Genetic diversity analysis of sesame (Sesamum indicum L.) genotypes in Türkiye using SSR markers

Abstract

This study aimed to analyze the genetic diversity of 25 different sesame (Sesamum indicum L.) genotypes cultivated in Türkiye, including 16 registered cultivars, 6 local populations, 1 Indian population adapted to the ecological conditions of Konya, and 2 genotypes of Indian origin, using SSR markers. Genetic diversity was assessed using 10 different SSR primers, resulting in a total of 79 polymorphic bands. The CUESTSSR02 primer was the most efficient one with high values for Polymorphic Allele Number (PA), Polymorphic Information Content (PIC), Expected Heterozygosity (He), and Marker Index (MI). Genetic relationships between genotypes were analyzed and visualized using a circular phylogenetic tree, PCoA, and a heatmap. The findings revealed that the local populations are genetically distinct from both registered cultivars and Indian genotypes. Notably, the Akören genotype was identified as genetically isolated from all other genotypes. This study highlights the crucial role of local populations in preserving and enhancing genetic diversity. The integration of Indian genotypes with local populations may contribute to the development of more resilient and productive cultivars. The findings emphasize that the effective use of genetic resources can support sustainable agriculture and improve agricultural performance.

Keywords

• Sesame (Sesamum inducum L.)
• SSR markers
• Genetic diversity
• Local populations

Türkiye’deki susam (Sesamum indicum L.) genotiplerinin genetik çeşitliliğinin SSR markörleri ile analizi

Öz

Bu çalışma, Türkiye’de yetiştirilen 16 tescilli çeşit, 6 yerel popülasyon, Konya ekolojik koşullarına uyum sağlamış 1 Hint popülasyonu ve Hindistan kökenli 2 genotip olmak üzere toplam 25 farklı susam genotipinin genetik çeşitliliğini SSR (Simple Sequence Repeat) markörleri kullanarak analiz etmeyi amaçlamıştır. Araştırmada, 10 farklı SSR primeri ile yapılan genetik çeşitlilik değerlendirmesi sonucunda toplam 79 polimorfik bant tespit edilmiştir. CUESTSSR02 primeri, yüksek Polimorfik Allel Sayısı (PA), Polimorfik Bilgi İçeriği (PIC), Beklenen Heterozigotluk (He) ve Markör İndeksi (MI) değerleri ile en verimli primer olarak öne çıkmıştır.Genotipler arasındaki genetik ilişkiler, dairesel filogenetik ağaç, Temel Koordinatlar Analizi (TKoA) ve ısı haritası gibi yöntemlerle görselleştirilerek analiz edilmiştir. Elde edilen bulgular, yerel popülasyonların tescilli çeşitlerden ve Hindistan genotiplerinden genetik olarak farklılaştığını ortaya koymuştur. Özellikle Akören genotipi, tüm diğer genotiplerden genetik olarak izole bir yapıya sahip bulunmuştur. Çalışma, yerel popülasyonların genetik çeşitliliğin korunması ve artırılmasında önemli bir rol oynadığını göstermektedir. Hindistan genotiplerinin yerel popülasyonlarla birleştirilmesi, daha dayanıklı ve verimli varyetelerin geliştirilmesine katkı sağlayabilir. Sonuçlar, genetik kaynakların etkin kullanımının sürdürülebilir tarımı destekleyerek tarımsal performansı artırabileceğini ortaya koymaktadır.

Anahtar Kelimeler

• Susam (Sesamum indicum L.)
• SSR markörleri
• Genetik çeşitlilik
• Yerel popülasyon

Kaynakça

1. Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D., & Sorrells, M.E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36 (1), 181-186. https://doi.org/10.1139/g93-024
2. Andrade, P.B.d., Freitas, B.M., Rocha, E.E.d.M., Lima, J.A.d., & Rufino, L.L. (2014). Floral biology and pollination requirements of sesame (Sesamum indicum L.). Acta Scientiarum. Animal Sciences, 36 (1), 93-99. https://doi.org/10.4025/actascianimsci.v36i1.21838
3. Anggraeni, T., Fadilah, S., Kusnadi, J., & Basuki, S. (2022). The use of ISSR markers for clustering sesame genotypes based on geographical origin. IOP Conference Series: Earth and Environmental Science, 974, 012031.
4. Asekova, S., Kulkarni, K.P., Oh KiWon, O.K., Lee MyungHee, L.M., Oh EunYoung, O.E., Kim JungIn, K.J., Yeo UnSang, Y.U., Pae SukBok, P.S., Ha TaeJoung, H.T., & Kim SungUp, K.S. (2018). Analysis of molecular variance and population structure of sesame (Sesamum indicum L.) genotypes using simple sequence repeat markers. Plant Breeding and Biotechnology, 6, 321-336. https://doi.org/10.9787/PBB.2018.6.4.321
5. Ashfaq, M., Rani, K.J., Padmaja, D., Yadav, P., & Betha, U.K. (2024). Analysis of genetic diversity in sesame (Sesamum indicum L.) germplasm lines based on agro-morphological traits and SSR markers. Electronic Journal of Plant Breeding, 15 (4), 962-971. https://doi.org/10.37992/2024.1504.105
6. Ashri, A. (2006). Sesame (Sesamum indicum L.). Genetic Resources, Chromosome Engineering, and Crop Improvement: Oilseed Crops, 4, 231-289.
7. Bhattacharjee, M., Prakash, S., Roy, S., Soumen, S., Begum, T., & Dasgupta, T. (2020). SSR-based DNA fingerprinting of 18 elite Indian varieties of sesame (Sesamum indicum L.). The Nucleus, 63, 67-73. https://doi.org/10.1007/s13237-019-00290-3
8. Botstein, D., White, R.L., Skolnick, M., & Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32 (3), 314-331. https://www.ncbi.nlm.nih.gov/pubmed/6247908

9. Chesnokov, Y.V., & Artemyeva, A. (2015). Evaluation of the measure of polymorphism information of genetic diversity. Сельскохозяйственная биология, (5 (eng)), 571-578. https://doi.org/10.15389/agrobiology.2015.5.571eng
10. Cornea-Cipcigan, M., Pamfil, D., Sisea, C.R., & Margaoan, R. (2023). Characterization of Cyclamen genotypes using morphological descriptors and DNA molecular markers in a multivariate analysis. Frontiers in Plant Science, 14, 1100099. https://doi.org/10.3389/fpls.2023.1100099
11. Dossa, K., Wei, X., Zhang, Y., Fonceka, D., Yang, W., Diouf, D., Liao, B., Cisse, N., & Zhang, X. (2016). Analysis of genetic diversity and population structure of sesame accessions from Africa and Asia as major centers of its cultivation. Genes (Basel), 7 (4), 14. https://doi.org/10.3390/genes7040014
12. Doyle, J.J. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13-15. https://doi.org/10016746787
13. Elston, R.C., Olson, J.M., & Palmer, L. (2002). Biostatistical genetics and genetic epidemiology (Vol. 1). John Wiley & Sons.
14. Emon, R.M., Sakib, M.N., Khatun, M.K., Malek, M.A., Haque, M.S., & Alam, M.A. (2023). Microsatellite marker assisted molecular and morpho-physiological genetic diversity assessment in 38 genotypes of sesame (Sesamum indicum L.). Journal of Phytology, 15, 43-51. https://doi.org/10.25081/jp.2023.v15.7902
15. Guo, X., & Elston, R.C. (1999). Linkage information content of polymorphic genetic markers. Human Heredity, 49 (2), 112-118. https://doi.org/10.1159/000022855
16. Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles, 44, 223-270.
17. Liang, J., Sun, J., Ye, Y., Yan, X., Yan, T., Rao, Y., Zhou, H., & Le, M. (2021). QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing. PLoS One, 16 (2), e0247681. https://doi.org/10.1371/journal.pone.0247681
18. Liu, K., Goodman, M., Muse, S., Smith, J.S., Buckler, E., & Doebley, J. (2003). Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics, 165 (4), 2117-2128. https://doi.org/10.1093/genetics/165.4.2117
19. Meena, R., Singh, B., Meena, K., Meena, R., Singh, B., & Gurjar, P. (2018). Performance of front-line demonstrations on sesame (Sesamum indicum L.) in Karauli District of Rajasthan, India. International Journal of Current Microbiology and Applied Sciences, 7 (3), 1507-1511. https://doi.org/10.20546/ijcmas.2018.703.179
20. Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89 (3), 583-590. https://doi.org/10.1093/genetics/89.3.583
21. Porebski, S., Bailey, L.G., & Baum, B.R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 15, 8-15. https://doi.org/10.1007/Bf02772108
22. Powell, W., Machray, G.C., & Provan, J. (1996). Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1 (7), 215-222. https://doi.org/1360-1385(96)86898-1
23. Teklu, D.H., Shimelis, H., & Abady, S. (2022). Genetic improvement in sesame (Sesamum indicum L.): Progress and outlook: A review. Agronomy, 12 (9), 2144. https://doi.org/10.3390/agronomy12092144
24. Uncu, A.O., Gultekin, V., Allmer, J., Frary, A., & Doganlar, S. (2015). Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame. Plant Genome, 8 (2), eplantgenome2014 2011 0087. https://doi.org/10.3835/plantgenome2014.11.0087
25. Williams, S.E., & Hoffman, E.A. (2009). Minimizing genetic adaptation in captive breeding programs: A review. Biological Conservation, 142 (11), 2388-2400. https://doi.org/10.1016/j.biocon.2009.05.034
26. Yaseen, G., Ahmad, M., Zafar, M., Akram, A., Sultana, S., Ahmed, S.N., & Kilic, O. (2021). Sesame (Sesamum indicum L.). In green sustainable process for chemical and environmental engineering and science (pp. 253-269). Elsevier. https://doi.org/10.1016/B978-0-12-821886-0.00005-1
27. Yepuri, V., Surapaneni, M., Kola, V.S.R., Vemireddy, L., Jyothi, B., Dineshkumar, V., Anuradha, G., & Siddiq, E. (2013). Assessment of genetic diversity in sesame (Sesamum indicum L.) genotypes, using EST-derived SSR markers. Journal of Crop Science and Biotechnology, 16 (2), 93-103. https://doi.org/10.1007/s12892-012-0116-9
28. Yi, L., Dong, Z., Lei, Y., Zhao, J., Xiong, Y., Yang, J., Xiong, Y., Gou, W., & Ma, X. (2021). Genetic diversity and molecular characterization of worldwide prairie grass (Bromus catharticus Vahl) accessions using SRAP markers. Agronomy, 11 (10), 2054. https://doi.org/10.3390/agronomy11102054
29. Zhang, H., Wei, L., Miao, H., Zhang, T., & Wang, C. (2012). Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics, 13, 316. https://doi.org/10.1186/1471-2164-13-316