Investigation of Triticum boeoticum Boiss. ve T. urartu Thum. ex Gandil. populations with next generation sequencing methods

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.