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Sivas University of Science and Technology, Faculty of Agricultural Sciences and Technology, Department of Field Crops, Sivas
Abstract
This study aimed to evaluate the effectiveness of RAPD (Random Amplified Polymorphic DNA) markers in determining the genetic diversity among 18 sugar beet (Beta vulgaris L. subsp. vulgaris) genotypes. Of the 11 RAPD primers initially tested, 6 primers showing the highest level of polymorphism were selected and analyses were performed across all genotypes. A total of 49 bands were obtained, 40 of which were identified as polymorphic, corresponding to a polymorphism level of 81.6%. As a result of the RAPD analyses applied, it was determined that there were significant levels of genetic differences among the genotypes. To visualize genetic relationships, UPGMA cluster analysis based on the Jaccard similarity coefficient and Principal Component Analysis (PCA) were performed. Diversity parameters such as the effective number of alleles, gene diversity, and Shannon’s diversity index as well as Nei’s genetic distance were calculated using POPGENE version 1.32 software. In terms of PIC, the highest values were found in OPA-18 (0.30) and OPA-2 / OPA-5 (0.29), while the lowest PIC value was observed in OPA-3 (0.20). The pairwise genetic distance matrix was obtained using MVSP 3.22 software, while the Q-matrix bar plot was generated with STRUCTURE software. The results of the analyses showed that genetically similar genotypes clustered together, whereas distinct genotypes were separated. In particular, the differentiation of SB-2 as the most genetically distant individual revealed that this genotype has the potential to increase genetic variation in breeding programs. In contrast, SB-10 and SB-12 genotypes exhibited high genetic similarity. The fact that commercial cultivars were distributed in different clusters demonstrated that these materials have different genetic origins and may share common alleles with gene bank accessions. The findings obtained revealed that RAPD markers are a reliable method for the characterization of sugar beet genetic resources and provide important information for parent selection and sustainable breeding strategies.
ÇİLESİZ, Y. (2025). Utilization of Rapd Markers for Determining Genetic Diversity in Sugar Beet. ISPEC Journal of Agricultural Sciences, 9(3), 936–946. https://doi.org/10.5281/zenodo.16947565
📄Abbasi, Z., Arzani, A., Majidi, M.M., 2014. Evaluation of genetic diversity of sugar beet (Beta vulgaris L.) crossing parents using agro-morphological traits and molecular markers. Journal of Agricultural Science and Technology, 16(6): 1397-1411.
📄Baloch, F.S., Guizado, S.J.V., Altaf, M.T., Yüce, I., Çilesiz, Y., Bedir, M., Gómez, J.C.C., 2022. Applicability of inter-primer binding site iPBS-retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm. Molecular Biology Reports, 49(4): 2553-2564.
📄Broccanello, C., Stevanato, P., Biscarini, F., Cantu, D., Saccomani, M., 2015. A new polymorphism on chromosome 6 associated with bolting tendency in sugar beet. BMC genetics, 16(1): 142.
📄Çelik, C., Seraj, N.A., Yasak, S., Karakurt, Y., Telci, İ., Sevindik, E., 2024. Molecular characterization and genetic relationships in different Mint (Mentha L.) species with ISSR marker technique. Biology Bulletin, 51(4): 959-968.
📄Çetin, B., Sevindik, E., Özkara, Z., Filiz, E., Baş, E., 2025. ISSR marker based genetic variation analysis in the riparian relict tree pterocarya fraxinifolia (Juglandaceae) genotypes in Türkiye. Biology Bulletin, 52(2): 66.
📄Çilesiz, Y., Altaf, M.T., Nadeem, M.A., Ali, A., Sesiz, U., Alsaleh, A., Baloch, F.S., 2025. Identification of phenotypic diversity and dartseq loci associated with vitamin a contents in Turkish common bean germplasm through GWAS. Plants, 14(5): 776.
📄Çilesiz, Y., 2025. Genetic diversity assessment of walnut (Juglans regia L.) genotypes from inner Anatolia region Türkiye using ISSR and RAPD markers. Scientific Reports, 15(1): 30850.
📄Doyle, J.J., Doyle, J.L., 1990. Isolation of plant DNA from fresh tissue. Focus, 12: 13-15.
📄Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8): 2611-2620.
📄Ghasemi, A.R., Golparvar, A.R., Isfahani, M.N., 2014. Analysis of genetic diversity of sugar beet genotypes using random amplified polymorphic DNA marker. Genetika, 46(3): 975-984.
📄Gülay, M., Sevindik, E., Sofyalıoglu, E., Cayır, M.E., Filiz, E., 2023. Molecular characterization of Prunus spinosa L. (Rosaceae) populations from the west black sea region in Turkey using Inter-simple Sequence Repeat Polymerase Chain Reaction. Erwerbs-Obstbau, 65(6): 2337-2343.
📄Holtgräwe, D., Sörensen, T.R., Viehöver, P., Schneider, J., Schulz, B., Borchardt, D., Weisshaar, B., 2014. Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris). PLoS One, 9(10): e110113.
📄Hromadová, Z., Mikolasova, L., Balazova, Z., Vivodík, M., Chnapek, M., Gálová, Z., 2022. Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes using scot polymorphism. Journal of Microbiology, Biotechnology and Food Sciences, 12(1): e5919-e5919.
📄Karaköy, T., Toklu, F., Karagöl, E.T., Uncuer, D., Çilesiz, Y., Ali, A., Özkan, H., 2024. Genome-wide association studies revealed DArTseq loci associated with agronomic traits in Turkish faba bean germplasm. Genetic Resources and Crop Evolution, 71(1): 181-198.
📄Kovach, W.L., 2007. MVSP-A MultiVariate Statistical Package for Windows, ver. 3.1. Kovach Computing Services, Pentraeth Wales, UK
📄Küçük, R., Sevindik, E., Çayır, M.E., Murathan, Z.T., 2024. Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye. Genetic Resources and Crop Evolution, 71(8): 4739-4747.
📄Nagl, N., Taški-Ajduković, K., Popović, A., Ćurčić, Ž., Danojević, D., Kovačev, L., 2011. Estimation of genetic variation among related sugar beet genotypes by using RAPD. Genetika-belgrade, 43(3): 575-582.
📄Nosair, H., 2016. SCoT polymorphism reveals genetic diversity in some important Fabaceae species. Current Science International, 5(4): 592-598.
📄Ouchar, M.A.A., Dağ, B., Aytekin, İ., 2023. HaeIII polymorphism of growth hormone (GH-1) gene in some goat breeds reared in turkey by using PCR-RFLP method. ISPEC Journal of Agricultural Sciences, 7(3): 693-700.
📄Ovalıoglu, G., Çilesiz, Y., 2025. SCoT marker-based evaluation of genetic diversity in selected walnut (Juglans regia L.) accessions. International Journal of Agriculture Environment and Food Sciences, 9(2): 570-576.
📄Panella, L., 2010. Sugar beet as an energy crop. Sugar Tech, 12(3): 288-293.
📄Peng, F., Pi, Z., Li, S., Wu, Z., 2024. Genetic diversity and population structure analysis of excellent sugar beet (Beta vulgaris L.) germplasm resources. Horticulturae, 10(2): 120.
📄Rayan, W.A., Osman, S.A., 2019. Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern. Bulletin of the National Research Centre, 43(1): 161.
📄Richards, C.M., Brownson, M., Mitchell, S.E., Kresovich, S., Panella, L., 2004. Polymorphic microsatellite markers for inferring diversity in wild and domesticated sugar beet (Beta vulgaris). Molecular Ecology Notes, 4(2): 243-245.
📄Roldan-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A., De Loose, M., 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6: 125–134.
📄Sayed Ibrahim, A., Çelik, C., Karakurt, Y., Sevindik, E., 2024. Physiological, biochemical, and molecular characterization of some cucumber (Cucumis sativus L.) genotypes. International Journal of Vegetable Science, 30(6): 673-694.
📄Schneider, K., Kulosa, D., Soerensen, T.R., Möhring, S., Heine, M., Durstewitz, G., Ganal, M., 2007. Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics, 115(5): 601-615.
📄
📄Sevindik, E., Okan, K., Sevindik, M., Ercisli, S., 2023. Genetic diversity and phylogenetic analyses of Juglans regia L. (Juglandaceae) populations using RAPD, ISSR markers and nrDNA ITS regions. Erwerbs-Obstbau, 65(2): 311-320.
📄Sevindik, E., Yangılar, F., Atasagun, B., Sofyalıoğlu, E., Şimşek, S.A., Çayır, M.E., Vivodík, M., 2024. Genetic diversity and structure analysis of ‘Ak Sakı’and ‘Kara Sakı’apple cultivars growing in Erzincan Türkiye. Biologica Nyssana, 15(2).
📄Shimira, F., Boyaci, H.F., Çilesiz, Y., Nadeem, M.A., Baloch, F.S., Taşkin, H., 2021. Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers. Molecular Biology Reports, 48(9): 6323-6333.
📄Smulders, M.J., Esselink, G.D., Everaert, I., De Riek, J., Vosman, B., 2010. Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers. BMC genetics, 11(1): 41.
📄Sönmez, E., Çilesiz, Y., 2025. Genetic variation analysis of selected grape (Vitis vinifera L.) accessions through SCoT markers. Selcuk Journal of Agriculture and Food Sciences, 39(2): 418-426.
📄Stevanato, P., Chiodi, C., Broccanello, C., Concheri, G., Biancardi, E., Pavli, O., Skaracis, G., 2019. Sustainability of the sugar beet crop. Sugar Tech, 21(5): 703-716.
📄Susar, A., Şatana, A., 2024. Investigating the ımpacts of nitrogen doses and rhizobacteria on sugar beet (Beta vulgaris L.) yield and quality parameters for sustainable cultivation. ISPEC Journal of Agricultural Sciences, 8(3): 789-803.
📄Şahin, N.K., 2024. Stimulatory effects of different seed priming treatments on germination and early seedling growth of Sugar beet. ISPEC Journal of Agricultural Sciences, 8(4): 1056-1067.
📄Temrel, T.M., Çilesiz, Y., 2025. Investigation of genetic polymorphism in selected thyme (Thymus vulgaris L.) accessions using SCoT molecular markers. Selcuk Journal of Agriculture and Food Sciences, 39(2): 459-466.
📄Yeh, F.C., Yang, R., Boyle, T.J., Ye, Z., Xiyan, J.M., 2000. ‘PopGene32. Microsoft Windows-based freeware for population genetic analysis, version 1.32.’ (Molecular Biology and Biotechnology Centre, University of Alberta: Edmonton, Alberta, Canada).
