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Геном Solanum tuberosum L.: от удвоенного моноплоида к пангеному картофеля

Аннотация

Обзорная статья представляет результаты исследования генома картофеля за последние 15 лет: с момента секвенирования первого генома Solanum tuberosum L. до настоящего времени – создания линейного и графического пангеномов сортов и родственных  видов секции Petota Dumort. рода Solanum L. Геномный анализ селекционных и местных сортов, гибридных линий и диких видов картофеля обнаружил колоссальное аллельное разнообразие генного пула, комплексность и динамичность наследственной основы одной их ключевых для мирового и российского агропроизводства культур. Анализ структурной вариабельности геномов культурного картофеля и его диких родичей выявил их сложную эволюционную историю и влияние доместикации на разнообразие геномов, локусы и аллели, связанные с важными агрономическими признаками, с устойчивостью к абиотическим и биотическим стрессорам, генетическую основу инбридинговой депрессии. Прогресс в развитии геномики картофеля способствует лучшему пониманию природы фенотипического разнообразия этой важной продовольственной культуры, расширяет возможности исследователей, которые занимаются решением проблем эволюции клубнеобразующих видов рода Solanum, частной генетикой и селекцией новых сортов, отвечающих современным требованиям.

Об авторе

Е. В. Рогозина
Федеральный исследовательский центр Всероссийский институт генетических ресурсов растений имени Н.И. Вавилова
Россия

Елена Вячеславовна Рогозина, доктор биологических наук, ведущий научный сотрудник, отдел генетических ресурсов картофеля

190000 Россия, Санкт-Петербург, ул. Б. Морская, 42, 44 rogozinaelena@gmail.com



Список литературы

1. Abbas Q., Wilhelm M., Kuster B., Poppenberger B., Frishman D. Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies. BMC Genomics. 2024;25(1):619. DOI: 10.1186/s12864-024-10521-w

2. Achakkagari S.R., Kyriakidou M., Gardner K.M., De Koeyer D., De Jong H., Strömvik M.V. et al. Genome sequencing of adapted diploid potato clones. Frontiers in Plant Science. 2022;13:954933. DOI: 10.3389/fpls.2022.954933

3. Agha H.I., Shannon L.M., Morrell P.L. Unloading potatoes: Potato breeding moves forward with only half the genome. Cell Genomics. 2023;3(6):100343. DOI: 10.1016/j.xgen.2023.100343

4. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796-815. DOI: 10.1038/35048692

5. Aversano R., Contaldi F., Ercolano M.R., Grosso V., Iorizzo M., Tatino F. et al. The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. The Plant Cell. 2015;27(4):954-968. DOI: 10.1105/tpc.114.135954

6. Bao Z., Li C., Li G., Wang P., Peng Z., Cheng L. et al. Genome architecture and tetrasomic inheritance of autotetraploid potato. Molecular Plant. 2022;15(7):1211-1226. DOI: 10.1016/j.molp.2022.06.009

7. Bayer P.E., Golicz A.A., Scheben A., Batley J., Edwards D. Plant pan-genomes are the new reference. Nature. Plants. 2020;6(8):914-920. DOI: 10.1038/s41477-020-0733-0

8. Bernal-Gallardo J.J., de Folter S. Plant genome information facilitates plant functional genomics. Planta. 2024;259(5):117. DOI: 10.1007/s00425-024-04397-z

9. Bonthala V.S., Stich B. Genetic divergence of lineage-specific tandemly duplicated gene clusters in four diploid potato genotypes. Frontiers in Plant Science. 2022;13:875202. DOI: 10.3389/fpls.2022.875202

10. Bozan I., Achakkagari S.R., Anglin N.L., Ellis D., Tai H.H., Strömvik M.V. Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(31):e2211117120. DOI: 10.1073/pnas.2211117120

11. Bradshaw J.E. Potato breeding: theory and practice. Cham: Springer International Publishing; 2021. DOI: 10.1007/978-3-030-64414-7

12. Cheng L., Wang N., Bao Z., Zhou Q., Guarracino A., Yang Y. et al. Leveraging a phased pangenome for haplotype design of hybrid potato. Nature. 2025;640(8058):408-417. DOI: 10.1038/s41586-024-08476-9

13. DRYAD. Potato super pangenome v1.0: [website]. Available from: https://datadryad.org/dataset/doi:10.5061/dryad.cfxpnvxbn [accessed Jan. 25, 2026].

14. Freire R., Weisweiler M., Guerreiro R., Baig N., Hüttel B., Obeng-Hinneh E. et al. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. G3 (Bethesda). 2021;11(12):jkab330. DOI: 10.1093/g3journal/jkab330

15. Fulton T.M., Van der Hoeven R., Eannetta N.T., Tanksley S.D. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. The Plant Cell. 2002;14(7):1457-1467. DOI: 10.1105/tpc.010479

16. Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Frontiers in Genetics. 2023;14:1197206. DOI: 10.3389/fgene.2023.1197206

17. Gebhardt C. The historical role of species from the Solanaceae plant family in genetic research. Theoretical and Applied Genetics. 2016;129(12):2281-2294. DOI: 10.1007/s00122-016-2804-1

18. Godec T., Beier S., Rodriguez-Granados N.Y., Sasidharan R., Abdelhakim L., Teige M. et al. Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée. Scientific Data. 2025;12(1):1044. DOI: 10.1038/s41597-025-05372-3

19. Gong L., Zhang L., Zhang H., Nie F., Liu Z., Liu X. et al. Haplotype-resolved genome assembly and genome-wide association study identifies the candidate gene closely related to sugar content and tuber yield in Solanum tuberosum. Horticulture Research. 2025;12(6):uhaf075. DOI: 10.1093/hr/uhaf075

20. Hardigan M.A., Bamberg J., Buell C.R., Douches D.S. Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. The Plant Genome. 2015;8(1):eplantgenome2014.06.0025. DOI: 10.3835/plantgenome2014.06.0025

21. Hardigan M.A., Crisovan E., Hamilton J.P., Kim J., Laimbeer P., Leisner C.P. et al. Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. The Plant Cell. 2016;28(2):388-405. DOI: 10.1105/tpc.15.00538

22. Hardigan M.A., Laimbeer F.P.E., Newton L., Crisovan E., Hamilton J.P., Vaillancourt B. et al. Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. Proceedings of the National Academy of Sciences of the United States of America. 2017;114(46):E9999-E10008. DOI: 10.1073/pnas.1714380114

23. Henry R.J. Progress in plant genome sequencing. Applied Biosciences. 2022;1(2):113-128. DOI: 10.3390/applbiosci1020008

24. Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E. et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Molecular Plant. 2022;15(3):520-536. DOI: 10.1016/j.molp.2022.01.003

25. Hou M., Pang S. Plant pan-genomics: opportunities, advances, and challenges. Journal of Data Science and Intelligent Systems. 2024;00(00):1-10. DOI: 10.47852/bonviewJDSIS42023107

26. Huang B., Spooner D.M., Liang Q. Genome diversity of the potato. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(28):E6392-E6393. DOI: 10.1073/pnas.1805917115

27. Jiang X., Li D., Du H., Wang P., Guo L., Zhu G. et al. Genomic features of meiotic crossovers in diploid potato. Horticulture Research. 2023;10(6):uhad079. DOI: 10.1093/hr/uhad079

28. Karetnikov D.I., Vasiliev G.V., Toshchakov S.V., Shmakov N.A., Genaev M.A., Nesterov M.A. et al. Analysis of genome structure and its variations in potato cultivars grown in Russia. International Journal of Molecular Sciences. 2023;24(6):5713. DOI: 10.3390/ijms24065713

29. Knapp S., Bohs L., Nee M., Spooner D.M. Solanaceae – a model for linking genomics with biodiversity. Comparative and Functional Genomics. 2004;5(3):285-291. DOI: 10.1002/cfg.393

30. Kyriakidou M., Achakkagari S.R., Gálvez López J.H., Zhu X., Tang C.Y., Tai H.H. et al. Structural genome analysis in cultivated potato taxa. Theoretical and Applied Genetics. 2020a;133(3):951-966. DOI: 10.1007/s00122-019-03519-6

31. Kyriakidou M., Anglin N., Ellis D., Tai H.H., Strömvik M.V. Genome assembly of six polyploid potato genomes. Scientific Data. 2020b;7(1):88. DOI: 10.1038/s41597-020-0428-4

32. Leisner C.P., Hamilton J.P., Crisovan E., Manrique-Carpintero N.C., Marand A.P., Newton L. et al. Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. The Plant Journal. 2018;94(3):562-570. DOI: 10.1111/tpj.13857

33. Matthews C.A., Watson-Haigh N.S., Burton R.A., Sheppard A.E. A gentle introduction to pangenomics. Briefings in Bioinformatics. 2024;25(6):bbae588. DOI: 10.1093/bib/bbae588

34. Michael T.P., VanBuren R. Building near-complete plant genomes. Current Opinion in Plant Biology. 2020;54:26-33. DOI: 10.1016/j.pbi.2019.12.009

35. Morgante M., De Paoli E., Radovic S. Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology. 2007;10(2):149-155. DOI: 10.1016/j.pbi.2007.02.001

36. Nature: [website]. Available from: https://www.nature.com/nature/articles [accessed Jan. 09, 2026].

37. NGDC. National Genomics Data Center: [website]. Available from: https://ngdc.cncb.ac.cn/gwh/submit/27179/step?status=1 [accessed Jan. 09, 2026].

38. NIH. National Library of Medicine. National Center for Biotechnology Information. NCBI Datasets: [website]. Available from: https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=4113 [accessed Jan. 09, 2026].

39. NIH. National Library of Medicine. National Center for Biotechnology Information. GenBank: [website]. Available from: https://www.ncbi.nlm.nih.gov/genbank [accessed Jan. 09, 2026].

40. Paz M.M., Veilleux R.E. Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breeding. 1999;118(1):53-57. DOI: 10.1046/j.1439-0523.1999.118001053.x

41. Pham G.M., Hamilton J.P., Wood J.C., Burke J.T., Zhao H., Vaillancourt B. et al. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience. 2020;9(9):giaa100. DOI: 10.1093/gigascience/giaa100

42. Pham G.M., Newton L., Wiegert-Rininger K., Vaillancourt B., Douches D.S., Buell C.R. Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato. The Plant Journal. 2017;92(4):624-637. DOI: 10.1111/tpj.13706

43. Phytozome 14. The Plant Genomics Resource: [website]. Available from: https://phytozome-next.jgi.doe.gov [accessed Jan. 09, 2026].

44. PLAZA. A resource for plant comparative genomics: [website]. Available from: https://bioinformatics.psb.ugent.be/plaza [accessed Jan. 09, 2026].

45. Potato Genome Sequencing Consortium; Xu X., Pan S., Cheng S., Zhang B., Mu D. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475(7355):189-195. DOI: 10.1038/nature10158

46. Rabanus-Wallace M.T., Stein N. Why 2022 is a revolutionary year for potato genomics. Molecular Plant. 2022;15(8):1257-1259. DOI: 10.1016/j.molp.2022.06.015

47. Reyes-Herrera P.H., Delgadillo-Duran D.A., Flores-Gonzalez M., Mueller L.A., Cristancho M.A., Barrero L.S. Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region. G3 (Bethesda). 2024;14(9):jkae139. DOI: 10.1093/g3journal/jkae139

48. Рогозина Е.В., Хавкин Э.Е. Межвидовые гибриды картофеля как доноры долговременной устойчивости к патогенам. Вавиловский журнал генетики и селекции. 2017;21(1):30-41. DOI: 10.18699/VJ17.221

49. Serra Mari R., Schrinner S., Finkers R., Ziegler F.M.R., Arens P., Schmidt M.H. et al. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biology. 2024;25(1):26. DOI: 10.1186/s13059-023-03160-z

50. Sharma S.K., Bolser D., de Boer J., Sønderkær M., Amoros W., Carboni M.F. et al. Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3 (Bethesda). 2013;3(11):2031-2047. DOI: 10.1534/g3.113.007153

51. Sigaux F. Cancer genome or the development of molecular portraits of tumors. Bulletin de l’Academie Nationale de Medecine. 2000;184(7):1441-1447 (discussion 1448-1449). [in French]

52. Spooner D.M., Ghislain M., Simon R., Jansky S.H., Gavrilenko T. Systematics, diversity, genetics, and evolution of wild and cultivated potatoes. The Botanical Review. 2014;80(4):283-383. DOI: 10.1007/s12229-014-9146-y

53. SpudDB. Potato Genomics Resource: [website]. Available from: https://spuddb.uga.edu/index.shtml [accessed Jan. 21, 2026].

54. Sun H., Jiao W.B., Krause K., Campoy J.A., Goel M., Folz-Donahue K. et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nature Genetics. 2022;54(3):342-348. DOI: 10.1038/s41588-022-01015-0

55. Sun Н., Tusso S., Dent C.I., Goel M., Wijfjes R., Baus L.C. et al. The phased pan-genome of tetraploid European potato. Nature. 2025;642:389-397. DOI: 10.1038/s41586-025-08843-0

56. Tang D., Jia Y., Zhang J., Li H., Cheng L, Wang P. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature. 2022;606(7914):535-541. DOI: 10.1038/s41586-022-04822-x

57. Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(39):13950-13955. DOI: 10.1073/pnas.0506758102

58. The European Cultivated Potato Database: [website]. Available from: https://www.europotato.org/varieties/view/Otava-E [accessed Jan. 09, 2026].

59. Uitdewilligen J.G.A.M.L., Wolters A.M.A., D’hoop B.B., Borm T.J., Visser R.G., van Eck H.J. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One. 2013;8(5):e62355. DOI: 10.1371/journal.pone.0062355

60. Van Lieshout N., van der Burgt A., de Vries M.E., Ter Maat M., Eickholt D., Esselink D. et al. Solyntus, the new highly contiguous reference genome for potato (Solanum tuberosum). G3 (Bethesda). 2020;10(10):3489-3495. DOI: 10.1534/g3.120.401550

61. Van Os H., Andrzejewski S., Bakker E., Barrena I., Bryan G., Caromel B. et al. Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map. Genetics. 2006;173(2):1075-1087. DOI: 10.1534/genetics.106.055871

62. Visser R.G.F., Bachem C.W.B., Borm T., de Boer J., van Eck H.J., Finkers R. et al. Possibilities and challenges of the potato genome sequence. Potato Research. 2014;57(3-4);327-330. DOI: 10.1007/s11540-015-9282-8

63. Wageningen University & Research. Potato Pedigree Database: [website]. Available from: https://www.plantbreeding.wur.nl/PotatoPedigree [accessed Jan. 09, 2026].

64. Wang F., Xia Z., Zou M., Zhao L., Jiang S., Zhou Y. et al. The autotetraploid potato genome provides insights into highly heterozygous species. Plant Biotechnology Journal. 2022;20(10):1996-2005. DOI: 10.1111/pbi.13883

65. Yang X., Zhang L., Guo X., Xu J., Zhang K., Yang Y. et al. The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions. Molecular Plant. 2023;16(2):314-317. DOI: 10.1016/j.molp.2022.12.010

66. Zhang C., Yang Z., Tang D., Zhu Y., Wang P., Li D. et al. Genome design of hybrid potato. Cell. 2021;184(15):3873-3883. DOI: 10.1016/j.cell.2021.06.006

67. Zhou Q., Tang D., Huang W., Yang Z., Zhang Y., Hamilton J.P. et al. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nature Genetics. 2020;52(10):1018-1023. DOI: 10.1038/s41588-020-0699-x

68. Zhu X., Yang R., Liang Q., Yu Y., Wang T., Meng L. et al. Graph-based pangenome provides insights into the structural variation and genetic basis of metabolic traits in potato. Molecular Plant. 2025;18(4):590-602. DOI: 10.1016/j.molp.2025.01.017


Рецензия

Для цитирования:


Рогозина Е.В. Геном Solanum tuberosum L.: от удвоенного моноплоида к пангеному картофеля. Бюллетень ВИР. 2025;(246):19-37.

For citation:


Rogozina E.V. The genome of Solanum tuberosum L.: from a doubled monoploid to the potato pangenome. VIR Bulletin. 2025;(246):19-37. (In Russ.)

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