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    Genes involved in mRNA surveillance are induced in Brachypodium distachyon under cadmium toxicity
    (Springer, 2022) Aksoy, Emre; Uncu, Ali Tevfik; Filiz, Ertugrul; Orman, Sule; Cetin, Durmus; Akbudak, M. Aydin
    Background Cd accumulation in plant cells results in dramatic problems including oxidative stress and inhibition of vital enzymes. It also affects mineral uptakes by disrupting membrane permeability. Interaction among Cd and other plant nutrient elements changes the nutritional contents of crops and reduces their yield. Methods and results In the present study, Cd stress in Brachypodium distachyon led to the upregulation of some heavy metal transport genes (influx or efflux) encoding cation-efflux proteins, heavy metal-associated proteins and NRAMP proteins. The Arabidopsis orthologs of the differentially expressed B. distachyon genes (DEGs) under Cd toxicity were identified, which exhibited Bradi4g26905 was an ortholog of AtALY1-2. Detailed co-expression network and gene ontology analyses found the potential involvement of the mRNA surveillance pathway in Cd tolerance in B. distachyon. These genes were shown to be downregulated by sulfur (S) deficiency. Conclusions This is the first transcriptomic study investigating the effect of Cd toxicity in B. distachyon, a model plant for genomic studies in Poaceae (Gramineae) species. The results are expected to provide valuable information for more comprehensive research related to heavy metal toxicity in plants.
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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.
  • Küçük Resim Yok
    Öğe
    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.