Assessment of genetic diversity on tomato (Lycopersicon esculentum Mill.) landraces using SSR molecular markers in Turkey

Year 2021, , 51 - 59, 30.08.2021

Ahmet Okumuş , Şenay Dağıdır

https://doi.org/10.51753/flsrt.957055

Cited By: 3

Abstract

Genetic diversity is getting have been increasingly narrowed by the dense bred cultivar usage for production, on the other hand, genetic variation created by the landraces is known as the raw material of plant breeding. A collection of 21-landrace and three-commercial tomato (Lycopersicon esculentum Mill.) genotypes were screened for allele profile, genetic definition and genetic similarity with the aim of identifying genetic variability in genetic level with 40 SSR loci. Number of alleles per locus ranged from 3 (SSR50, SSR80, SSR9, LEtat002) to 13 (LEat018). Expected and observed heterozygosity values were scored between He: 0.753 and Ho: 0.714 respectively and the mean value of polymorphism information content (PIC) value of these loci was found as 0.694. Considering distribution of alleles at loci, the highest allele frequency was observed from SSR75 with % 62.5 LEat014 with % 58.3 LEga004 with % 50.0 locus, while the lowest was in AI491065 with 16.6% LEta024 locus. UPGMA (Unweighted Pair-Group Method using Arithmetic Means) method was conducted for cluster analysis. The dendrogram was consisted 2 main groups; Group 2 was the largest and contained many sub-groups. The highest genetic similarity level of genotypes from Bafra-Merkez and Sivas-Yukarıkale Village was found as 0.776. The lowest similarity ratio was observed between Sivas-Yıldızeli-Emirler Village and Samsun-Carsamba genotypes with 0.136. The obtained results are indicated that genetic diversity information of landraces with effective SSR loci will help to manage tomato genetic resources for tomato breeding.

Keywords

Genetic diversity, landraces, PIC value, Solanum lycopersicum L., SSR, tomato

Project Number

PYO.ZRT.1904.10.032.

References

• Benor, S., Zhang, M., Wang, Z., & Zhang, H. (2008). Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. Journal of Genetics and Genomics, 35(6), 373-379.
• Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314.
• Brookfield, J. F. Y. (1996). A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology, 5(3), 453-455.
• Can, H., Kal, U., Ozyigit, I. I., Paksoy, M., & Turkmen, O. (2019). Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. Journal of Genetics, 98(3), 86.
• Castellana, S., Ranzino, L., Beritognolo, I., Cherubini, M., Luneia, R., Villani, F., & Mattioni, C. (2020). Genetic characterization and molecular fingerprint of traditional Umbrian tomato (Solanum lycopersicum L.) landraces through SSR markers and application for varietal identification. Genetic Resources and Crop Evolution, 67(7), 1807-1820.
• Cox, S. (2000). From discovery to modern commercialism: the complete story behind Lycopersicon esculentum, Colorado State, USA. http://www.landscapeimagery.com/articles.html, Last accessed on July 18, 2021.
• Dilbirligi, E., (2007). Bitkisel biyolojik çeşitlilik ve genetik kaynaklarının sürdürülebilir kullanım stratejilerinin değerlendirilmesi. Ankara Üniversitesi, Fen Bilimleri Enstitüsü, Doktora Tezi.
• Doyle, J. J., & Doyle, J. L. (1991). Isolation of plant DNA from fresh tissue plant. Plant Molecular Biology, 9, 340-342.
• Fentik, D. A. (2017). Review on genetics and breeding of tomato (Lycopersicon esculentum Mill). Advances in Crop Science and Technology, 5(5), 1-6.
• He, C., Poysa, V., & Yu, K. (2003). Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical and Applied Genetics, 106(2), 363-373.
• Hennink, S., & Zeven, A. C. (1990). The interpretation of Nei and Shannon-Weaver within population variation indices. Euphytica, 51(3), 235-240.
• Henareh, M., Dursun, A., & Mandoulakani, B. A. (2015). Genetic diversity in tomato landraces collected from Turkey and Iran revealed by morphological characters. Acta Scientiarum Polonorum Hortorum Cultus, 14(2), 87-96.
• Henareh, M., Dursun, A., Abdollahi-Mandoulakani, B., & Haliloğlu, K. (2016). Assessment of genetic diversity in tomato landraces using ISSR markers. Genetika, 48(1), 25-35.
• Hocaoglu-Ozyigit, A., Ucar, B., Altay, V., & Ozyigit, I. I. (2020). Genetic diversity and phylogenetic analyses of Turkish cotton (Gossypium hirsutum L.) lines using ISSR markers and chloroplast trnL-F regions. Journal of Natural Fibers, 1-14.
• Kaemmer, D., Weising, K., Beyermann, B., Borner, T., Epplen, J. T., & Kahlm, G. (1995). Oligonucleotide fingerprinting of tomato DNA. Plant Breeding, 114(1), 12-17.
• Garcia-Martinez, S., Andreani, L., Garcia-Gusano, M., Geuna, F., & Ruiz, J. J. (2006). Evaluation of amplified fragment length polymorphism and simple sequence repeats for tomato germplasm fingerprinting: utility for grouping closely related traditional cultivars. Genome, 49(6), 648-656.
• Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106(949), 283-292. Nei, M., & Li, W. H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 76(10), 5269-5273.
• Nei, M. (1987). Molecular evolutionary genetics. (pp. 1-512). Columbia University Press, New York. Okumus, A. (2007). Genetic variation and relationship between Turkish flint maize landraces by RAPD markers. American Journal of Agricultural and Biological Sciences, 2(2), 49-53.
• Osma, E., Ozyigit, I. I., Leblebici, Z., Demir, G., & Serin, M. (2012). Determination of heavy metal concentrations in tomato (Lycopersicon esculentum Miller) grown in different station types. Romanian Biotechnological Letters, 17(1), 6962-6974.
• Ozgen, M., Adak, S., Karagoz, A. Ulukan, H. (1995). Bitkisel gen kaynaklarının korunma ve kullanımı. Türkiye Ziraat Mühendisliği 4. Teknik Kongresi, Ankara, Ziraat Bankası Kültür Yayınları, 26, 309-343.
• Peakall, R., & Smouse, P. (2010). GenAlEx 6.4. Appendix 1: Methods and statistics. http://wenku.baidu.com/view/f483ee3243323968011c927c.html, Last accessed on July 18, 2021.
• Rohlf, F. J. (1998). NTSyS-p.c. Numerical Taxonomy and Multivariate Analysis System (Version 2.0). Exeter Software Publishers Ltd., Setauket.
• Schouten, H. J., Tikunov, Y., Verkerke, W., Finkers, R., Bovy, A., Bai, Y., & Visser, R. G. (2019). Breeding has increased the diversity of cultivated tomato in The Netherlands. Frontiers in Plant Science, 10, 1606.
• Sefc, K. M., Lefort, F., Grando, M. S., Scott, K. D., Steinkellner, H., & Thomas, M. R. (2001). Microsatellite markers for grapevine: a state of the art. In: Roubelakis-Angelakis, K. A., (eds) Molecular Biology & Biotechnology of the Grapevine (pp. 433-463). Springer, Dordrecht.
• Sol Genomics, (2021). The Official Website of Sol Genomics Network, https://solgenomics.net/about/tomato_project/nsf_9872617/index.pl, Last accessed on July 18, 2021.
• Tam, S. M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S. R., & Grandbastien, M. A. (2005). Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theoretical and Applied Genetics, 110(5), 819-831.
• Tridge, (2021). The Official Website of Global Sourcing Hub of Food & Agriculture, https://www.tridge.com/intelligences/tomato/production, Last accessed on July 18, 2021.
• Vural, H., Esiyok, D., & Duman, I. (2000). Kültür sebzeleri (sebze yetiştirme). (pp. 1-440). Ege Üniv., Ziraat Fak., Bornova, İzmir.
• Wien, H. C. (1987). The physiology of vegatable crops. (pp. 1-207). Cornel University, Ithaca N.Y., USA.
• World’s Top Exports, (2021). The Official Website of World’s Top Exports, http://www.worldstopexports.com/tomatoes-exports-country, Last accessed on July 18, 2021.
• Yazgan, A., & Fidan, S. (1996). Tokat kosullarina uygun kiraz domates (Lycopersicon esculentum Mill. var. cerasiforme) çesitlerinin belirlenmesi. GAP I. Sebze Tarimi Sempozyumu, Sanliurfa, 19-23.