Özet
In this thesis study, it was aimed to reveal the intra- and inter-species differences among 94 accessions representing the populations of Triticum baeoticum Boiss. and Triticum urartu Thum. Ex. Gandil. by using the DArTseq sequencing method. The 59 Triticum urartu accessions used in the thesis study were obtained from the USDA (U.S. Department of Agriculture), and the 34 Triticum baeoticum accessions were obtained from the TTGB (Turkey Seed Gene Bank). After germination in the TTGB climate chamber, DNA isolations were performed at the TTGB Molecular Biology Laboratory. The purified DNAs were sent to Diversity Arrays Technologies for DArTseq sequencing. SNP and SilicoDArT datasets provided by DArT are file formats that store genotype data in two different ways. The SNP dataset stores genotype data as 0, 1, and 2, while SilicoDArT data stores it as 0/1 (presence/absence). A total of 56,188 and 105,260 SNP and SilicoDArT loci were obtained from the SNP and SilicoDArT datasets provided by DArT. After the necessary quality filtering, the number of loci in the SNP and SilicoDArT datasets dropped to 16,898 and 100,103, respectively. The ADMIXTURE program was used to reveal population structures with high-quality and reproducible genotype data. The Q matrices with the lowest cross-validation error K-value and the highest log-likelihood K-value were transformed into dendrograms for examining population structure. An AMOVA analysis was performed to reveal the variance between the populations of T. urartu and T. baeoticum. A PCoA analysis was performed to visualize the main sources of variation between populations on a two-dimensional plane. To reveal the evolutionary relationship between the 94 accessions, the FASTA file obtained from the SNP dataset was transformed into dendrograms using the maximum likelihood statistical method and UPGMA clustering algorithm and visualized using iToL v6.8. As a result of the analyses, it was observed that the accessions of T. urartu and T. baeoticum belong to different populations of two different species. The analyses showed that there is a high level of genetic diversity between Triticum urartu and Triticum baeoticum species. This high diversity is also supported by the high Phi-statistics value in the AMOVA analysis and the wide variance in the PCoA analysis. In addition, it was understood that the DArTseq sequencing method is a powerful technique in terms of cost and speed, capable of molecularly distinguishing species that are difficult to morphologically distinguish from each other.
Künye
1. Soreng, R.J., Peterson, P.M., Romaschenko, K., Davidse, G., Zuloaga, F.O., Judziewicz, E.J., Filgueiras, T.S., Davis, J.I., & Morrone, O. A worldwide phylogenetic classification of the Poaceae (Gramineae). Journal of Systematics and Evolution, 53(2), 117-137, 2015.
2. Peng, J., Sun, D., & Nevo, E., Domestication evolution, genetics and genomics in wheat. Molecular Breeding, 28(3), 281-301., 2011.
3. Humphreys, M., Genetic improvement of forage crops-past, present and future. Journal of Agricultural Science, 143(4), 233-246 2005.
4. Brackenridge, G.R., Kandeler, E., & Wienand, K., The role of grasslands in the global carbon cycle. Grassland Science, 53(1), 1-10 2007.
5. Jasechko, S., Sharp, Z.D., Gibson, J.J., Birks, S.J., Yi, Y., & Fawcett, P.J., Terrestrial water fluxes dominated by transpiration. Nature, 496(7445), 347-350 2013.
6. Kellogg, E.A., Evolutionary history of the grasses. Plant Physiology, 125(3), 1198-1205 2001.
7. Clark, L.G., & Londoño, X., Bamboo taxonomy and habitat. In Gielis, J., & Potters, G. (Eds.), Compendium of ornamental foliage plant diseases (pp. 25-32). St. Paul, MN: APS Press., 2013.
8. Tzvelev, N. N., The System of Grasses (Poaceae) and Their Evolution. Botanical Review, 55(3), 141-204, 1989.
9. Djajadi, D. T., Hansen, A. R., Jensen, A., Thygesen, L. G., Pinelo, M., Meyer, A. S., Jørgensen, H., Surface properties correlate to the digestibility of hydrothermally pretreated lignocellulosic Poaceae biomass feedstocks. Biotechnology for Biofuels, 10, Article 49, 2017.
10. Wand, S. J. E., Midgley, G. F., Jones M. H., Curtis, P.S. Responses of wild C4 and C3 grass (Poaceae) species to elevated atmospheric CO2 concentration: a meta-analytic test of current theories and perceptions, Vol. 5 (6), 723-741, 1999.
11. Chen, I., Li, K., Tsang, C. (2020). Silicified bulliform cells of Poaceae: morphological characteristics that distinguish subfamilies. Botanical Studies, 61(1), 2020.
12. Rudall, P.J., Stuppy, W., Cunniff, J., Kellogg, E.A., Briggs, B.G., Evolution of reproductive structures in grasses (Poaceae) inferred by sister-group comparison with their putative closest living relatives, Ecdeiocoleaceae. American Journal of Botany, 92(9), 1432-1443, 2005.
13. Tsujimoto, H., Tsunewaki, K., & Gupta, P.K., DArTseq-based analysis of genomic relationships among species of tribe Triticeae. Scientific Reports, 8(1), 2018.
14. Goncharov, N.P., Genus Triticum L. taxonomy: the present and the future. Plant Systematics and Evolution, 295(1-4), 1-11, 2011.
15. Tan, K., Triticum L. In: Davis, P.H. (Ed.), Flora of Turkey and the East Aegean Islands. University of Edinburgh Press, 245-255, 1985.
16. Cabi, E., Triticeae dumortier (Poaceae) oymağının Türkiye'deki revizyonu, Doktora Tezi, Orta Doğu Teknik Üniversitesi Fen Bilimleri Enstitüsü, Ankara, 2010.
17. Kilian, B., Özkan, H., Pozzi, C., & Salamini, F., Domestication of the Triticeae in the Fertile Crescent. In Genetics and Genomics of the Triticeae (pp. 81-119), 2009.
18. Braidwood, R.J., & Braidwood, L., Jarmo: A Village Early Farmers in Iraq. Antiquity, 24(96), 189-195, 1950.
19. Braidwood, R. J., Çamlıbel, H., Watson, P.J., Prehistoric Investigations in Southeastern Turkey, 164(3885), 1275-1276, 1969.
20. Kilian, B., Martin, W., & Salamini, F., Genetic Diversity, Evolution and Domestication of Wheat and Barley in the Fertile Crescent. Evolution in Action, 137-166, 2010.
21. Özberk, F., Karagöz, A., Özberk, İ., & Atlı, A., Buğday Genetik Kaynaklarından Yerel ve Kültür Çeşitlerine; Türkiye'de Buğday ve Ekmek. Tarla Bitkileri Merkez Araştırma Enstitüsü Dergisi, 25(2), 218-233, 2016.
22. Dahm, R., Friedrich Miescher and the discovery of DNA. Developmental Biology, 278(2), 274-288, 2005.
23. Dahm, R., From discovering to understanding: Friedrich Miescher's attempts to uncover the function of DNA. EMBO Reports, 11(2), 153-160. 2010.
24. Lederberg, J., The Transformation of Genetics by DNA: An Anniversary Celebration of Avery, Macleod and Mccarty (1944). Genetics, 136(2), 423-426, 1994.
25. Klug, A., Rosalind Franklin and the Discovery of the Structure of DNA. Nature, 219, 808-810, 1968.
26. Pauling, L., Corey, R.B., A Proposed Structure For The Nucleic Acids. Proceedings of the National Academy of Sciences of the United States of America, 39(2), 1953.
27. Watson, J.D., & Crick, F.H.C., Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738, 1953.
28. Sanger, F., & Coulson, A.R., A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase, Journal of Molecular Biology, 94(3), 441-448, 1975.
29. Maxam, A.M., & Gilbert, W., A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America, 74(2), 560-564, 1977.
30. Sanger, F., Nicklen, S., & Coulson, A.R., DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74(12), 5463-5467, 1977.
31. Hood, L. E., Hunkapiller, M. W., Smith, L. M., Automated DNA sequencing and analysis of the human genome, Genomics, 1(3), 201-212, 1987.
32. Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen M., Nyren, P., Real-Time DNA Sequencing Using Detection of Pyrophosphate Release, ANALYTICAL BIOCHEMISTRY, 242, 84-89, 1996.
33. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921, 2001.
34. Rothberg, M., Leamon, J., H., The development and impact of 454 sequencing, Nat Biotechnol, 26(10), 1117-24, 2008.
35. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., Dewinter, A., Dixon, J., Foquet, M., … Turner, S., Real-time DNA sequencing from single polymerase molecules. Science (New York, N.Y.), 323(5910), 133–138, 2009.
36. Eisenstein, M. Oxford Nanopore announcement sets sequencing sector abuzz., Nat Biotechnol, 30, 295–296, 2012.
37. Abbasov, M., Akparov, Z., Gross, T., Babayeva, S., Izzatullayeva, V., Hajiyev, E., Rustamov, K., Gross, P., Tekin, M., Akar, T., Chao, S., Brueggeman, R., Genetic relationship of diploid wheat (Triticum spp.) species assessed by SSR markers, Genetic Resources and Crop Evolution, 65, 1441-1453, 2018.
38. Taheri, M., Alavi-Kia, S., Mohammadi, S., Vahed, M., Assessment of genetic diversity and relationships among Triticum urartu and Triticum boeoticum populations from Iran using IRAP and REMAP markers, Genetic Resources and Crop Evolution, 65, 1867-1868, 2018.
39. Hammer, K., Filatenko, A., Korzun, V., Microsatellite markers – a new tool for distinguishing diploid wheat species, 47, 497-500, 2000.
40. Peng, H., J., Sun, D., Nevo, E., Domestication evolution, genetics and genomics in wheat, 28, 281-301, 2011.
41. Jasechko, S., Sharp, Z., Gibson, J., Birks, S., Yi, Y., Fawcett, P., Terrestrial water fluxes dominated by transpiration, 496, 347-350, 2013.
42. Judziewicz, E., Londoño, X., Clark, L., TWO NEW NORTHERN ANDEAN SPECIES OF AULONEMIA (POACEAE: BAMBUSOIDEAE: BAMBUSEAE: ARTHROSTYLIDIINAE) WITH VERRUCOSE CULMS, 7, 137-143, 2013.
43. Djajadi, D., Hansen, A., Jensen, A., Thygesen, L., Pinelo, M., Meyer, A., Jørgensen, H., Surface properties correlate to the digestibility of hydrothermally pretreated lignocellulosic Poaceae biomass feedstocks, 49, 2017.
44. Wand, S., Midgley, G., Jones, M., Curtis, P., Responses of wild C4 and C3 grass (Poaceae) species to elevated atmospheric CO2 concentration: a meta-analytic test of current theories and perceptions, 5, 723-741, 1999.
45. Briggs, J., Knapp, A., Blair, J., Heisler, J., Hoch, G., Lett, M., McCarron, J., An Ecosystem in Transition: Causes and Consequences of the Conversion of Mesic Grassland to Shrubland, 55, 243-254, 2005.
