The ancient DNA and archaeobotanical analysis suggest cultivation of Triticum aestivum subsp. spelta at Yumuktepe and Yenikapı Pottery Neolithic sites in Turkey

Archaeobotanical materials subject to aDNA analysis were recovered from Yumuktepe and Yenikapı, two important archaeological sites in Anatolia and date back to the Pottery Neolithic Period i.e., 7th millennium BC. Many charred ancient seeds representing various cereal species including a great number of wheat grains were documented in mentioned sites. Among the cereal seeds, charred wheat samples were tentatively identified as Triticum aestivum subsp. spelta L. or Triticum new glume wheat (NGW) or atypical emmer or naked wheat in Yumuktepe and Yenikapı showed similarities with the morphological characteristics of T. aestivum subsp. spelta wheat, but it was difficult to reach a firm conclusion. This study aimed to provide genetic data to enable more precise identification of charred wheat seeds using an ancient DNA (aDNA) approach. aDNAs were successfully extracted from the representative charred seeds of T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat. The PCR amplification of 26SrDNA and IGS gene regions with aDNA was carried out and sequenced. The expected product sizes of IGS 158 bp for the D genome and 87 bp for the A or B genomes and DNA sequence comparisons with other wheat species revealed that T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat samples included the D genome from Aegilops tauschii and is more likely to be T. aestivum subsp. spelta. The discovery of T. aestivum subsp. spelta grains in the Yenikapı and Yumuktepe suggest that the cultivation of hexaploid wheat was widespread. Further, spelta hulled wheat, which is the progenitor of the hexaploid wheat, might have been cultivated in these settlements. © 2022, The Author(s), under exclusive licence to Springer Nature B.V

Göksu nehir ekosisteminde Populus euphratica populasyonlarının genetik yapılanması.

Poplar is one of the economically most important plants growing in Anatolia. Developing and growing world population and ascending demand for energy sources increased the genetic studies on poplars. There are four poplar species that have economical value and distributed naturally in Turkey; Populus nigra, Populus tremula, Populus alba and Populus euphratica. Populus euphratica, which can survive in salty and calciferous soils and known as Euphrates poplar, is resistant for low moisture and long summer drought. Having economical value for these respects, this species is distributed in East Mediterranean and Southeastern Anatolia. The species possesses great importance for both renewable energy resources and persistence of a healthy river ecosystem. Due to decreasing water resources with increased population and habitat destructions by human activities, the distribution area of this species become narrower gradually as well as loss of gene sources. Hence, searching for potential genetic diversity present in species’ genetic resources is of great importance in terms of conservation (in situ and ex situ), breeding and use. In this PhD Thesis, genetic structure and diversity of Populus euphratica populations in the Göksu river ecosystem were studied with 21 microsatellite DNA (SSR: single sequence repeats) markers. Results demonstrated reduced level of genetic diversity with low heterozygosity values (Ho:0.50±0.07, uHe:0.49±0.06). Severe past reductions in population sizes have resulted in loss of genetic variation for the species. Native populations of this species in the Göksu river are experiencing gene pool shrinkage and are in great danger of collapsing, mainly because of anthropogenic pressures. With great number of private alleles and slightly higher heterozygosity values The Euphrates river population is shown to be an effective candidate of genetic resource for future conservation studies. Effective breeding and conservation programs including in situ conservation of Euphrates poplar stands in the Göksu river and ex situ conservation by establishing gene banks and clone banks in order to preserve germplasm resources should be initiated immediately. The conservation of these genetic resources is of great importance and priority should be given for fast and reproducible actions.Ph.D. - Doctoral Progra

Kara pas ve sarı pas hastalıklarına dayanıklı ve hassas durum buğday hatlarının moleküler düzeyde biyofiziksel metodlarla karakterizasyonu

Stem rust and Yellow rust diseases are the two major wheat fungal diseases causing considerable yield losses in Turkey and all around the world. There are studies which are carried out to identify and utilize resistance sources in order to obtain resistant lines of wheat. However, virulent pathotypes are continuously being important threats to wheat production and yield. For that reason, new approaches for rapid identification are needed. The aim of this study was to investigate and to understand the structural and functional differences between the resistant and sensitive durum wheat cultivars to the plant fungal diseases of stem and yellow (stripe) rusts. To aim this, forty durum wheat recombinant inbred lines (RILs), which were previously determined to be resistant or sensitive to stem and yellow rust diseases, were investigated by the noninvasive Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) Spectroscopy. Also, classification of the resistant and sensitive lines depending on the structural and functional differences has been attempted. The FTIR spectra for stem rust disease showed that, resistant durum wheat lines had a significant increase in the population of unsaturation in acyl chains of lipid molecules, an increase in lipid and in total protein content and also an increase in carboxylic acids and alcohols. For yellow rust disease, resistant lines had a significant increase in hydrogen bonding and they had also a more ordered membrane structure. In Principal Component Analysis for stem rust disease, according to 3700-650 cm-1 region, amide III band (1213-1273 cm-1 region) and C-H stretching region (3020- 2800 cm-1), the resistant and sensitive groups were separated successfully. For yellow rust disease, according to 3700-650 cm-1 region, Amide A and Amide III bands, the resistant and sensitive lines were grouped distinctly. FTIR spectroscopy provides a useful approach to determine the differences in molecular structure of durum wheat RILs regarding resistance of lines to fungal diseases. However, further research is still needed to ensure if the structural and functional differences in biomolecules of the samples could be used as molecular markers for discrimination of rust resistant materials from rust sensitive ones.M.S. - Master of Scienc

Genetic diversity of marginal populations of Populus euphratica Oliv. from highly fragmented river ecosystems

Populus euphratica Oliv. (Euphrates poplar) is one of the naturally distributed poplar species and limited to south and southwestern Turkey. The species possesses great importance for both renewable energy resources and persistence of a healthy river ecosystem. Due to increased habitat destructions and fragmentation by human activities, the distribution area of this species has become narrower. Hence, searching for potential genetic diversity present in species' genetic resources is of great importance in terms of its resilience to changing environment as well as breeding and use. To explore genetic structure and diversity of Euphrates poplar, natural populations in the GOksu and Euphrates river ecosystems were studied with 21 microsatellite DNA loci. Results demonstrated reduced level of genetic diversity (Ho:0.44, uHe:0.45) and low differentiation among two river populations (F-ST = 0.07), suggesting a common origin. It appears that severe past reductions in population sizes have resulted in loss of genetic variation in the species. Native populations of this species in two rivers seemed to be marginal with continued gene pool shrinkage. Therefore, they are in great danger of collapsing, mainly because of continued habitat loss and fragmentation. Genetic data generated with the current study provide important information which could be useful for future restoration and conservation studies of the species.Scientific and Technological Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [KBAG 117Z018]We sincerely thank Sadi Siklar for his contributions to the field studies. We are also indebted to Abdulbaki Coban, Asiye Ciftci and Funda Ozdemir Degirmenci for their contributions to the statistical analysis. We also thank anonymous reviewers for helpful comments on the manuscript. This study was funded by The Scientific and Technological Council of Turkey (TUBITAK), Project #: KBAG 117Z018

MOLECULAR PHYLOGENY OF TRITICUM AND AEGILOPS GENERA BASED ON ITS AND MATK SEQUENCE DATA

Understanding the phylogenetic relationship between Triticum and Aegilops species, which form a vast gene pool of wheat, is very important for breeding new cultivated wheat varieties. In the present study, phylogenetic relationships between Triticum (12 samples from 4 species) and Aegilops (24 samples from 8 species) were investigated using sequences of the nuclear ITS rDNA gene and partial sequences of the matK gene of chloroplast genome. The phylogenetic relationships among species were reconstructed using Maximum Likelihood method. The constructed tree based on the sequences of the nuclear component (ITS) displayed a close relationship between polyploid wheats and Aegilops speltoides species which provided new evidence for the source of the enigmatic B genome donor as Ae. speltoides. Concurrent clustering of Ae. cylindrica and Ae. tauschii and their close positioning to polyploid wheats pointed the source of the D genome as one of these species. As reported before, diploid Triticum species (i.e. T. urartu) were identified as the A genome donors and the positioning of these diploid wheats on the constructed tree are meaningful. The constructed tree based on the chloroplastic matK sequences displayed same relationship between polyploid wheats and Ae. speltoides species providing evidence for the later species being the chloroplast donors for polyploid wheats. Therefore, our results supported the idea of coinheritance of nuclear and chloroplast genomes where Ae. speltoides was the maternal donor. For both trees the remaining Aegilops species produced a distinct cluster whereas with the exception of T. urartu, diploid Triticum species displayed a monophyletic structure

Phylogeography and phylogeny of genus Quercus L. (Fagaceae) in Turkey implied by variations of trnT (UGU) -L (UAA) -F (GAA) chloroplast DNA region

The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT(UGU)-L(UAA) IGS, trnL(UAA)intron, trnL(UAA)-F(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT(UGU)-L(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and hT > vT observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely “Ilex” and “Coccifera.” Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex

A Molecular Phylogeny Of Salvia Euphratica Sensu Lato (Salvia L., Lamiaceae) And Its Closely Related Species With A Focus On The Section Hymenosphace

To investigate the phylogenetic relationships of Salvia euphratica sensu lato and its closely related species with a focus on the section Hymenosphace, we screened five different regions; one nuclear ribosomal DNA region (Internal Transcribed Spacer, ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and trnV intron]. Based on 19 sequences of 7 Salvia taxa produced in the study and different number of sequences obtained from GenBank, our results supported latest taxonomic treatments on Salvia pseudeuphratica and S. cerino-pruinosa as they are resurrected and accepted different species from S. euphratica. The results confirmed the latest phylogenetic findings as “the section Hymenosphace is a non-monophyletic group, originated thick textured, non-expanding ancestral group, and expanding calyces with widely diverging lips in fruiting stage evolved several times in parallel, not only in Salvia but also in the Iranian genus Zhumeria”. The species of the sect. Hymenosphace are mostly distributed in three different geographic regions [(1) Southwest Asia, Turkey, Russia and Iran, (2) Canary Islands, (3) Southern Africa] with different morphological characters. The results showed that ITS had the highest resolution power for discriminating studied taxa and the highest number of haplotypes was also observed in this region. The resolutions of the chloroplast regions were too low for taxa native to Turkey, but quite enough to discriminate species from the different clades whose sequences were obtained from database. © 2015, Springer-Verlag Wien

Mitochondrial Dna Analysis in The Turkish Leber'S Hereditary Optic Neuropathy Population

Purpose To define the prevalence of a panel of mitochondrial DNA (mtDNA) mutations associated with Leber's hereditary optic neuropathy (LHON) in the Turkish LHON population. LHON-associated mtDNA mutations have been found in LHON patients from around the world, but the Turkish LHON population has not been studied. Methods Thirty-two Turkish patients were defined clinically as having LHON on the basis of painless, subacute, bilateral optic neuropathy and the exclusion of other causes of subacute optic neuropathy. mtDNA was extracted from blood of the 32 probands and assayed for a panel of primary and secondary LHON-associated mtDNA mutations by polymerase chain reaction (PCR)-based methods. We studied three well-known LHON-associated primary mutations (at nucleotide positions 11778, 3460 and 14484) and one common secondary mutation (at nucleotide 15257) in all 32 probands. In addition to these mutations, 18 of the 32 probands were tested for the Complex IV, COX III gene, LHON associated 9804 and 9438 mutations and secondary LHON mutations at nucleotide positions 3394, 4160, 4216, 4917, 5244, 7444, 7706, 13708, 13730 and 15812. Results Among the 32 probands tested for four common LHON mutations, 3 carried the 14484 mutation, 1 carried the 11778 mutation, 1 carried the 3460 mutation and 1 carried the 15257 mutation. Among the 18 LHON patients who tested for additional mutations, 1 proband harboured the 9804 mutation and 4 carried the secondary mutations at nucleotide positions 4216, 4917 and 13708. Conclusion The results of mtDNA analysis of the Turkish LHON patients appear to be different from those of previous reports.WoSScopu