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

  • O. Y. Antonova
  • N. A. Shvachko
  • L. Y. Novikova
  • O. Y. Shuvalov
  • L. I. Kostina
  • N. S. Klimenko
  • A. R. Shuvalova
  • T. A. Gavrilenko
Article
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Abstract

The genetic diversity of potato varieties from the collection of Vavilov Institute of Plant Genetic Resources (VIR) was analyzed based on microsatellite analysis. These varieties have been bred in Russia and its neighboring countries since 1931. Application of 14 highly polymorphic nuclear microsatellites (SSRs) has enabled 113 varieties to be fully distinguished. Additionally, we have studied these varieties for the distribution of 8 DNA markers associated with three R-genes involved in controlling resistance to two quarantine objects: potato wart Synchytrium endobioticum and golden potato cyst nematode Globodera rostochiensis, occurring locally in some regions of the Russian Federation. All the analyzed varieties with resistance to the S. endobioticum pathotype 1 revealed the diagnostic marker Nl251400 of the Sen1 gene, while a few susceptible cultivars lost this diagnostic fragment. The tested markers of the H1 and Gro1-4 genes, which confer resistance to the G. rostochiensis pathotype Ro1 revealed different predictability. In the molecular screening of potato varieties, it is better to use several markers of these genes. The results of molecular screening using six markers of H1 and Gro1-4 genes allowed us to detect six haplotypes in the tested subset. Five haplotypes include varieties with different combinations of the markers tested; the majority (87.9%) of these varieties were highly resistant or moderately resistant to G. rostochiensis. The most numerous haplotype H1/0 included 76 varieties, which did not possess any marker of H1 and Gro1-4 genes; 96.1% of these varieties were susceptible to G. rostochiensis. Predictive associations between the haplotype content, wart and nematode resistance, pedigree, and the variety in their age are discussed.

Keywords

Solanum potato SSR-genotyping MAS Globodera rostochiensis Synchytrium endobioticum 

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References

  1. Asano, K. and Tamiya, S., Breeding of pest and disease resistant potato cultivars in Japan by using classical and molecular approaches, JARQ, 2016, vol. 50, no. 1, pp. 1–6.CrossRefGoogle Scholar
  2. Baayen, R.P., Cochius, G., Hendriks, H., Meffert, J.P., Bakker, J., Bekker, M., Boogert, P.H., Stachewicz, H., and van Leeuwen, G.C.M., History of potato wart disease in Europe—a proposal for harmonization in defining pathotypes, Eur. J. Plant Pathol., 2006, vol. 116, pp. 21–31. doi 10.1007/s10658-006-9039-yCrossRefGoogle Scholar
  3. 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., and Goverse, A., A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis, Theor. Appl. Genet., 2004, vol. 109, no. 1, pp. 146–152. doi 10.1007/s00122-004-1606-zCrossRefPubMedGoogle Scholar
  4. Ballvora, A., Flath, K., Lubeck, J., Strahwald, J., Tacke, E., Hofferbert, H.-R., and 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, vol. 123, pp. 1281–1292.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Ballvora, A., Hesselbach, J., Niewohner, J., Leister, D., Salamini, F., and Gebhardt, C., Marker enrichment and high-resolution map of the segment of potato chromosome VII harboring the nematode resistance gene Gro1, Mol. Gen. Genet., 1995, vol. 249, pp. 82–90.CrossRefPubMedGoogle Scholar
  6. Barone, A., Ritter, E., Schachtschabel, U., Debener, T., Salamini, F., and 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. Gen. Genet., 1990, vol. 224, no. 2, pp. 177–182.CrossRefPubMedGoogle Scholar
  7. Biryukova, V.A., Shmyglya, I.V., Abrosimova, S.B., Zapekina, T.I., Meleshin, A.A., Mityushkin, A.V., and Manankov, V.V., Search for sources of genes for resistance to pathogens among breeding clones and genetic collections of VNIIKhH using molecular markers, Zashch. Kartofelya, 2015, vol. 1, pp. 3–7.Google Scholar
  8. Biryukova, V.A., Zhuravlev, A.A., Abrosimova, S.B., Kostina, L.I., Khromova, L.M., Shmyglya, I.V., Morozova, N.N., and Kirsanova, S.N., Use of molecular markers of potato golden nematode resistance genes H1 and GRO1, Russ. Agric. Sci., 2008, vol. 34, no. 6, pp. 365–368.CrossRefGoogle Scholar
  9. Bornet, B., Goraguer, F., Joly, G., and Branchard, M., Genetic diversity in European and Argentinian cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs), Genome, 2002, vol. 45, no. 3, pp. 481–484.CrossRefPubMedGoogle Scholar
  10. Bradshaw, J.E., Bryan, G.J., and Ramsay, G., Genetic recourses (including wild and cultivated Solanum species) and progress in their utilization in potato breeding, Potato Res., 2006, vol. 49, pp. 49–65. doi 10.1007/s11540-006-9002-5CrossRefGoogle Scholar
  11. Braun, A. and Wenzel, G., Molecular analysis of genetic variation in potato (Solanum tuberosum L.). I. German cultivars and advanced clones, Potato Res., 2004, vol. 47, no. 5, pp. 81–92. doi 10.1007/BF02731971CrossRefGoogle Scholar
  12. Bukasov, S.M. and Kameraz, A.Ya., Osnovy selektsii kartofelya (Fundamentals of Potato Breeding), Moscow: Sel’khozgiz, 1959.Google Scholar
  13. Cote, M.-J., Leduc, L., and Reid, A., Evaluation of simple sequence repeat (SSR) markers established in Europe as a method for the identification of potato varieties grown in Canada, Am. J. Potato Res., 2013, vol. 90, pp. 340–350. doi 10.1007/s12230-013-9310-7CrossRefGoogle Scholar
  14. Dice, L., Measures of the amount of ecologic association between species, Ecology, 1945, vol. 26, pp. 297–302.CrossRefGoogle Scholar
  15. Ellenby, C., Tuber forming species and varieties of the genus Solanum tested for resistance to the potato root eelworm Heterodera rostochiensis Wollenweber, Euphytica, 1954, vol. 3, pp. 195–202. doi 10.1007/BF00055593CrossRefGoogle Scholar
  16. Feingold, S., Lloyd, J., Norero, N., Bonierbale, M., and Lorenzen, J., Mapping and characterization of new ESTderived microsatellites for potato (Solanum tuberosum L.), Theor. Appl. Genet., 2005, vol. 111, pp. 456–466. doi 10.1007/s00122-005-2028-2CrossRefPubMedGoogle Scholar
  17. Finkers-Tomczak, A., Bakker, E., Boer, J., Vossen, E., Achenbach, U., Golas, T., Suryaningrat, S., Smant, G., Bakker, J., and 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, vol. 122, pp. 595–608. doi 10.1007/s00122-010-1472-9CrossRefPubMedGoogle Scholar
  18. Fu, Y., Peterson, G., Richards, K., Tarn, T., and Percy, J., Genetic diversity of Canadian and exotic potato germplasm revealed by simple sequence repeat markers, Am. J. Potato Res., 2009, no. 1, pp. 38–48. doi 10.1007/s12230-008-9059-6CrossRefGoogle Scholar
  19. Gadzhiev, N.M. and Lebedeva, V.A., Origin of some of the Belogorsk varieties of potatoes, Kartofel’ Ovoshchi, 2010, vol. 8, pp. 21–22.Google Scholar
  20. Gaevskii, N.A., Znakomstvo s evolyutsionnoi genetikoi (Introduction to Evolutionary Genetics), Krasnoyarsk, 2002.Google Scholar
  21. Gavrilenko, T., Antonova, O., Ovchinnikova, A., Novikova, L., Krylova, E., Mironenko, N., Pendinen, G., Islamshina, A., Shvachko, N., Kiru, S., Kostina, L., Afanasenko, O., and Spooner, D., A microsatellite and morphological assessment of the Russian national cultivated potato collection, Genet. Resour. Crop Evol., 2010, vol. 57, pp. 1151–1164. doi 10.1007/s10722-010-9554-8CrossRefGoogle Scholar
  22. Gavrilenko, T., Antonova, O., Shuvalova, A., Krylova, E., Alpatyeva, N., Spooner, D., and Novikova, L., Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism, Genet. Resour. Crop Evol., 2013, vol. 60, pp. 1997–2015. doi 10.1007/s10722-013-9968-1CrossRefGoogle Scholar
  23. GCDT (The Global Crop Diversity Trust) Background on the development of “Global Strategy for the Ex situ Conservation of Potato,” 2006. https://www.croptrust.org/wp-content/uploads/2014/2/Potato-Strategy-FINAL-30Jan07.pdf.Google Scholar
  24. Gebhardt, C., Bellin, A., Henselewski, A., Lehmann, W., Schwarzfischer, A., and Valkonen, J., Marker-assisted combination of major genes for pathogen resistance in potato, Theor. Appl. Genet., 2006, vol. 112, pp. 1458–1464. doi 10.1007/s00122-006-0248-8CrossRefPubMedGoogle Scholar
  25. Gebhardt, C., Bridging the gap between genome analysis and precision breeding in potato, Trends Genet., 2013, vol. 29, no. 4, pp. 248–256. doi 10.1016/j.tig.2012.11.006CrossRefPubMedGoogle Scholar
  26. Ghislain, M., Nunez, J., Herera, M. del R., Rignataro, J., Guzman, F., Bonierbale, M., and Spooner, D.M., Robust and hightly informative microsatellite-based genetic identity kit for potato, Mol. Breed., 2009, vol. 23, pp. 377–388. doi 10.1007/s11032-008-9240-0CrossRefGoogle Scholar
  27. Gorji, A.M., Poczai, P., Polgar, Z., and Taller, J., Efficiency of arbitrarily amplified dominant markers (SCOT,ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato, Am. J. Pot. Res., 2011, vol. 88, pp. 226–237. doi 10.1007/s12230-011-9187-2CrossRefGoogle Scholar
  28. Hehl, R., Faurie, E., Hesselbach, J., Salamini, F., and Witham, S., TMV resistance gene N homologues are linked to Synchytrium endobioticum resistance in potato, Theor. Appl. Genet., 1999, vol. 98, pp. 379–386. doi 10.1007/s001220051083CrossRefGoogle Scholar
  29. Hirsch, C.D., Hamilton, J.P., Childs, K.L., Cepela, J., Crisovan, E., Vaillancourt, B., and Hirsch, C.N., A resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding, Plant Genome, 2014, vol. 7, pp. 1–12. doi 10.3835/plantgenome2013.12.0042CrossRefGoogle Scholar
  30. Kawchuk, I.M., Lynch, D.R., Thomas, J., Penner, B., Silito, D., and Kulcsar, F., Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification, Am. Potato J., 1996, vol. 73, pp. 325–335. doi 10.1007/BF02849164CrossRefGoogle Scholar
  31. Khiutti, A., Afanasenko, O., Antonova, O., Shuvalov, O., Novikova, L., Krylova, E., Chalaya, N., Mironenko, N., Spooner, D.M., and Gavrilenko, T., Characterization of resistance to Synchytrium endobioticum in cultivated potato accessions from the collection of Vavilov Institute of Plant Industry (VIR) collection, Plant Breed., 2012, vol. 131, pp. 744–750. doi 10.1111/j.1439-0523.2012.02005.xCrossRefGoogle Scholar
  32. Kort, J., Ross, H., Rumpenhorst, H.J., and Stone, A.R., An international scheme for the identification of pathotypes of potato cyst nematodes Globodera rostochiensis and G. pallid, Nematologica, 1977, vol. 23, pp. 333–339.CrossRefGoogle Scholar
  33. Kuz’minova, O.A., Stashevski, Z., Vologin, S.G., and Gimaeva, E.A., Study of potato selection material by molecular genetic analysis for the presence of resistance genes to Globodera rostochiensis, Sovremennye tekhnologii vyrashchivaniya sel’skokhozyaistvennykh kul’tur. Mater. Vseros. zaoch. nauch.-prakt. konf. molodykh uchenykh, posvyashch. pamyati R.G. Gareeva (Modern Technologies of Cultivation of Agricultural Crops. Proc. All-Russian Sci.-Pract. Conf. Young Scientists Dedicated to the Memory of R.G. Gareyeva), Kazan: Tsentr innovatsionnykh tekhnologii,2015, pp. 88–97.Google Scholar
  34. Limantseva, L., Mironenko, N., Shuvalov, O., Antonova, O., Khiutti, A., Novikova, L., Afanasenko, O., Spooner, D., and Gavrilenko, T., Characterization of resistance to Globodera rostochiensis pathotype Ro1 in cultivated and wild potato species accessions, Plant Breed., 2014, vol. 133, no. 5, pp. 660–665. doi 10.1111/pbr.12195CrossRefGoogle Scholar
  35. Loeschcke, V. and Stegemann, H., The application of PAG electrophoresis for studying of the potato proteins, Z. Naturforschung, 1966, vol. 21, pp. 879–888.Google Scholar
  36. McGregor, C., Lambert, C., Greyling, M., Louw, H., and Warnich, L., A comparative assessment of fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm, Euphytica, 2000, vol. 113, pp. 135–144.CrossRefGoogle Scholar
  37. Milczarek, D., Flis, B., and Przetakiewicz, A., Suitability of molecular markers for selection of potatoes resistant to Globodera spp., Am. J. Potato Res., 2011, vol. 88, pp. 245–255. doi 10.1007/s12230-011-9189-0CrossRefGoogle Scholar
  38. Moisan-Thiery, M., Marhadour, S., Kerlan, M., Dessenne, N., Perramant, M., Gokelaere, T., and LeHingrat, Y., Potato cultivar identification using simple sequence repeats markers (SSR), Potato Res., 2005, vol. 48, pp. 191–200. doi 10.1007/BF02742376CrossRefGoogle Scholar
  39. Nei, M., Analysis of gene diversity in subdivided populations, Proc. Natl. Acad. Sci. U.S.A., 1973, vol. 70, pp. 3321–3323.CrossRefPubMedPubMedCentralGoogle Scholar
  40. Paal, J., Henselewski, H., Muth, J., Meksem, K., Menendez, C., Salamini, F., Ballvora, A., and Gebhardt, C., Molecular cloning of the potato Gro 1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach, Plant J., 2004, vol. 38, pp. 285–297.PubMedGoogle Scholar
  41. Provan, J., Powell, W., and Waugh, R., Analysis of cultivated potato (Solanum tuberosum) using intermicrosatellite amplification, Genome, 1996, vol. 39, pp. 767–769.CrossRefPubMedGoogle Scholar
  42. Ramakrishnan, A.P., Ritland, C.E., Blas Sevillano, R.H., and Riseman, A., Review of potato molecular markers to enhance trait selection, Am. J. Potato Res., 2015, vol. 92, no. 4, pp. 455–472. doi 10.1007/s12230-015-9455-7CrossRefGoogle Scholar
  43. Ross, H., Potato breeding—problems and perspectives, J. Plant Breed., 1986, suppl. 13.Google Scholar
  44. Ryzhova, N.N., Martirosyan, E.V., and Kochieva, E.Z., Analysis of microsatellite locus polymorphism in potato (Solanum tuberosum) cultivars of Russian breeding, Russ. J. Genet., 2010, vol. 46, no. 4, pp. 425–430.CrossRefGoogle Scholar
  45. Salaman, R.N., Potato Varieties, Cambrige Univ. Press, 1926.Google Scholar
  46. Schultz, L., Cogan, N.O.I., Mclean, K., Dale, M.F.B., Bryan, G.J., Forster, J.N.W., and Slater, A.T., Evaluation and implementation of a potential diagnostic molecular marker for H1-conferred potato cyst nematode resistance in potato, Plant Breed., 2012, vol. 131, pp. 315–321. doi 10.1111/j.1439-0523.2012.01949.xCrossRefGoogle Scholar
  47. Shanina, E.P., Klyukina, E.M., Koksharov, V.P., and Shanin, A.A., The creation of nematode-resistant varieties is a priority in the selection of potatoes in the Middle Urals, Agrar. Vestn. Urala, 2011, vol. 2, no. 81, pp. 59–61.Google Scholar
  48. Simakov, E.A., Yakovleva, V.A., Abrosimova, S.B., D’yachenko, A.A., and Biryukova, V.A., How to assess potato resistance to Globodera rostochiensis?, Zashch. Karantin Rast., 2009, vol. 1, pp. 28–29.Google Scholar
  49. Spooner, D.M., Nunez, J., Trujillo, G., del Rosario Herrera, M., Guzman, F., and Ghislain, M., Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification, Proc. Natl. Acad. Sci. U.S.A., 2007, vol. 104, pp. 19398–19403. doi 10.1073/pnas.0709796104CrossRefPubMedPubMedCentralGoogle Scholar
  50. Stuart, W., The Potato: Its Culture, Uses, History and Classification, Stuart, W. and Lippincott, J.B., Eds., Philadelphia, Pennsylvania:1937.Google Scholar
  51. Takeuchi, T., Sasaki, J., Suzuki, T., Horita, H., Hiura, S., Iketani, S., Fujita, R., and Senda, K., DNA Markers for Efficient Selection of Disease and Pests Resistance Genes in Potato, Hokkaido Nogyo-Shiken-Kaigi-Shiryo, 2009, pp. 1–26.Google Scholar
  52. Uitdewilligen, J.G., Wolters, A.-M.A., D’Hoop, B.B., Borm, T.J.A., Visser, R.G.F., and Eck, H.J., A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato, PLoS ONE,2013. doi 10.1371/journal.pone.0062355Google Scholar
  53. van Berloo, R., Hutten, R., van Eck, H., and Visser, R.G.F., An online potato pedigree database resource, Potato Res., 2007, vol. 50, pp. 45–57. doi 10.1007/s11540-007-9028-3CrossRefGoogle Scholar
  54. Vos, P.G., Uitdewilligen, J., Visser, R.G.F., and Eck, H.J., Development and analysis of a 20k SNP array for potato: An insight into the breeding history, Theor. Appl. Genet., 2015, vol. 128, pp. 2387–2401. doi 10.1007/s00122-015-2593-yCrossRefPubMedPubMedCentralGoogle Scholar
  55. Yashina, I.M., Kukushkina, L.N., Derevyagina, M.K., Babaitseva, O.V., et al., Katalog novykh iskhodnykh form donorov polevoi (gorizontal’noi) ustoichivosti kartofelya k fitoftorozu (The Catalog of New Initial Forms of Donors of Field (Horizontal) Resistance of Potato to Late Blight), Moscow: Ros. akad. s.-kh. nauk VNIIKKh,2007.Google Scholar
  56. Zaitseva, N.D., Rukovodstvo po opredeleniyu sortov kartofelya (Guidelines for the Identification of Potato Varieties), Moscow,1965.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2017

Authors and Affiliations

  • O. Y. Antonova
    • 1
  • N. A. Shvachko
    • 1
  • L. Y. Novikova
    • 1
  • O. Y. Shuvalov
    • 1
  • L. I. Kostina
    • 1
  • N. S. Klimenko
    • 1
  • A. R. Shuvalova
    • 1
  • T. A. Gavrilenko
    • 1
    • 2
  1. 1.Vavilov Institute of Plant Genetic Resources (VIR)St. PetersburgRussia
  2. 2.St. Petersburg State UniversitySt. PetersburgRussia

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