Finding RB/Rpi-blb1/Rpi-sto1-like sequences in conventionally bred potato varieties

The main objectives in potato breeding are increasing yield abilities and improving resistance to numerous pathogens and pests. Among them, the late blight caused by the Phytophthora infestans oomycete is one of the most destructive potato diseases both in Russia and worldwide. Wild relatives of cultivated potato are traditionally used in breeding as the source of valuable R genes conferring resistance to pathogens. Of particular interest are Mexican wild species because Mexico is the centre of origin and diversity of P. infestans and at the same time, it is the centre of potato species diversity.  Mexican wild potato species S. bulbocastanum and S. stoloniferum are an important source of the R genes conferring broad-spec trum resistance against various isolates of P. infestans (Rpi-blb1,  Rpi-blb2, Rpi-sto1). Recently these genes have been transferred into cultivated potato gene pool using the cisgene  approach. At the same time there is a high probability of finding geno types with the Rpi-sto1 gene (functional homologues of  Rpi-blb1) among conventionally bred varieties because for about 40 years S. stoloniferum has been used in breeding as a source of the Rysto and Ry-fsto genes of the extreme resistance to the most important viral pathogen PVY. In this study 188 potato varieties bred in Russia and in near-abroad countries were screened for the presence of six gene-specific markers of the RB/Rpi-blb1 =  Rpi-sto1 and Rpi-blb2 genes conferring broad-spectrum resistance against P. infestans, and for the markers linked to the Rysto and Ry-fsto genes conferring extreme resistance to PVY. In addition, a marker for detecting male sterile mitochondrial DNA type gamma derived from S. stoloniferum was used. The genotypes selected through the molecular markers were divided into four groups: (A) 13 PVY resistant varieties carrying diagnostic markers of the Rysto, Ry-fsto genes and having sterile mt-type gamma; (B) four varieties possessing mt-type gamma and not having the markers of the R genes introgressed from S. stoloniferum; (C) eight genotypes carrying five gene-specific markers for the RB/Rpi-blb1/= Rpi-sto1; (D) the rest 166 (86.9 %) varieties not possessing any of the diagnostic markers associated with the S. stoloniferum genetic material. The sequences of the Rpi-sto1- and BLB1 F/R-amplicons were identical in all the genotypes of group ‘C’ and showed respective 99 % and 100 % similarity to the corresponding fragments of the Rpi-sto1 and Rpi-blb1 genes from the GenBank database. Among the genotypes of group ‘C’ various mt-types were detected, and some of them were male fertile.

potato, Solanum stoloniferum, marker assisted selection, R genes, RB/Rpi-blb1/Rpi-sto1, male sterility

1. Biryukova V.A., Shmyglya I.V., Abrosimova S.B., Zapekina T.I., Meleshin A.A., Mityushkin A.V., Manankov V.V. Search for sources of genes for resistance to pathogens among samples of selection and genetic collections of VNIIKhH using molecular markers. Zashchita Kartofelya = Potato Protection. 2015;1:3-7.

2. Colton L.M., Groza H.I., Wielgus S.M., Jiang J. Marker-assisted selection for the broad-spectrum potato late blight resistance conferred by gene RB derived from a wild potato species. Crop Sci. 2006;46:589594. DOI 10.2135/cropsci2005.0112.

3. Elanskij S. Features of late blight in Russia. Zashhita Kartofelya = Potato Protection. 2015;1:8-11. Fact Series. A late blight resistance for Europe, 2014. www.vib.be.

4. Flis B., Hennig J., Strzelczyk-Żyta D., Gebhardt C., Marczewski W. The Ry-fsto gene from Solanum stoloniferum for extreme resistant to Potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122718 in PVY resistant potato cultivars. Mol. Breed. 2005;15(1):95-101. DOI 10.1007/s11032-004-2736-3.

5. Fry W.E. Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant Pathol. 2008;9(3):385-402. DOI 10.1111/j.1364-3703.2007. 00465.x.

6. Fry W.E., Goodwin S.B. Re-emergence of potato and tomato late blight in the United States. Plant Dis. 1997;81(12):1349-1357. DOI 10.1094/PDIS.1997.81.12.1349.

7. Fry W.E., Goodwin S.B., Dyer A.T., Matuszak J.M., Drenth A., Tooley P.W., Sujkowski L.S., Koh Y.J., Cohen B.A., Spielman L.J., Deahl K.L., Inglis D.A., Sandlan K.P. Historical and recent migrations of Phytophthora infestans; chronology, pathways and implications. Plant Dis. 1993;77(7):653-661.

8. Gavrilenko T., Antonova O., Shuvalova A., Krylova E., Alpatyeva N., Spooner D., Novikova L. Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism. Genet. Resour. Crop Evol. 2013;60(7):1997-2015. DOI 10.1007/s10722-013- 9968-1.

9. 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).

10. Goss E.M., Tabima J.F., Cooke D.E., Restrepo S., Fry W.E., Forbes G.A., Fieland V.J., Cardenas M., Grünwald N.J. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proc. Natl. Acad. Sci. USA. 2014;111(24):87918796. DOI 10.1073/pnas.1401884111.

11. Hajianfar R., Kolics B., Cernák I., Wolf I., Polgár Z., Taller J. Expression of biotic stress response genes to Phytophthora infestans inoculation in White Lady, a potato cultivar with race-specific resistance to late blight. Physiol. Mol. Plant Pathol. 2016;93:22-28. DOI 10.1016/j.pmpp.2015.12.001.

12. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 1999;41:95-98.

13. Hanneman R.E., Bamberg J.B. Inventory of tuber-bearing Solanum species. Madison: Univ. of Wisconsin, WI, USA, 1986. Haverkort A.J., Boonekamp P.M., Hutten R., Jacobsen E., Lotz L.A.P., Kessel G.J.T., Visser R.G.F., van der Vossen E.A.G. Societal costs of late blight in potato and prospects of durable resistance through cisgenic modification. Potato Res. 2008;51(1):47-57. DOI 10.1007/ s11540-008-9089-y.

14. Haverkort A.J., Boonekamp P.M., Hutten R., Jacobsen E., Lotz L.A.P., Kessel G.J.T., Vossen J.H., Visser R.G.F. Durable late blight resistance in potato through dynamic varieties obtained by cisgenesis: scientific and societal advances in the DuRPh Project. Potato Res. 2016;59(1):35-66. DOI 10.1007/s11540-015-9312-6.

15. Haverkort A.J., Struik P.C., Visser R.G.F., Jacobsen E. Applied biotechnology to combat late blight in potato caused by Phytophthora infestans. Potato Res. 2009;52(3):249-264. DOI 10.1007/s11540009-9136-3.

16. Hawkes J.G. The potato: evolution, biodiversity and genetic resources. London: Belhaven Press, 1990. Helgeson J.P., Pohlman J.D., Austin S., Haberlach G.T., Wielgus S.M., Ronis D., Zambolim L., Tooley P., McGrath J.M., James R.V., Stevenson W.R. Somatic hybrids between Solanum bulbocastanum and potato: A new source of resistance to late blight. Theor. Appl. Genet. 1998(6-7);96:738-742. DOI 10.1007/s001220050796.

17. Hermsen J.G.Th., Ramanna M.S. Double-bridge hybrids of Solanum bulbocastanum and cultivars of Solanum tuberosum. Euphytica. 1973;22(3):457-466. http://evrogen.ru http://www.ncbi.nlm.nih.gov/

18. Jackson S.A., Hanneman R.E.Jr. Crossability between cultivated and wild tuber-and non-tuber-bearing Solanums. Euphytica. 1999; 109(1):51-67. DOI 10.1023/A:1003710817938.

19. Kostina L.I., Koroleva L.V., Kosareva O.S., Fomina V.E. Breeding potato varieties from Russia and near-abroad countries. Catalogue. Saint Petersburg, 2016. Issue 829:43.

20. Levy A.V., Voronkova E.V., Poljuhovich Ju.V., Ermishin A.P. DNA markers of genes of resistance to late blight and Y-virus in samples of wild allotetraploid species of potato Solanum stoloniferum. Vesci Nacyjanal’naj Akadjemii Navuk Belarusi. 2017;2:46-54. DOI 10.29235/1029-8940-2017-0-2-46-54.

21. Lokossou A.A., Rietman H., Wang M.Q., Krenek P., Schoot H., Henken B., Hoekstra R., Vleeshouwers V.G.A.A., Vossen E.A.G., Visser R.G.F., Jacobsen E., Vosman B. Diversity, distribution, and evolution of Solanum bulbocastanum late blight resistance genes. Mol. Plant Microbe Interact. 2010;23(9):1206-1216. DOI 10.1094/ MPMI-23-9-1206.

22. Lössl A., Götz M., Braun A., Wenzel G. Molecular markers for cytoplasm in potato: male sterility and contribution of different plastidmitochondrial configurations to starch production. Euphytica. 2000; 116:221-230. DOI 10.1023/A:1004039320227.

23. Malcolmson J.F., Black W. New R genes in Solanum demissum Lindl. and their complementary races of Phytophthora infestans (Mont.) de Bary. Euphytica. 1966;15(2):199-203.

24. Naess S.K., Bradeen J.M., Wielgus S.M., Haberlach G.T., McGrath J.M., Helgeson J.P. Resistance to late blight in Solanum bulbocastanum is mapped to chromosome 8. Theor. Appl. Genet. 2000;101(5-6):697704. DOI 10.1007/s001220051533.

25. Okonechnikov K., Golosova O., Fursov M., UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012; 28(8):1166-1167. DOI 10.1093/bioinformatics/bts091.

26. Ortiz R. Potato breeding via ploidy manipulations. Ed. J. Janicks. Plant Breeding Reviews. New York: John Viley & Sons, 1998. 16:15-86.

27. Pankin A., Sokolova E., Rogozina E., Kuznetsova M., Deahl K., Jones R., Khavkin E. Allele mining in the gene pool of wild Solanum species for homologues of late blight resistance gene RB/ Rpi-blb1. Plant Genet. Res. 2011;9(2):305-308. DOI 10.1017/ S1479262111000414.

28. Pavlyuchuk N.V., Voluevich E.A., Mahanko V.L., Ruseckij N.V. Method of multiplex PCR for the detection of potato genotypes, resistant to PVY and to PVS. [Potato-growing. Proc. RUE “Research and practical center of NAS of Belarus for potato, fruit and vegetable growing”]. 2013;21(1):184-192.

29. Potatoes. Selection Potato Varieties of Russia and CIS Countries. Issue 829. Catalog of the world collection of VIR. SPb, 2016. (in Russian)

30. Ross H. Potato Breeding – Problems and Perspectives. Berlin: V.P. Parey, 1986. Russian Varieties of Potatoes. Catalog. Cheboksary, 2011. (in Russian)

31. Sanetomo R., Gebhardt C. Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits. BMC Plant Biol. 2015;15:162. DOI 10.1186/s12870-015-0545-y.

32. Simakov E.A., Anisimov B.V., Sklyarova N.P., Yashina I.M., Elanskiy S.N. Potato Cultivars in Russia. Moscow: Agrospas, 2009. (in Russian)

33. Simakov E.A., Yashina I.M., Sklyarova N.P. Potato breeding in Russia: history, general trends and achievements. Ed. A. Haverkort, B. Anisimov. Potato Production and Innovative Technologies. Wageningen Academic Publishers, The Netherlands. 2007;353-363. DOI 10.3920/978-90-8686-608-3.

34. Simko I. Comparative analysis of quantitative trait loci for foliage resistance to Phytophthora infestans in tuber-bearing Solanum species. Am. J. Potato Res. 2002;79:125-132.

35. Song J., Bradeen J.M., Naess S.K., Raasch J.A., Wielgus S.M., Haberlach G.T., Liu J., Kuang H., Austin-Phillips S., Buell C.R., Helgeson J.P., Jiang J. Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight. Proc. Natl. Acad. Sci. USA. 2003;100(16):9128-9133. DOI 10.1073/pnas.1533501100.

36. Song Y.-S., Schwarzfischer A. Development of STS markers for selection of extreme resistance (Rysto) to PVY and maternal pedigree analysis of extremely resistant cultivars. Am. J. Potato Res. 2008; 85(2):159-170. DOI 10.1007/s12230-008-9012-8.

37. Valkonen J.P.T., Wiegmann K., Hamalainen J.H., Marczewski W., Watanabe K.N. Evidence for utility of the same PCR-based markers for selection of extreme resistance to potato virus Y controlled by Rysto of Solanum stoloniferum derived from different sources. Ann. Appl. Biol. 2008;152(1):121-130. DOI 10.1111/j.1744-7348. 2007.00194.x.

38. van der Vossen E.A.G., Gros J., Sikkema A., Muskens M., Wouters D., Wolters P., Pereira A., Allefs S. The Rpi-blb2 gene from Solanum bulbocastanum is an Mi-1 gene homolog conferring broad-spectrum late blight resistance in potato. Plant J. 2005;44(2):208-222. DOI 10.1111/j.1365-313X.2005.02527.x.

39. van der Vossen E.A.G., Sikkema A., Hekkert B., Gros J., Stevens P., Muskens M., Wouters D., Pereira A., Stiekema W., Allefs J. An ancient R gene from the wild potato species Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans in cultivated potato and tomato. Plant J. 2003;36(6):867-882. DOI 10.1046/j.1365-313X.2003.01934.x.

40. van Hove L., Gillund F. Is it only the regulatory status? Broadening the debate on cisgenic plants. Environ. Sci. Eur. 2017;29(1):22. DOI 10.1186/s12302-017-0120-2.

41. Vleeshouwers V.G.A.A., Raffaele S., Vossen J.H., Champouret N., Oliva R., Segretin M.E., Rietman H., Cano L.M., Lokossou A.A., Kessel G.J.T., Pel M., Kamoun S. Understanding and exploiting late blight resistance in the age of effectors. Annu. Rev. Phytopatol. 2011;49:507-531. DOI 10.1146/annurev-phyto-072910-095326.

42. Vleeshouwers V.G.A.A., Rietman H., Krenek P., Champouret N., Young C., Oh S.K., Wang M., Bouwmeester K., Vosman B., Visser R.G.F., Jacobsen E., Govers F., Kamoun S., van der Vossen E.A.G. Effector genomics accelerates discovery and functional profiling of potato disease resistance and Phytophthora infestans avirulence genes. PLoS ONE. 2008;3(8):e2875. DOI 10.1371/journal. pone.0002875.

43. Wang M., Sjefke A., van den Berg R.G., Vleeshouwers V.G.A.A., van der Vossen E.A.G., Vosman B. Allele mining in Solanum: conserved homologues of Rpi-blb1 are identified in Solanum stoloniferum. Theor. Appl. Genet. 2008;116(7):933-943. DOI 10.1007/s00122008-0725-3.

44. Wastie R.L. Breeding for resistance. Eds. D.S. Ingram, P.H. Williams. Phytophthora infestans, the Cause of Late Blight of Potato. Vol. 7. Advances in Plant Pathology. London: Academic Press Ltd, 1991.

45. Yashina I.M. The importance of variety in modern technologies of potato production. Actual Problems of the Modern Potato Industry. Cheboksary: PMC CR “Agro-Innovations”, 2010;41-48.

46. Zhu S., Li Y., Vossen J.H., Visser R.G., Jacobsen E. Functional stacking of three resistance genes against Phytophthora infestans in potato. Transgenic Res. 2012;21(1):89-99. DOI 10.1007/s11248-011-9510-1.

47. Zoteyeva N., Antonova O., Klimenko N., Apalikova O., Carlson-Nilsson U., Karabitsina Yu., Ukhatova Yu., Gavrilenko T. Facilitation of introgressive hybridization of wild polyploid mexican potato species using DNA markers of R genes and of different cytoplasmic types. Sel’skokhozyaistvennaya Biologiya = Agricultural Biology. 2017; 52(5):964-975.

48. Zoteyeva N., Chrzanowska M., Flis B., Zimnoch-Guzowska E. Resistance to pathogens of the potato accessions from the collection of N.I. Vavilov Institute of Plant Industry (VIR). Am. J. Potato Res. 2012;89(4):277-293. DOI 10.1007/s12230-012-9252-5.