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Samarina L.S., Shkhalakhova R.M., Malyukova L.S., Bobrovskikh A.V., Malyuchenko O.P., Koninskayа N.G., Malyarovskaya V.I., Gvasaliya M.V., Tsaturyan G.A., Shurkina E.S., Ryndin A.V. SNP and InDel markers of chloroplast and nuclear DNA for the analysis of genetic diversity in tea plants Camellia sinensis (L.) Kuntze from commercial plantations and a core collection. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2026, Vol. 61, № 1, p. 89-105.
(how to cite this article)

doi: 10.15389/agrobiology.2026.1.89eng

UDC: 633.72:577.22:577.2

Acknowledgements:
Analysis of the tea plants genetic diversity was supported financially by grant No. 23-46-00002 from the Russian Science Foundation. Validation of the universal primers was performed within the state assignment of the Federal Research Center Subtropical Scientific Center RAS No. FGRW-2024-0005, registration No. 124022000092-4. The tea collection was provided within the state assignment of the Federal Research Center Subtropical Scientific Center RAS No. FGRW-2024-0003, registration No. 124022000093-1.1.

 

SNP AND InDel MARKERS OF CHLOROPLAST AND NUCLEAR DNA FOR THE ANALYSIS OF GENETIC DIVERSITY IN TEA PLANTS Camellia sinensis (L.) Kuntze FROM COMMERCIAL PLANTATIONS AND A CORE COLLECTION

L.S. Samarina1, R.M. Shkhalakhova1✉, L.S. Malyukova1,
A.V. Bobrovskikh2, O.P. Malyuchenko3, N.G. Koninskayа1,
V.I. Malyarovskaya1, M.V. Gvasaliya1, G.A. Tsaturyan1,
E.S. Shurkina1, A.V. Ryndin1

1Federal Research Centre the Subtropical Scientific Centre RAS, 2/28, ul. Yana Fabritsiusa, Sochi, 354002 Russia, e-mail q11111w2006@yandex.ru, shhalahova1995@mail.ru (✉ corresponding author), malukovals@mail.ru, natakoninskaya@mail.ru, malyrovskaya@yandex.ru, m.v.gvasaliya@mail.ru, grisha.tsaturyan@yandex.ru,
shurkinaekaterina@mail.ru, ryndin@subtropras.ru;
2Federal Research Center Institute of Cytology and Genetics SB RAS, 10, prosp. Akademika Lavrentyeva, Novosibirsk, 630090 Russia, e-mail alex-bobrovskih@mail.ru;
3All-Russia Research Institute of Agricultural Biotechnology, 42, ul. Timiryazevskaya, Moscow, 127550 Russia, e-mail seq@syntol.ru

ORCID:
Samarina L.S. orcid.org/0000-0002-0500-1198
Malyarovskaya V.I. orcid.org/0000-0003-4213-8705
Shkhalakhova R.M. orcid.org/0000-0001-5262-7866
Gvasaliya M.V. orcid.org/0000-0001-7394-4377
Malyukova L.S. orcid.org/0000-0003-1531-5745
Tsaturyan G.A. orcid.org/0000-0002-6277-1105
Bobrovskikh A.V. orcid.org/0000-0002-1826-2864
Shurkina E.S. orcid.org/0000-0003-2305-3327
Mayuchenko O.P. orcid.org/0009-0009-8727-9967
Ryndin A.V. orcid.org/0000-0001-9640-4840
Koninskaya N.G. orcid.org/0000-0002-2126-5863

Final revision received April 23, 2025
Accepted August 11, 2025

Characterization of genetic resources of subtropical crops in atypical growing regions can shed light on the molecular mechanisms of plant adaptation to unfavorable conditions and can be used in breeding programs. The Northwestern Caucasus of Russia, as a northernmost region of commercial tea Camellia sinensis (L.) Kuntze cultivation in the world could be a source of the most frost-resistant tea forms. However, an understanding of the genetic diversity of local tea plantations, their molecular genetic characterization, and the origin of local cultivars and forms is still lacking. In this study, we identified effective SNP and InDel markers for the nuclear and chloroplast genomes of the tea plants, characterized by a high level of intraspecific polymorphism. Among eight universal primer pairs for the chloroplast genome of flowering plants, 23S.4.5S/32S.5S, 16S, rpl23/rpl2.l, rpoC1 intron, and trnE-UUC/trnT-GUU the most effective and enabled the detection of genomic polymorphism among domestic tea cultivars and forms. DNA fragments that contain the selected effective nuclear and chloroplast DNA markers were sequenced by Sanger’s method. With these markers, we assessed the genetic diversity of tea plants from four commercial plantations and from the core collection of the Federal Research Centre the Subtropical Scientific Centre RAS (Sochi). Specimens from commercial plantations of the Republic of Abkhazia and from Sri Lanka served as external controls. For nuclear SNP markers, the highest discriminatory power was D = 0.90-0.92, and the average polymorphism level identified based on population samples was P = 83 %. For chloroplast SNP/InDel markers, the highest discriminatory power was D = 0.36-0.68, and the average polymorphism level was P = 62 %. The greatest genetic diversity was found in the tea core collection, the polymorphism level was P = 100 %, h values for chloroplast and nuclear DNA were 0.330 and 0.335, respectively, and in populations of commercial plantations from Kalinovoye Ozero settlement, with P = 100 % and h values of 0.346 and 0.401, respectively. We revealed phylogenetic similarities of collection and commercial genotypes to the control cv. Kolkhida and form A2019 contrasting in their response to cold stress. We also found variation in genetic diversity within tea populations growing in different geographic regions. The data obtained reveal the genetic diversity of C. sinensis in the humid subtropics of Russia, which will allow for the improvement of conservation programs for this promising gene pool. The identified genotype-specific SNP and InDel markers can also be used for molecular certification of tea cultivars and forms.

Keywords: Camellia sinensis, germ plasm collections, genotyping, single nucleotide polymorphism, SNP, InDel.

 

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