold (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Elrosa (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Prima (1) | T/T | T/T | T/T | G/G | G/G | C/C | A/A | 0 | 0 | |||
Red Elstar (1) | T/T | C/C | No AMP | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Maria Red (1) | T/T | C/C | No AMP | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Jonaprints (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Synap Almatinsky (1) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Wilton Star (2) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 0 |
Deljonca (2) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | N/A | N/A |
Santana (2) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
Pinova (2,7) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 1 |
Red Topaz (2) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 1 | 1 |
SQ159 (2) | T/T | C/C | T/T | T/T | T/T | G/G | G/G | C/C | C/C | A/A | 0 | 0 |
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Kairova, G.; Daulet, N.; Solomadin, M.; Sandybayev, N.; Orkara, S.; Beloussov, V.; Kerimbek, N.; Gritsenko, D.; Sapakhova, Z. Identification of Apple Varieties Resistant to Fire Blight (Erwinia amylovora) Using Molecular Markers. Horticulturae 2023, 9, 1000. https://doi.org/10.3390/horticulturae9091000
Kairova G, Daulet N, Solomadin M, Sandybayev N, Orkara S, Beloussov V, Kerimbek N, Gritsenko D, Sapakhova Z. Identification of Apple Varieties Resistant to Fire Blight (Erwinia amylovora) Using Molecular Markers. Horticulturae. 2023; 9(9):1000. https://doi.org/10.3390/horticulturae9091000
Chicago/Turabian StyleKairova, Gulshariya, Nurzhan Daulet, Maxim Solomadin, Nurlan Sandybayev, Shynggys Orkara, Vyacheslav Beloussov, Nazym Kerimbek, Dilyara Gritsenko, and Zagipa Sapakhova. 2023. "Identification of Apple Varieties Resistant to Fire Blight (Erwinia amylovora) Using Molecular Markers" Horticulturae 9, no. 9: 1000. https://doi.org/10.3390/horticulturae9091000