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    Evaluation of Sodium Azide as a Chemical Mutagen in Developing Cold-Tolerant Quinoa (Chenopodium quinoa Willd.) Lines
    (Springer Int Publ Ag, 2023) Ilhan, Emre; Kasapoglu, Ayse Gul; Turkoglu, Aras; Aygoren, Ahmed Sidar; Muslu, Selman; Aydin, Murat; Aldaif, Muhammed
    Quinoa (Chenopodium quinoa Willd.) is an allotetraploid grain crop belonging to the Amaranthaceae family. With a nutritionally well-balanced nature and rich oil, protein, vitamin, carbohydrate, and amino acid content, it has various health benefits. Hybridization programs to induce genetic variation are difficult processes in quinoa plants; however, the introduction of variations through mutation to obtain promising genotypes is much easier. In this research, quinoa cultivar Atlas seeds were exposed to different doses and application durations of sodium azide (NaN3) were cultivated in pots. The present findings revealed distinctive differences in all studied traits between native and mutant plants. NaN3 mutagenesis caused genetic variations that were categorized based on studied traits and RAPD data, which led to two distinct groups during M-2. It was noted that 2 mM + 3 h NaN3 treatments had the greatest effects on genetic variations and germination parameters. Present findings were also confirmed by molecular analysis. This research will provide new insights into molecular breeding programs to be conducted to improve present quinoa genotypes and produce better genotypes.
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    Genetic Diversity and Population Structure of Barley Cultivars Released in Turkey and Bulgaria using iPBS-retrotransposon and SCoT markers
    (Galenos Publ House, 2022) Gungor, Huseyin; Ilhan, Emre; Kasapoglu, Ayse Gul; Filiz, Ertugrul; Hossein-Pour, Arash; Valchev, Dragomir; Valcheva, Darina
    To improve quantitative traits, it is essential to acknowledge genetic structure and diversity of the crop plants. In this study, 54 barley cultivars released from 1963 to date by different institutes in both Turkey and Bulgaria were screened with 18 iPBS and four SCoT markers to evaluate population structure and genetic diversity. According to the results, while total polymorphic band numbers was identified as 560, the polymorphic ones were found as 530 (438 and 92 amplified bands for iPBS and SCoT markers, respectively). In addition, the average polymorphic band number was found as 24.09. While the average polymorphism information content (PIC) value was 0.48, the average PIC value was 0.48 for iPBS and 0.48 for SCoT markers. The highest PIC value was determined as 0.50. The highest effective number of alleles, Shannon's information index, and Nei's genetic diversity were detected from the iPBS2271 marker at 1.61, 0.52 and 0.35, respectively among the iPBS markers while the highest values were obtained from SCoT-71 marker as 1.55, 0.32 and 0.48, respectively. As a result of a distribution of the 530 amplified bands in 54 barley cultivars, structure analysis showed that the subpopulations in the barley cultivars as a value of k=5. The average expected heterozygosity and fixation indices were identified as 0.234 and 0.322, respectively. Based on DICE similarity index, Marti and Zahir cultivars were found the most similar barley cultivars with 75% genetic similarity, whereas Ozdemir and Karatay 94 and Tosunpasa and Konevi cultivars were found 73% similar. On the other hand, Bayrak and Avci-2002 were found the most diverse cultivars with 19.9% genetic similarity. As a result, the barley cultivars released in Turkey and Bulgaria were found varying and, the genetic diversity and statistics index analysis indicated that iPBS and SCoT markers are powerful markers to perform genetic diversity analysis.
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    Genetic Diversity and Population Structure of Barley Cultivars Released in Turkey and Bulgaria using iPBS-retrotransposon and SCoT markers
    (Galenos Publ House, 2022) Gungor, Huseyin; Ilhan, Emre; Kasapoglu, Ayse Gul; Filiz, Ertugrul; Hossein-Pour, Arash; Valchev, Dragomir; Valcheva, Darina
    To improve quantitative traits, it is essential to acknowledge genetic structure and diversity of the crop plants. In this study, 54 barley cultivars released from 1963 to date by different institutes in both Turkey and Bulgaria were screened with 18 iPBS and four SCoT markers to evaluate population structure and genetic diversity. According to the results, while total polymorphic band numbers was identified as 560, the polymorphic ones were found as 530 (438 and 92 amplified bands for iPBS and SCoT markers, respectively). In addition, the average polymorphic band number was found as 24.09. While the average polymorphism information content (PIC) value was 0.48, the average PIC value was 0.48 for iPBS and 0.48 for SCoT markers. The highest PIC value was determined as 0.50. The highest effective number of alleles, Shannon's information index, and Nei's genetic diversity were detected from the iPBS2271 marker at 1.61, 0.52 and 0.35, respectively among the iPBS markers while the highest values were obtained from SCoT-71 marker as 1.55, 0.32 and 0.48, respectively. As a result of a distribution of the 530 amplified bands in 54 barley cultivars, structure analysis showed that the subpopulations in the barley cultivars as a value of k=5. The average expected heterozygosity and fixation indices were identified as 0.234 and 0.322, respectively. Based on DICE similarity index, Marti and Zahir cultivars were found the most similar barley cultivars with 75% genetic similarity, whereas Ozdemir and Karatay 94 and Tosunpasa and Konevi cultivars were found 73% similar. On the other hand, Bayrak and Avci-2002 were found the most diverse cultivars with 19.9% genetic similarity. As a result, the barley cultivars released in Turkey and Bulgaria were found varying and, the genetic diversity and statistics index analysis indicated that iPBS and SCoT markers are powerful markers to perform genetic diversity analysis.
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    Identification of Novel QTLs Associated with Frost Tolerance in Winter Wheat (Triticum aestivum L.)
    (Mdpi, 2023) Bolouri, Parisa; Haliloglu, Kamil; Mohammadi, Seyyed Abolghasem; Turkoglu, Aras; Ilhan, Emre; Niedbala, Gniewko; Szulc, Piotr
    Low temperature (cold) and freezing stress is a major problem during winter wheat growth. Low temperature tolerance (LT) is an important agronomic trait in winter wheat and determines the plants' ability to cope with below-freezing temperatures; thus, the development of cold-tolerant cultivars has become a major goal of breeding in various regions of the world. In this study, we sought to identify quantitative trait loci (QTL) using molecular markers related to freezing tolerance in winter. Thirty-four polymorphic markers among 425 SSR markers were obtained for the population, including 180 inbred lines of F-12 generation wheat, derived from crosses (Norstar x Zagros) after testing with parents. LT50 is used as an effective selection criterion for identifying frost-tolerance genotypes. The progeny of individual F-12 plants were used to evaluate LT50. Several QTLs related to wheat yield, including heading time period, 1000-seed weight, and number of surviving plants after overwintering, were identified. Single-marker analysis illustrated that four SSR markers with a total of 25% phenotypic variance determination were linked to LT50. Related QTLs were located on chromosomes 4A, 2B, and 3B. Common QTLs identified in two cropping seasons based on agronomical traits were two QTLs for heading time period, one QTL for 1000-seed weight, and six QTLs for number of surviving plants after overwintering. The four markers identified linked to LT50 significantly affected both LT50 and yield-related traits simultaneously. This is the first report to identify a major-effect QTL related to frost tolerance on chromosome 4A by the marker XGWM160. It is possible that some QTLs are closely related to pleiotropic effects that control two or more traits simultaneously, and this feature can be used as a factor to select frost-resistant lines in plant breeding programs.
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    Phylogenetic relationship among taxa in the genus Adonis L. collected from Turkiye based on nrDNA internal transcribed spacer (ITS) markers
    (Springer, 2022) Karahan, Faruk; Ilcim, Ahmet; Turkoglu, Aras; Ilhan, Emre; Haliloglu, Kamil
    Background Genus Adonis L. contain approximately 40 annual and perennial species, which are widely distributed in the temperate zones of Asia and Europe, and less frequently in southwestern Asia, northern Africa and the Mediterranean region. The aim of the study was to evaluate the phylogenetic relationship among Adonis taxa collected from Turkiye based on nrDNA Internal transcribed spacer (ITS) markers. Methods Samples of 64 individual genotypes from 21 populations of 10 Adonis taxa were collected from different regions of the country during vegetation period between 2014 and 2018. ITS1, ITS4, P16 and P25 primers within ITS technique was used to genotype the plant materials. Then, genotypic data was used to estimate magnitude and organization of infraspecific variation in different populations of Adonis. Results About 600 bp DNA sequences were obtained from each 64 Adonis genotypes belonging to 21 different populations. The dendrogram obtained from Adonis taxa and out-group sequences had two large main groups. While the out-group species were placed in the first large main group, the sect. Consiligo (perennial) and sect. Adonis (annuals) were placed in different sub-groups of the second large main group. Genetic similarity among Adonis taxa varied between A. microcarpa and A. dentata (98.46%). Principal component analysis indicated that two important components in Adonis taxa genotypes. The expected heterozygosity ranged from 0.0252 (sub-population A) to 0.3460 (sub-population C), with an average of 0.1154. In addition, population differentiation measurements (Fst) ranged from 0.0025 (sub-population C) to 0.9016 (sub-population A) with a relatively high average 0.6601. Conclusions Present analyses revealed that phylogenetic classification (grouping) of Adonis taxa largely depended on morphological structure and present ITS primers were quite efficient in putting forth the genetic diversity of such species. The results of this study suggested that ITS markers could be used in the identification of genetic diversity among the Adonis taxa. The results obtained from molecular data can be used to explore the genetic variation pattern, population structure, and the evolutionary history of genus Adonis in the future.