Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

Male sterility in potato is little studied since traditional breeding is based  on the vegetative reproduction of highly heterozygous tetraploid varieties. The rapid development of hybrid diploid breeding contributes to growing interest in studying the male sterility of this important crop. In this work, a set of 6 cytoplasmic markers was employed to describe cytoplasmic genetic diversity of 185 potato cultivars bred in Russia and FSU countries. Three cytoplasm types were identified, T (40.0 %), D (50.8 %) and W/γ (8.7 %), which according to literature  are associated with male sterility. With a single exception (0.5 %), cytoplasm types characteristic of male fertile forms (A, P) were not found in the subset  of 185 cultivars. A comparison of these results with previously published data suggested expanding the subset  to up to 277 cultivars, all developed in Russia or FSU countries;  however,  the resulting  differentiation into three cytoplasm  types (T, D and W/γ) was nearly the same. Fertility phenotyping helped identify both  male-sterile and male-fertile genotypes within the three groups  of varieties with T-, D- and W/γ-type cytoplasm. Fifteen genotypes differing in cytoplasm  type and male sterility/fertility traits were selected for direct sequencing of 8 mtDNA loci. Fragments of the  nad2, nad7, cox2, atp6 and  CcmFc genes  were identical  in all 15 selected genotypes. The polymorphism, detected in the rps3, atp9 and CcmFc loci, was not associated with male sterility. Two SNPs in the nad1/atp6 and nad2 loci differentiated 7 genotypes with W/γ-type cytoplasm into five genotypes with tetrad sterility, and two with fertile pollen. The results of an NGS analysis confirmed  the association of these  SNPs with tetrad sterility in a larger set of 28 genotypes of different origin, all with W/γ-type cytoplasm.  A heteroplasmy state  was observed both in male-sterile and in male-fertile genotypes.

1. Anisimova I.N., Alpatieva N.V., Karabitsina Y.I., Gavrilenko T.A. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J. Genet. 2019;98:87. DOI 10.1007/s12041-019-1130-1.

2. Anisimova I.N., Gavrilenko T.A. Cytoplasmic male sterility and prospects for its utilization in potato breeding, genetic studies and hybrid seed production. Russ. J. Genet.: Appl. Res. 2017;7(7):721-735. DOI 10.1134/S2079059717070024.

3. Antonova O.Y., Klimenko N.S., Evdokimova Z.Z., Kostina L.I., Gavrilenko T.A. Finding RB/Rpi-blb1/Rpi-sto1-like sequences in conventionally bred potato varieties. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2018;22(6):693-702. DOI 10.18699/VJ18.412.

4. 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):489-500. DOI 10.1134/S2079059717050021.

5. Ballvora A., Ercolano M.R., Weiss J., Meksem K., Bormann C.A., Oberhagemann P., Salamini F., Gebhardt C. The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes. Plant J. 2002;30(3):361-371. DOI 10.1046/j.1365-313X.2001.01292.x.

6. Beketova M.P., Khavkin E.E. The R1 gene of late blight resistance in susceptible and resistant potato cultivars. Sel’skokhozyaistvennaya Biologiya = Agricultural Biology. 2006;3:109-114. (in Russian)

7. Bentolila S., Stefanov S. A reevaluation of rice mitochondrial evolution based on the complete sequence of male-fertile and male-sterile mitochondrial genomes. Plant Physiol. 2012;158(2):996-1017. DOI 10.1104/pp.111.190231.

8. 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 breeding and genetic collections of the Lorch Potato Research Institute using molecular markers. Zashchita Kartofelya = Potato Protection. 2015;1:3-7. (in Russian)

9. Bragin A.G., Ivanov M.K., Fedoseeva L.A., Dymshits G.M. Analysis of mitochondrial DNA heteroplasmy of fertile and male-sterile sugar beet plants (Beta vulgaris). Russ. J. Genet.: Appl. Res. 2012;2(1):53-57. DOI 10.1134/S2079059712010030.

10. Bryan G.J., McNicoll J., Ramsay G., Meyer R.C., De Jong W.S. Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theor. Appl. Genet. 1999;99(5):859-867. DOI 10.1007/s001220051306.

11. Chen J., Guan R., Chang S., Du T., Zhang H., Xing H. Substoichiometrically different mitotypes coexist in mitochondrial genomes of Brassica napus L. PLoS One. 2011;6(3):e17662. DOI 10.1371/journal.pone.0017662.

12. Das S., Sen S., Chakraborty A., Chakraborti P., Maiti M.K., Basu A., Basu D., Sen S.K. An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of Oryza sativa L. subsp. indica. BMC Plant Biol. 2010;10(1):39. DOI 10.1186/1471-2229-10-39.

13. De Vries M., ter Maat M., Lindhout P. The potential of hybrid potato for East-Africa. Open Agriculture. 2016;1(1):151-156. DOI 10.1515/opag-2016-0020.

14. Dionne L.A. Cytoplasmic sterility in derivatives of Solanum demissum. Am. Potato J. 1961;38(4):117-120. DOI 10.1007/BF02870217.

15. Ducos E., Touzet P., Boutry M. The male sterile G cytoplasm of wild beet displays modifed mitochondrial respiratory complexes. Plant J. 2001;26(2):171-180. DOI 10.1046/j.1365-313x.2001.01017.x.

16. Feng X., Kaur A.P., Mackenzie S.A., Dweikat I.M. Substoichiometric shifting in the fertility reversion of cytoplasmic male sterile pearl millet. Theor. Appl. Genet. 2009;118(7):1361-1370. DOI 10.1007/s00122-009-0986-5.

17. 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.

18. Gavrilenko T.A., Afanasenko O.S., Antonova O.Ju., Rogozina E.V., Hjutti A.V., Shuvalov O.Ju., Islamshina A.R., Chalaya N.A. Development of a protocol for assessing the genetic diversity of cultivated and wild potato species for resistance to viral diseases and cancer based on modern molecular and phytopathological methods. In: Proceedings of the conference “Targeted Basic Studies and their Implementation in the Agricultural Sector of Russia”. 2009;94-100. (in Russian)

19. Gavrilenko T.A., Antonova O.Yu., Kostina L.I. Study of genetic diversity in potato cultivars using PCR analysis of organelle DNA. Russ. J. Genet. 2007;43(11):1301-1305. DOI 10.1134/S1022795407110130.

20. 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.

21. 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)

22. Gavrilenko T.A., Yermishin A.P. Interspecific hybridization of potato: theoretical and applied aspects. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2017;21(1): 16-29. DOI 10.18699/VJ17.220. (in Russian)

23. 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(1):93-102. DOI 10.1023/B:MOLB.0000012878.89855.df.

24. Grun P., Aubertin M., Radlow A. Multiple differentiation of plasmons of diploid species of Solanum. Genetics. 1962;47(10):1321-1333.

25. Grun P., Ochoa C., Capage D. Evolution of cytoplasmic factors in tetraploid cultivated potatoes (Solanaceae). Am. J. Bot. 1977;64(4):412-420. DOI 10.2307/2441770.

26. Hosaka K. Who is the mother of the potato? – restriction endonuclease analysis of chloroplast DNA of cultivated potatoes. Theor. Appl. Genet. 1986;72(5):606-618. DOI 10.1007/BF00288998.

27. Hosaka K. T-type chloroplast DNA in Solanum tuberosum L. ssp. tuberosum was conferred from some populations of S. tarijense Hawkes. Am. J. Potato Res. 2003;80(1):21-32. DOI 10.1007/BF02854553.

28. Hosaka K., Sanetomo R. Development of a rapid identification method for potato cytoplasm and its use for evaluating Japanese collections. Theor. Appl. Genet. 2012;125(6):1237-1251. DOI 10.1007/s00122-012-1909-4.

29. Hosaka K., Sanetomo R. Application of a PCR-based cytoplasm genotyping method for phylogenetic analysis in potato. Am. J. Potato Res. 2014;91(3):246-253. Publ. online 2013; DOI 10.1007/s12230-013-9344-x.

30. Huang S., van der Vossen E.A.G., Kuang H., Vleeshouwers V.G., Zhang N., Borm T.J.A., van Eck H.J., Baker B., Jacobsen E., Visser R.G.F. Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. Plant J. 2005;42(2):251-261. DOI 10.1111/j.1365-313X.2005.02365.x.

31. Irikura Y. Studies on interspecific crosses of tuber-bearing Solanums. I. Overcoming cross-incompatibility between Solanum tuberosum and other Solanum species by mean of induced polyploids and haploids. Hokkaido Agr. Exp. Sta. Shuho. 1968;92:21-37.

32. Iwanaga M., Ortiz R., Cipar M.S., Peloquin S.J. A restorer gene for genetic-cytoplasmic male sterility in cultivated potatoes. Am. Potato J. 1991;68(1):19-28. DOI 10.1007/BF02893338.

33. Jansky S.H., Charkowski A.O., Douches D.S., Gusmini G., Richael C., Bethke P.C., Spooner D.M., Novy R.G., De Jong H., De Jong W.S., Bamberg J.B., Thompson A.L., Bizimungu B., Holm D.G., Brown C.R., Haynes K.G., Sathuvalli V.R., Veilleux R.E., Miller J.C., Jr., Bradeen J.M., Jiang J. Reinventing potato as a diploid inbred line. Crop Sci. 2016;56(4):1412-1422. DOI 10.2135/cropsci2015.12.0740.

34. Khalafyan A.A. Statistica 6. Statistical Data Analysis. Moscow: Binom Publ., 2010. (in Russian)

35. Kim D.H., Kim B.-D. The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.). Curr. Genet. 2006;49(1):59-67. DOI 10.1007/s00294-005-0032-3.

36. Klimenko N.S., Antonova O.Y., Kostina L.I., Mamadbokirova F.T., Gavrilenko T.A. Marker-associated selection of Russian potato varieties with using markers of resistance genes to the golden potato cyst 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)

37. Klimenko N.S., Gavrilenko Т.А., Kostina L.I., Mamadbokirova F.T., Antonova O.Yu. Search for resistance sources to Globodera pallida and Potato Virus X in the collection of potato varieties using molecular markers. Biotekhnologiya i Selektsiya Rasteniy = Plant Biotechnology and Breeding. 2019;2(1):42-48. DOI 10.30901/2658-6266-2019-1-42-48. (in Russian)

38. Lindhout P., De Vries M., ter Maat M., Ying S., Viquez-Zamora M., van Heusden S. Hybrid potato breeding for improved varieties. In: Achieving Sustainable Cultivation of Potatoes. Vol. 1. 2018;99-122. DOI 10.19103/AS.2016.0016.04.

39. Lindhout P., Meijer D., Schotte T., Hutten R.C.B., Visser R.G.F., Eck H.J. Towards F1 hybrid seed potato breeding. Potato Res. 2011;54(4):301-312. DOI 10.1007/s11540-011-9196-z.

40. Liu H., Cui P., Zhan K., Lin Q., Zhuo G., Guo X., Ding F., Yang W., Liu D., Hu S., Yu J., Zhang A. Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line. BMC Genomics. 2011;12(1):163. DOI 10.1186/1471-2164-12-163.

41. Lössl A., Adler N., Horn R., Frei U., Wenzel G. Chondriometype characterization of potato: mt α, β, γδε and novel plastidmitochondrial configurations in somatic hybrids. Theor. Appl. Genet. 1999;91(1-2):1-10. DOI 10.1007/s001220051202.

42. Lössl A., Götz M., Braun A., Wenzel G. Molecular markers for cytoplasm in potato: male sterility and contribution of different plastid-mitochondrial configurations to starch production. Euphytica. 2000;116(3):221-230. DOI 10.1023/A:1004039320227.

43. Mihovilovich E., Sanetomo R., Hosaka K., Ordoñez B., Aponte M., Bonierbale M. Cytoplasmic diversity in potato breeding: case study from the International Potato Center. Mol. Breed. 2015;35(6):137-146. DOI 10.1007/s11032-015-0326-1.

44. Mori K., Sakamoto Y., Mukojima N., Tamiya S., Naka 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(3):347-355. DOI 10.1007/s10681-011-0381-6.

45. Ochoa C.M. The Potatoes of South America: Peru. Part I: The Wild Species. Lima, 2004.

46. Ortiz R., Iwanaga M., Peloquin S.J. Male sterility and 2n pollen in 4x progenies derived from 4x × 2x and 4x × 4x crosses in potatoes. Potato Res. 1993;36(3):227-236. DOI 10.1007/BF02360531.

47. Ortiz R., Simon P., Jansky S., Stelly D. Ploidy manipulation of the gametophyte, endosperm and sporophyte in nature and for crop improvement: a tribute to Professor Stanley J. Peloquin (1921–2008). Ann. Bot. 2009;104(5):795-807. DOI 10.1093/aob/mcp207.

48. Phumichai C., Mori M., Kobayashi A., Kamijima O., Hosaka K. Toward the development of highly homozygous diploid potato lines using the self-compatibility controlling Sli gene. Genome. 2005;48(6):977-984. DOI 10.1139/g05-066.

49. Plaisted R.L. Utilization of germplasm in breeding programs – use of cultivated tetraploids. In: French E.R. (Ed.). Prospect for the Potato in the Developing World. Lima, 1972;90-99.

50. Provan J., Powell W., Dewar H., Bryan G., Machray G.C., Waugh R. An extreme cytoplasmic bottleneck in the modern European cultivated potato (Solanum tuberosum) is not reflected in decreased levels of nuclear diversity. Proc. R. Soc. Lond. 1999;266(1419):633-639. DOI 10.1098/rspb.1999.0683.

51. Ross H. Potato Breeding – Problems and Perspectives. Berlin, 1986.

52. Sanetomo R., Gebhardt C. Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits. BMC Plant Biol. 2015;15(1):162. DOI 10.1186/s12870-015-0545-y.

53. Sanetomo R., Hosaka K. A maternally inherited DNA marker, descended from Solanum demissum (2n = 6x = 72) to S. tuberosum (2n = 4x = 48). Breed. Sci. 2011;61(4):426-434. DOI 10.1270/jsbbs.61.426.

54. Sanetomo R., Hosaka K. A recombination-derived mitochondrial genome retained stoichiometrically only among Solanum verrucosum Schltdl. and Mexican polyploid wild potato species. Genet. Resour. Crop Evol. 2013;60(8):2391-2404. DOI 10.1007/s10722-013-0007-z.

55. Sanetomo R., Ono S., Hosaka K. Characterization of crossability in the crosses between Solanum demissum and S. tuberosum, and the F1 and BC1 progenies. Am. J. Potato Res. 2011;88:500-510. DOI 10.1007/s12230-011-9217-0.

56. Shishova M., Puzanskiy R., Gavrilova O., Kurbanniazov S., Demchenko K., Yemelyanov V., Pendinen G., Shavarda A., Gavrilenko T. Metabolic alterations in male-sterile potato as compared to male-fertile. Metabolites. 2019;9:24. DOI 10.3390/metabo9020024.

57. 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.

58. Spooner D.M., Núñez J., Trujillo G., Del Rosario Herrera M., Guzmán F., 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. USA. 2007;104(49):19398-19403. DOI 10.1073/pnas.0709796104.

59. State Register of Breeding Achievements Authorized for Use for Production Purposes, 2010–2018. Available at: http://reestr.gossort.com/ (in Russian)

60. Zhang C., Wang P., Tang D., Yang Z., Lu F., Qi J., Tawari N.R., Shang Y., Li C., Huang S. The genetic basis of inbreeding depression in potato. Nat. Genet. 2019;51(3):374-378. DOI 10.1038/s41588-018-0319-1.

61. Zoteyeva N.M., Antonova O.Yu., Klimenko N.S., Apalikova O.V., Carlson-Nilsson U., Karabitsina Yu.I., Ukhatova Yu.V., Gavrilenko T.A. 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. DOI 10.15389/agrobiology.2017.5.964rus. (in Russian)