SSR-BASED ASSESSMENT OF GENETIC DIVERSITY IN TOMATO CULTIVARS AND LINES GROWN IN KAZAKHSTAN
Main Article Content
Authors
Yu. Genievskaya
Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
S. Jantasov
Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
E. Nurbayeva
Kazakh Research Institute of Fruit and Vegetable Growing, Almaty 050060, Kazakhstan
Ye. Turuspekov
al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
Abstract
Tomato (Solanum lycopersicum L.) is a versatile crop known for its nutritional value and health benefits, thriving in diverse climates worldwide. Nevertheless, regional variations persist in tomato yield, with Kazakhstan serving as an example of lower productivity in contrast to global averages. Closing this disparity requires comprehensive genetic studies and breeding efforts. This study is focused on the genetic diversity of 49 tomato cultivars and hybrids sourced from Kazakh Research Institute of Fruit and Vegetable Growing (Almaty), employing 10 SSR markers associated with important agronomic traits. SSR genotyping unveiled polymorphisms across 6 markers with variable allele numbers. Genetic diversity metrics highlighted significant genetic diversity within both outdoor and greenhouse tomato cultivars and lines. Bayesian clustering, Neighbor-joining (NJ) clustering, and principal coordinate analysis (PCoA) delineated genetic differentiation between outdoor and greenhouse tomatoes with small admixture, indicating distinct breeding directions for these two types. Highly polymorphic SSRs (PIC > 0.5) associated with essential fruit traits emerge as promising targets for marker-assisted selection (MAS) that can be used to enhance tomato breeding efficiency in Kazakhstan. According to 8 SSRs, 22 out of 30 outdoor accessions and 8 greenhouse tomato accessions were genetically uniform. This study offers comprehensive insights into the genetic diversity and population structure of tomato cultivars and lines in Kazakhstan, laying the foundation for informed breeding endeavors aimed at bolstering yield and resilience in tomato crops.
Keywords
Solanum lycopersicum L., microsatellites, population structure, outdoor tomato, greenhouse tomato
Article Details
References
Bhuvaneswari V., Nagini S. Lycopene: a review of its potential as an anticancer agent // Current Medicinal Chemistry-Anti-Cancer Agents. – 2005. – Vol. 5. – No. 6. – P. 627-635.
The Food and Agriculture Organization Corporate Statistical Database (FAOSTAT). Available at: URL (Accessed 29.03.2024).
Tomato news. Available at: URL (Accessed 15.02.2024).
Бюро национальной статистики Агентства по стратегическому планированию и реформам Республики Казахстан. Официальный сайт: URL (От 15.02.2024).
Hernández-Leal E., Lobato-Ortiz R., García-Zavala J.J., Hernández-Bautista A., Reyes-López D., Bonilla-Barrientos O. Stability and breeding potential of tomato hybrids // Chilean journal of agricultural research. – 2019. – Vol. 79. – No. 2. – P. 181-189.
Kanaka K.K., Sukhija N., Goli R.C., Singh S., Ganguly I., Dixit S.P., et al. On the concepts and measures of diversity in the genomics era // Current Plant Biology. – 2023. – Vol. 33. – P. 100278.
Agrimonti C., Vietina M., Pafundo S., Marmiroli N. The use of food genomics to ensure the traceability of olive oil // Trends in Food Science & Technology. – 2011. – Vol. 22. – No. 5. – P. 237-244.
Rufo R., Alvaro F., Royo C., Soriano J. M. From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers // PloS one. – 2019. – Vol. 14. – No. 7. – P. e0219867.
Vanlalsanga S., Singh S.P., Singh Y.T. Rice of Northeast India harbor rich genetic diversity as measured by SSR markers and Zn/Fe content // BMC genetics. – 2019. – Vol. 20. – P. 1-13.
Priyanka V., Kumar R., Dhaliwal I., Kaushik P. Germplasm conservation: Instrumental in agricultural biodiversity — A review // Sustainability. – 2021. – Vol. 13. – No. 12. – P. 6743.
Кулакова А.В., Дьяченко Е.А., Щенникова А.В., Пышная О.Н., Джос Е.А. Вариабельность генома отечественных сортов томата: данные AFLP-анализа // Вавиловский журнал генетики и селекции. – 2022. – Т. 26. – №. 7. – С. 652-661.
Gonias E.D., Ganopoulos I., Mellidou I., Bibi A.C., Kalivas A., Mylona P. V., et al. Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers // Genetic Resources and Crop Evolution. – 2019. – Vol. 66. – P. 1295-1309.
Kandel D.R., Bedre R.H., Mandadi K.K., Crosby K., Avila C. Genetic diversity and population structure of tomato (Solanum lycopersicum) germplasm developed by Texas A&M breeding programs // American Journal of Plant Sciences. – 2019. – Vol. 10. – No. 7. – P. 1154-1180.
Tranchida-Lombardo V., Mercati F., Avino M., Punzo P., Fiore M.C., Poma I., et al. Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array // Plant Biosystems-An International Journal Dealing with all Aspects of Plant Biology. – 2019. – Vol. 153. – No. 2. – P. 288-297.
Vargas J.E.E., Aguirre N.C., Coronado Y.M. Study of the genetic diversity of tomato (Solanum spp.) with ISSR markers // Revista Ceres. – 2020. – Vol. 67. – P. 199-206.
Pidigam S., Thuraga V., Munnam S.B., Amarapalli G., Kuraba G., Pandravada, S.R., et al. Genetic diversity, population structure and validation of SSR markers linked to Sw-5 and I-2 genes in tomato germplasm // Physiology and Molecular Biology of Plants. – 2021. – Vol.. 27. – P. 1695-1710.
Gbadamosi A. E., Ajayi A.T., Osekita O.S., Omotuyi, I.O. Genetic diversity in tomato accessions [Solanum lycopersicum (L.) H. Karst] from Nigeria employing morphological and SSR markers // Plant Physiology Reports. – 2020. – Vol. 25. – P. 444-459.
Caramante M., Rouphael Y., Corrado G. The genetic diversity and structure of tomato landraces from the Campania region (Southern Italy) uncovers a distinct population identity // Agronomy. – 2021. – Vol. 11. – No. 3. – P. 564.
Ramesh P., Mallikarjuna G., Sameena S., Kumar A., Gurulakshmi K., Reddy B. V., et al. Advancements in molecular marker technologies and their applications in diversity studies // Journal of biosciences. – 2020. – Vol. 45. – P. 1-15.
Guler B. A., Imamoglu E. Molecular marker technologies in food plant genetic diversity studies: an overview. – 2023.
Vieira M.L.C., Santini L., Diniz A. L., Munhoz C.D.F. Microsatellite markers: what they mean and why they are so useful // Genetics and molecular biology. – 2016. – Vol. 39. – P. 312-328.
Foolad M.R. Genome mapping and molecular breeding of tomato // International Journal of Plant Genomics. – 2007. – Article ID 64358.
Tanksley S.D., Ganal M.W., Prince J.P., De Vicente M.C., Bonierbale M.W., Broun P., et al. High density molecular linkage maps of the tomato and potato genomes // Genetics. – 1992. – Vol. 132. – No. 4. – P. 1141-1160.
Frary A., Xu Y., Liu J., Mitchell S., Tedeschi E., Tanksley S. Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments // Theoretical and Applied Genetics. – 2005. – Vol. 111. – P. 291-312.
Liu Y., Zhou T., Ge H., Pang W., Gao L., Ren L., Chen H. SSR mapping of QTLs conferring cold tolerance in an interspecific cross of tomato // International Journal of Genomics. – 2016. – Article ID 3219276.
Shah L.R., Ahmed N., Hussain K., Mansoor S., Khan T., Khan I., et al. Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics // BMC Genomic Data. – 2024. – Vol. 25. – No. 1. – P. 9.
Kimbara J., Ohyama A., Chikano H., Ito H., Hosoi K., Negoro S., et al. QTL mapping of fruit nutritional and flavor components in tomato (Solanum lycopersicum) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross // Euphytica. – 2018. – Vol. 214. – P. 1-12.
Henareh M., Abdollahi Mandoulakani B., Dursun A., Haliloglu K. Genetic Structure and Mixed Linear Model-Based Association Analysis for Morphological Traits in a Collection of Tomato Landraces from Iran and Turkey // Journal of Agricultural Science and Technology. – 2020. – Vol. 22. – P.1067-1082.
Pozharskiy A., Kostyukova V., Taskuzhina A., Nizamdinova G., Kisselyova N., Kalendar R., et al. Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses // Heliyon. – 2022. – Vol. 8. – No. 8. – P. e10095.
Pozharskiy A., Kostyukova V., Khusnitdinova M., Adilbayeva K., Nizamdinova G., Kapytina A., et al. Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers // PeerJ. – 2023. – Vol. 11. – P. e15683.
Aboul-Maaty N.A.F., Oraby H.A.S. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method // Bulletin of the National Research Centre. – 2019. – Vol. 43. – No. 1. – P. 1-10.
Scintu A., Characterization of a wide collection of tomato (Solanum lycopersicum L.) for morpho-phenological, quality and resistance traits. – 2014. – 127 p.
Mazzucato A., Papa, R., Bitocchi, E., Mosconi, P., Nanni, L., Negri, V., et al. Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces // Theoretical and Applied Genetics. – 2008. – Vol. 116. – P. 657-669.
Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms // American journal of human genetics. – 1980. – Vol. 32. – P. 314.
Peakall R.. Smouse P.E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research // Mol. Ecol. Notes. – 2012. – Vol. 6. – P. 288–295.
Hammer Ø., Harper D.A.T. Past: paleontological statistics software package for educaton and data anlysis // Palaeontologia electronica. – 2001. – Vol. 4. – No. 1. – P. 1.
Porras-Hurtado L., Ruiz Y., Santos C., Phillips C., Carracedo Á., Lareu M. V. An overview of STRUCTURE: applications, parameter settings, and supporting software // Frontiers in genetics. – 2013. – Vol. 4. – P. 98.
Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study // Molecular ecology. – 2005. – Vol. 14. – No. 8. – P. 2611-2620.
Avdikos I.D., Tsivelika N., Gallidou A., Koutsika-Sotiriou M., Traka-Mavrona E. Exploitation of heterosis through recurrent selection scheme applied in segregating generations of a tomato breeding program // Scientia horticulturae. – 2011. – Vol. 130. – No. 4. – P. 701-707.