Molecular marker analysis of genes of resistance to scab and fire blight in the apple cultivars bred at the Sverdlovsk Horticultural Breeding Station

Background. Unique apple cultivars have been created at the Sverdlovsk Horticultural Breeding Station and adapted to growing in the harsh natural and climatic conditions of the Middle Urals. Sharp temperature changes and a significant amount of precipitation in summer contribute to the development of fungal and bacterial diseases. Therefore, the main direction in breeding is the creation of forms with a complex of genes for resistance to various types of diseases. To search for sources of valuable features, the use of the molecular marker method remains relevant, which shortens the analysis time and allows for selection directly on the basis of gene presence instead of the external manifestation of а trait. The aim of our work was to search for scab and fire blight resistance genes in apple cultivars bred by the Sverdlovsk Breeding Station of Horticulture using DNA markers. The study used the VfC marker of the Rvi6 scab resistance gene, AE10-375 and GE-8019 QTL FBF7 markers of resistance to fire blight of apple trees. The results of molecular identification of the scab resistance gene were compared with those of evaluating the field resistance in the cultivars studied during the epiphytotic years. 21 apple cultivars were analyzed. Results. In the course of the research, the Rvi6 gene was identified in three apple cultivars – ‘Pervouralskaya’ ‘Aksyonaʼ and ʻBlagaya Vestʼ. An assessment of field resistance to scab showed that a number of cultivars were not affected. It was established that all varieties with a fragment indicating the presence of the Rvi6 gene were not affected by scab during epiphytotic years. The cultivars ʻTavatuyʼ, ʻRozochkaʼ, ʻDanilaʼ, ʻVEM Rozovyjʼ, and ‘Rodnikovayaʼ also showed no signs of the disease. The pedigree analysis showed that scab resistance donors carrying the Rvi5 gene were used to create these cultivars.In the analyzed collection, markers AЕ10-375 and GE-8019 QTL FBF7 of resistance to bacterial fire blight of apple trees were noted in almost the same number of cultivars (AЕ10-375 was identified in 12 accessions, and GE-8019 in 10). However, the presence of resistance is evidenced by the presence of two markers in one genotype. The five identified accessions are ʻIset Belaya’, ‘Pervouralskaya’, ʻAksyonaʼ, ʻSerebryanoye Kopyttseʼ, and ʻBlagaya Vest’. Conclusions. The performed research made it possible to establish the sources of valuable characters in apple cultivars bred in the Urals. The identified genotypes are promising for further use in breeding and industrial horticulture.

1. Afunian M.R., Goodwin P.H., Hunter D.M. Linkage of Vfa4 in Malus × domestica and Malus floribunda with Vf resistance to the apple scab pathogen Venturia inaequalis. Plant Pathology. 2004;53(4):461-467. DOI: 10.1111/j.1365-3059.2004.01047.x

2. Baldo J.L., Farrell R.E., Bassett C.L., Aldwinckle H.S., Malnoy M. Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus × domestica) with Erwinia amylovora. BMC Plant Biology. 2010;10(1):1. DOI: 10.1186/1471-2229-10-1

3. Baumgartner I.O., Patocchi A., Frey J.E., Peil A., Kellerhals M. Breeding elite lines of apple carrying pyramided homozygous resistance genes against apple scab and resistance against powdery mildew and fire blight. Plant Molecular Biology Reporter. 2015;33(5):1573-1583. DOI: 10.1007/s11105-015-0858-x

4. Boudichevskaia A., Flachowsky H., Dunemann F. Identification and molecular analysis of candidate genes homologous to HcrVf genes for scab resistance in apple. Plant breeding. 2009;128(1):84-91. DOI: 10.1111/j.1439-0523.2008.01537.x

5. Boudichevskaia A., Flachowsky H., Fischer C., Hanke V., Dunemann F. Development of molecular markers for Vr1, a scab resistance factor from R12740-7A apple. Acta Horticulturae. 2004;663:171-176. DOI: 10.17660/ActaHortic.2004.663.24

6. Bus V.G.M. Revision of the nomenclature of the differential host-pathogen inter-actions of Venturia inaequalis and Malus. Annual Review of Phytopathology. 2011;49(1):391-413. DOI: 10.1146/annurev-phyto-072910-095339

7. Calenge F., Drouet D., Denancé C., Van de Weg W.E., Brisset M.-N., Paulin J.-P., Durel C.-E. Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies. Theoretical and Applied Genetics. 2005;111(1):128-135. DOI: 10.1007/s00122-005-2002-z

8. Dolzhikova M.A. Analysis of the apple tree (Malus Mill.) hybrid fund for the presence of the DNA marker of the Vf gene of resistance to scab (Venturia inaequalis). Breeding and variety cultivation of fruit and berry crops. 2022;9(1):47-51. [in Russian]. DOI: 10.24411/25000454_2022_0109

9. Drenova N.V. Fire blight in the Russian Federation and current approaches to its diagnostics. Pomiculture and small fruits culture in Russia. 2019;58:131-137. [in Russian]. DOI: 10.31676/2073-4948-2019-58-131-137

10. Flachowsky H., Richter K., Kim W.S., Geider K., Hanke M.V. Transgenic expression of a viral EPS‐depolymerase is potentially useful to induce fire blight resistance in apple. Annals of Applied Biology. 2008;153(3):345-355. DOI: 10.1111/j.1744-7348.2008.00264.x

11. Karimova E.V., Shnejder E.Yu., Smirnova I.P. Predicting the spread of the bacterial blight pathogen in fruit crops (Prognozirovanie rasprostraneniya vozbuditelya bakterialnogo ozhoga plodovykh kul’tur). Zashchita i Karantin Rastenii = Plant Protection and Quarantine. 2013;9:40-43. [in Russian]. DOI: 10.1007/s11295-018-1226-4

12. Khan M.A., Durel C.E., Duffy B., Drouet D., Kellerhals M., Gessler C., Patocchi A. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome. 2007;50(6):568-577. DOI: 10.1139/G07-033

13. Kost T.D. Functionality of the FB_MR5 fire blight resistance gene of Malus × robusta 5 [dissertation]. ETH Zürich; 2016. DOI: 10.3929/ethz-a-010656323

14. Kotov L.A. Apple breeding in the Middle Urals. Contemporary horticulture.

15. 2019;2:13-21. [in Russian] (Котов Л.А. Селекционная работа по яблоне на Среднем Урале. Современное садоводство. 2019;2:13-21). DOI: 10.24411/2312-6701-2019-10203

16. Liebhard R., Koller B., Patocchi A., Kellerhals M., Pfammatter W., Jermini M., Gessler C. Mapping quantitative field resistance against apple scab in a ‘Fiesta’ × ‘Discovery’ progeny. Phytopathology. 2003;93(4):493-501. DOI: 10.1094/PHYTO.2003.93.4.493

17. Lyzhin A.S., Savel'eva N.N. Marker-assisted screening of scab resistant (Rvi6+Rvi4) apple genotypes. Fruit growing and viticulture of South Russia. 2021;67:1-9. [in Russian]. DOI: 10.30679/2219-5335-2021-1-67-1-9

18. Omasheva M.Y., Pozharskiy A.S., Maulenbay A.D., Ryabushkina N.A., Galiakparov N.N. SSR genotyping of Kazakhstani apple varieties: identification of alleles associated with resistance to highly destructive pathogens. Eurasian Journal of Applied Biotechnology. 2016;2:46-58. DOI: 10.11134/btp.2.2016.4

19. Patocchi A., Bigler B., Koller B., Kellerhals M., Gessler C. Vr2: a new apple scab resistance gene. Theoretical and Applied Genetics. 2004;109:1087-1092. DOI: 10.1007/s00122-004-1723-8

20. Patocchi A., Frei A., Frey J.E. Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes. Moleсular Breeding. 2009;24:337. DOI: 10.1007/s11032-009-9295-6

21. Patocchi A., Walser M., Tartarini S., Broggini G.A., Gennari F., Sansavini S., Gessler C. Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm. Genome. 2005;48(4):630-636. DOI: 10.1139/g05-036

22. Podwyszy´nska M.P., Markiewicz M., Broniarek-Niemiec A., Matysiak B., Marasek-Ciolakowska A. Apple autotetraploids with enhanced resistance to apple scab (Venturia inaequalis) due to genome duplication-phenotypic and genetic evaluation. International Journal of Molecular Sciences. 2021;22(2):527. DOI: 10.3390/ijms22020527

23. Sedov E.N., Ogoltsova T.P. (eds) Program and methodology for studying cultivars of fruit, berry and nut crops (Programma i metodika sortoizucheniya plodovykh, yagodnykh i orekhoplodnykh kul'tur). Orel: VNIISPK; 1999. [in Russian]

24. Shamshin I.N., Maslova M.V., Drenova N.V., Dubrovsky M.L., Parusova O.V. Assessment of fire blight resistance in apple clonal rootstocks using molecular markers. Proceedings on applied botany, genetics and breeding. 2020;181(4):185-191. [in Russian]. DOI: 10.30901/2227-8834-2020-4-185-191

25. Shamshin I.N., Savel'ev N.I., Kudryavtsev A.M. Application of molecular markers for identification of apple genotypes with scab resistance gene (Primeneniye molekulyarnykh markerov dlya identifikatsii genotipov yabloni s genom ustoychivosti k parshe). Pomiculture and small fruits culture in Russia. 2011;26:126-129. [in Russian]

26. Sheikh M.A., Mushtaq K., Mir J.I., Amin M., Nabi S.U. Introgression of scab resistance gene Vf (Rvi6) in commercially grown susceptible cultivar Fuji Azitec of apple (Malus domestica) using marker assisted selection. Research Journal of Biotechnology. 2020;15(9):50-56.

27. Slepneva T.N., Shlyavas A.V. Porfiry Afanasyevich Dibrova: at the origins of scientific pomiculture in the Urals. Proceedings on applied botany, genetics and breeding. 2021;182(2):163-172. [in Russian]. DOI: 10.30901/2227-8834-2021-2-163-172

28. Suprun I.I., Egorov E.A., Nasonov A.I., Lobodina E.V., Tokmakov S.V., Stepanov I.V. Marker-assisted selection in the development of advanced apple-tree forms and donors combining scab resistance with increased fruit storability. Proceedings on applied botany, genetics and breeding. 2023;184(3):135-145. [in Russian]. DOI: 10.30901/2227-8834-2023-3-135-145

29. Suprun I.I., Tokmakov S.V., Lobodina E.V. Assessment of prospects for the improvement of the VfC1 DNA marker for the Vf gene of scab resistance in apple (Otsenka perspektivnosti usovershenstvovaniya DNK-markera VfC1 gena ustoichivosti yabloni k parshe Vf). Nauchnyie trudy Severo-Kavkazskogo federalnogo nauchnogo tsentra sadovodstva, vinogradarstva, vinodeliya = Scientific works of the North-Caucasian Scientific Center of Horticulture, Viticulture and Wine-making. 2016;9:47-51. [in Russian]

30. Telezhinskiy D.D., Shlyavas A.V. Morphobiological features and agronomic advantages of the new apple cultivar ʻRozochka’. Agricultural Science Euro-North-East. 2025;26(1):82-89. [in Russian]. DOI: 10.30766/2072-9081.2025.26.1.82-89

31. Telezhinskiy D.D., Kotov L.A., Makarenko S.A., Tarasova G.N. Sverdlovchanin: a new apple cultivar for the Middle Urals. Proceedings on applied botany, genetics and breeding. 2020;181(1):93-96. [in Russian]. DOI: 10.30901/2227-8834-2020-1-93-96

32. Tóth M., Ficzek G, Király I., Honty K., Hevesi M. Evaluation of old Carpathian apple cultivars as genetic resources of resistance to fire blight (Erwinia amylovora). Trees. 2013;27:597-605. DOI: 10.1007/s00468-012-0814-4

33. Ulyanovskaya E.V., Chernutskaya E.A., Bogdanovich T.V., Stepanov I.V. Marker selection for genes Rvi6, Md-ACS1, Md-ACO1 promising for breeding of apple gene pool samples. Agrarian Scientific Journal. 2024;3:71-76. [in Russian]. DOI: 10.28983/asj.y2024i3pp71-76

34. Wöhner T.W., Flachowsky H., Richter K., Garcia-Libreros T., Trognitz F., Hanke M.- V., Peil A. QTL mapping of fire blight resistance in Malus × robusta 5 after inoculation with different strains of Erwinia amylovora. Molecular breeding. 2014;34(1):217-230. DOI: 10.1007/s11032-014-0031-5