Genotyping of potato samples from the GenAgro ICG SB RAS collection using DNA markers of genes conferring resistance to phytopathogens

Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis), which parasitize the roots of the host plant, cause significant damage to potato crop. Both of these disease factors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their most common races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties. An important step in this process is the selection of resistant genotypes from the population and the estimation of the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypic evaluation is associated with difficulties, for example, it is not always possible to work with pathogens, and phenotypic evaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes can significantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgro potato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wart resistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associated with nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were compared with the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation (Spearman R = 0.722008, p = 0.000000, p < 0.05) between resistance and the presence of a diagnostic fragment. The diagnostic efficiency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searching for resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presence of the DNA marker and resistance. The diagnostic efficiency of the CP113 marker was only 44.44 %. Spearman’s correlation coefficient (Spearman R = –0.109218, p = 0.361104, p < 0.05) did not show significant correlation between resistance and the DNA marker. The diagnostic efficiency of the NL25 marker was 61.11 %. No significant correlation was found between the NL25 marker and resistance (Spearman R = –0.017946, p = 0.881061, p < 0.05). The use of these markers for the search for resistant samples is not advisable.

1. Antonova O.Y., Shvachko N.A., Novikova L.Y., Shuvalov O.Y., Kostina L.I., Klimenko N.S., Shuvalova A.R., Gavrilenko T.A. Genetic diversity of potato varieties bred in Russia and its neighboring countries based on the polymorphism of SSR-loci and markers associated with resistance R-genes. Russ. J. Genet. Appl. Res. 2017;7(5):489500. DOI 10.1134/S2079059717050021.

2. Asano K., Kobayashi A., Tsuda S., Nishinaka M., Tamiya S. DNA marker-assisted evaluation of potato genotypes for potential resistance to potato cyst nematode pathotypes not yet invading into Japan. Breed. Sci. 2012;62(2):142-150. DOI 10.1270/jsbbs.62.142.

3. Baayen R.P., Cochius G., Hendriks H., Meffert J.P., Bakker J., Bekker M., van den Boogert P.H.J.F., Stachewicz H., van Leeuwen G.C.M. History of potato wart disease in Europe – a proposal for harmonisation in defining pathotypes. Eur. J. Plant Pathol. 2006;116(1):21-31. DOI 10.1007/s10658-006-9039-y.

4. Bakker E., Achenbach U., Bakker J., van Vliet J., Peleman J., Segers B., van der Heijden S., van der Linde P., Graveland R., Hutten R., van Eck H., Coppoolse E., van der Vossen E., Bakker J., Goverse A. A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis. Theor. Appl. Genet. 2004;109(1):146-152. DOI 10.1007/s00122-004-1606-z.

5. Epub 2004 Feb 25. Ballvora A., Flath K., Lubeck J., Strahwald J., Tacke E., Hofferbert H.-R., Gebhardt C. Multiple alleles for resistance and susceptibility modulate the defense response in the interaction of tetraploid potato (Solanum tuberosum) with Synchytrium endobioticum pathotypes 1, 2, 6 and 18. Theor. Appl. Genet. 2011;123(8):1281-1292. DOI 10.1007/s00122-011-1666-9.

6. Epub 2011 Aug 6. Ballvora A., Hesselbach J., Niewöhner J., Leister D., Salamini F., Gebhardt C. Marker enrichment and high-resolution map of the segment of potato chromosome VII harbouring the nematode resistance gene Gro1. Mol. General Genet. 1995;249:82-90. DOI 10.1007/BF00290239.

7. Barone A., Ritter E., Schachtschabel U., Debener T., Salamini F., Gebhardt C. Localization by restriction fragment length polymorphism mapping in potato of a major dominant gene conferring resistance to the potato cyst nematode Globodera rostochiensis. Mol. General Genet. 1990;224(2):177-182. DOI 10.1007/BF00271550.

8. Bartkiewicz A., Chilla F., Terefe-Ayana D., Lübeck J., Strahwald J., Tacke E., Hoferbert H.-R., Flath K., Linde M., Debener T. Improved genetic resolution for linkage mapping of resistance to potato wart in monoparental dihaploids with potential diagnostic value in tetraploid potato varieties. Theor. Appl. Genet. 2018;131:2555-2566. DOI 10.1007/s00122-018-3172-9.

9. Bormann C.A., Rickert A.M., Ruiz R.A.C., Paal J., Lübeck J., Strahwald J., Buhr K., Gebhardt C. Tagging quantitative trait loci for maturity-corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers. Mol. Plant-Microbe Interact. 2004;17(10):1126-1138. DOI 10.1094/MPMI.2004.17.10.1126.

10. Brugmans B., Hutten R.G.B., Rookmaker N., Visser R.G.F., van Eck H.J. Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene. Theor. Appl. Genet. 2006;112(2):269-277. DOI 10.1007/s00122-005-0125-x.

11. Finkers-Tomczak A., Bakker E., Boer J., Vossen E., Achenbach U., Golas T., Suryaningrat S., Smant G., Bakker J., Goverse A. Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). Theor. Appl. Genet. 2011;122: 595-608. DOI 10.1007/s00122-010-1472-9.

12. Finkers-Tomczak A., Danan S., van Dijk T., Beyene A., Bouwman L., Overmars H., van Eck H., Goverse A., Bakker J., Bakker E. A highresolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis. Theor. Appl. Genet. 2009;119(1):165-173. DOI 10.1007/s00122-009-1026-1.

13. Flor H.H. Current status of the gene-for-gene concept. Annu. Rev. Phytopathol. 1971;9:275-296. DOI 10.1146/annurev.py.09.090171.001423.

14. Food and Agriculture Organization of the United Nations. World Food and Agriculture – Statistical pocketbook 2019. Rome: FAO, 2019. Available at: http://www.fao.org/3/ca6463en/ca6463en.pdf.

15. Galek R., Rurek M., De Jong W.S., Pietkiewicz G., Augustyniak H., Sawicka-Sienkiewicz E. Application of DNA markers linked to the potato H1 gene conferring resistance to pathotype Ro1 of Globodera rostochiensis. J. Appl. Genet. 2011;52(4):407-411. DOI 10.1007/s13353-011-0056-y.

16. Gavrilenko Т.А., Klimenko N.S., Antonova O.Yu., Lebedeva V.A., Evdokimova Z.Z., Gadjiyev N.M., Apalikova O.V., Alpatyeva N.V., Kostina L.I., Zoteyeva N.M., Mamadbokirova F.T., Egorova K.V. Molecular screening of potato varieties bred in the northwestern zone of the Russian Federаtion. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2018;22(1):35-45. DOI 10.18699/VJ18.329. (in Russian)

17. Gebhardt C., Ballvora A., Walkemeier B., Oberhagemann P., Schüler K. Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol. Breed. 2004;13:93-102. DOI 10.1023/B:MOLB.0000012878.89855.df.

18. Gebhardt C., Bellin D., Henselewski H., Lehmann W., Schwarzfischer J., Valkonen J. Marker-assisted combination of major genes for pathogen resistance in potato. Theor. Appl. Genet. 2006; 112(8):1458-1464. DOI 10.1007/s00122-006-0248-8.

19. Epub 2006 Mar 15. Gebhardt C., Mugniery D., Ritter E., Salamini F., Bonnel E. Identification of RFLP markers closely linked to the H1 gene conferring resistance to Globodera rostochiensis in potato. Theor. Appl. Genet. 1993;85:541-544. DOI 10.1007/BF00220911.

20. Gebhardt C., Valkonen J.P.T. Organization of genes controlling disease resistance in the potato genome. Annu. Rev. Phytopathol. 2001;39: 79-102. DOI 10.1146/annurev.phyto.39.1.79.

21. Groth J., Song Y., Kellermann A., Schwarzfischer A. Molecular characterisation of resistance against potato wart races 1, 2, 6 and 18 in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). J. Appl. Genet. 2013;54(2):169-178. DOI 10.1007/s13353-013-0141-5. Epub 2013 Feb 24.

22. Hampson М.С. History, biology and control of potato wart disease in Canada. Can. J. Plant Pathol. 1993;15(4):223-244. DOI 10.1080/07060669309501918.

23. Hehl R., Faurie E., Hesselbach J., Salamini F., Whitham S., Baker B., Gebhardt C. TMV resistance gene N homologues are linked to Synchytrium endobioticum resistance in potato. Theor. Appl. Genet. 1999;98:379-386. DOI 10.1007/s001220051083.

24. Jacobs J.M.E., Eck H.J., Horsman K., Arens P.F.P., Verkerk-Bakker B., Jacobsen E., Pereira A., Stiekema W.J. Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei. Mol. Breed. 1996;2:51-60. DOI 10.1007/BF00171351.

25. Janssen R., Bakker J., Gommers F.J. Mendelian proof for a gene-forgene relationship between virulence of Globodera rostochiensis and the H1 resistance gene in Solanum tuberosum ssp. andigena CPC 1673. Rev. de Nematol. 1991;14(2):207-211.

26. Jones F.G.W., Parrott D.M., Perry J.N. The gene-for-gene relationship and its significance for potato cyst nematodes and their solanaceous hosts. In: Zuckerman B.M., Rohde R.A. (Eds.). Plant Parasitic Nematodes. Vol. 3. New York: Acad. Press, 1981;23-36.

27. Khiutti A., Afanasenko O., Antonova O., Shuvalov O., Novikova L., Krylova E., Chalaya N., Mironenko N., Spooner D., Gavrilenko T. Characterization of resistance to Synchytrium endobioticum in cultivated potato accessions from the collection of Vavilov Institute of Plant Industry. Plant Breed. 2012;131(6):744-750. DOI 10.1111/j.1439-0523.2012.02005.x.

28. Khiutti А.V., Antonova O.Yu., Mironenko N.V., Gavrilenko T.A., Afanasenko O.S. Potato resistance to quarantine diseases. Russ. J. Genet. Appl. Res. 2017;7(8):833-844. DOI 10.1134/S2079059717050094.

29. Klimenko N.S., Antonova O.Yu., Kostina L.I., Mamadbokirova F.T., Gavrilenko T.A. Marker-assisted selection of Russian potato varieties with markers of genes for resistance to potato golden nematode (pathotype Ro1). Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics, and Breeding. 2017;178(4):66-75. DOI 10.30901/2227-8834-2017-4-66-75. (in Russian)

30. Koretsky P.M. Harmfulness of potato wart in household plots in areas of widespread of the disease in Ukraine. Mikologiya i Fitopatologiya = Mycology and Phytopathology. 1970;4(4):366-369. (in Russian)

31. KortJ., StoneA.R., Rumpenhorst H.J., Ross H. An international scheme for identifying and classifying pathotypes of potato cyst-nematodes Globodera rostochiensis and G. pallida. Nematologica. 1977;23(3): 333-339. DOI 10.1163/187529277x00057.

32. Kreike C.M., De Koning J.R.A., Vinke J.H., Van Ooijen J.W., Stiekema W.J. Mapping of loci involved in quantitatively inherited resistance to the potato cyst-nematode Globodera rostochiensis pathotype Ro1. Theor. Appl. Genet. 1993;87:464-470. DOI 10.1007/BF00215092.

33. Kreike C.M., Kok-Westeneng A.A., Vinke J.H., Stiekema W.J. Mapping of QTLs involved in nematode resistance, tuber yield and root development. Theor. Appl. Genet. 1996;92:463-470. DOI 10.1007/BF00223694.

34. Kuhl J.C. Mapping and tagging of simply inherited traits. In: Bradeen J.M., Chittaranjan K. (Eds.). Genetics, Genomics and Breeding of Potato. Enfield, New Hampshire: Sci. Publishers, 2011;90-112.

35. Leister D., Ballvora A., Salamini F., Gebhardt C. A PCR based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nat. Genet. 1996;14:421-429. DOI 10.1038/ng1296-421.

36. Limantseva L., Mironenko N., Shuvalov O., Antonova O., Khiutti A., Novikova L., Afanasenko O., Spooner D., Gavrilenko T. Characterization of resistance to Globodera rostochiensis pathotype Ro1 in cultivated and wild potato species accessions from the Vavilov Institute of Plant Industry. Plant Breed. 2014;133(5):660-665. DOI 10.1111/pbr.12195.

37. Lopez-Pardo R., Barandalla L., Ritter E., de Galarreta J.I.R. Validation of molecular markers for pathogen resistance in potato. Plant Breed. 2013;132:246-251. DOI 10.1111/pbr.12062.

38. Milczarek D., Flis B., Przetakiewicz A. Suitability of molecular markers for selection of potatoes resistant to Globodera spp. Am. J. Potato Res. 2011;88:245-255. DOI 10.1007/s12230-011-9189-0.

39. Milczarek D., Przetakiewicz A., Kaminski P., Flis B. Early selection of potato clones with the H1 resistance gene – the relation of nematode resistance to quality characteristics. Czech J. Genet. Plant Breed. 2014;50(4):278-284. DOI 10.17221/114/2014-CJGPB.

40. Mori K., Sakamoto Y., Mukojima N., Tamiya S., Nakao T., Ishii T., Hosaka K. Development of a multiplex PCR method for simultaneous detection of diagnostic DNA markers of five disease and pest resistance genes in potato. Euphytica. 2011;180:347-355. DOI 10.1007/s10681-011-0381-6.

41. Niewöhner J., Salamini F., Gebhardt C. Development of PCR assays diagnostic for RFLP marker alleles closely linked to alleles Gro1 and H1, conferring resistance to the root cyst nematode Globodera rostochiensis in potato. Mol. Breed. 1995;1:65-78. DOI 10.1007/BF01682090.

42. Obidiegwu J.E., Flath K., Gebhardt C. Managing potato wart: a review of present research status and future perspective. Theor. Appl. Genet. 2014;127(4):763-780. DOI 10.1007/s00122-014-2268-0.

43. Obidiegwu J.E., Sanetomo R., Flath K., Tacke E., Hoferbert H.-R., Hofmann A., Walkemeier B., Gebhardt C. Genomic architecture of potato resistance to Synchytrium endobioticum disentangled using SSR markers and the 8.3 k SolCAP SNP genotyping array. BMC Genet. 2015;16:38. DOI 10.1186/s12863-015-0195-y.

44. OEPP/EPPO Standards PM 7/28. Diagnostic protocols for regulated pests: Synchytrium endobioticum. Bulletin OEPP/EPPO Bulletin. 2004;34:213-218. DOI 10.1111/j.1365-2338.2004.00722.x.

45. OEPP/EPPO Testing of potato varieties to assess resistance to Globodera rostochiensis and Globodera pallida. Bulletin OEPP/ EPPO Bulletin. 2006;36:419-420. DOI 10.1111/j.1365-2338.2006.01032.x.

46. Paal J., Henselewski H., Muth J., Meksem K., Menéndez C.M., Salamini F., Ballvora A., Gebhardt C. Molecular cloning of the potato Gro1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach. Plant J. 2004;38(2):285-297. DOI 10.1111/j.1365313X.2004.02047.x.

47. Pajerowska-Mukhtar K., Stich B., Achenbach U., Ballvora A., Lübeck J., Strahwald J., Tacke E., Hofferbert H.-R., Ilarionova E., Bellin D., Walkemeier B., Basekow R., Kersten B., Gebhardt C. Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics. 2009;181(3):1115-1127. DOI 10.1534/genetics.108.094268.

48. Pineda O., Bonierbale M.W., Plaisted R.L., Brodie B.B., Tanksley S.D. Identification of RFLP markers linked to the H1 gene conferring resistance to the potato cyst nematode Globodera rostochiensis. Genome. 1993;36(1):152-156. DOI 10.1139/g93-019.

49. Plich J., Przetakiewicz J., Śliwka J., Flis B., Wasilewicz-Flis I., Zimnoch-Guzowska E. Novel gene Sen2 conferring broad-spectrum resistance to Synchytrium endobioticum mapped to potato chromosome XI. Theor. Appl. Genet. 2018;131:2321-2331. DOI 10.1007/s00122-018-3154-y.

50. Prodhomme C., Esselink D., Borm T., Visser R.G.F., van Eck H.J., Vossen J.H. Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3. Plant Methods. 2019;15:60. DOI 10.1186/s13007-019-0445-5.

51. Prodhomme C., Peter G.V., Paulo M.J., Visser R.G.F., Vossen J.H., van Eck J.H. Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers. Theor. Appl. Genet. 2020;133:1859-1871. DOI 10.1007/s00122-020-03559-3.

52. Ramakrishnan A.P., Ritland C.E., Blas Sevillano R.H., Riseman A. Review of potato molecular markers to enhance trait selection. Am. J. Potato Res. 2015;92(4):455-472. DOI 10.1007/s12230-015-9455-7.

53. Rouppe van der Voort J., Lindeman W., Folkertsma R., Hutten R., Overmars H., van der Vossen E., Jacobsen E., Bakker J. A QTL for broadspectrum resistance to cyst nematode species (Globodera spp.) maps to a resistance gene cluster in potato. Theor. Appl. Genet. 1998;96: 654-661. DOI 10.1007/s001220050785.

54. Rouppe van der Voort J., van der Vossen E., Bakker E., Overmars H., van Zandvoort P., Hutten R., Klein Lankhorst R., Bakker J. Two additive QTLs conferring broadspectrum resistance in potato to Globodera pallida are localized on resistance gene clusters. Theor. Appl. Genet. 2000;101:1122-1130. DOI 10.1007/s001220051588.

55. Schultz L., Cogan N.О.I., McLean K., Dale M.F.B., Bryan G.J., Forster J.W., Slater A.T. Evaluation and implementation of a potential diagnostic molecular marker for H1-conferred potato cyst nematode resistance in potato (Solanum tuberosum L.). Plant Breed. 2012; 131:315-321. DOI 10.1111/j.1439-0523.2012.01949.x.

56. Skupinová S., Vejl P., Sedlák P., Domkářová J. Segregation of DNA markers of potato (Solanum tuberosum ssp. tuberosum L.) resistance against Ro1 pathotype Globodera rostochiensis in selected F1 progeny. Rostlinná Výroba. 2002;48(11):480-485. DOI 10.17221/4399-PSE.

57. State Register of Selection Achievements Authorized for Use for Production Purposes. Vol. 1. Plant Varieties (official publication). Moscow: Rosinformagrotech Publ., 2019. (in Russian)

58. Toxopeus H.J., Huijsman C.A. Breeding for resistance to potato root eelworm. I. Preliminary data concerning the inheritance and the nature of resistance. Euphytica. 1953;2(3):180-186. DOI 10.1007/BF00053725