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Öğe Association mapping for five agronomic traits in the common bean (Phaseolus vulgaris L.)(Wiley, 2014) Nemli, Seda; Asciogul, Tansel Kaygisiz; Kaya, Hilal Betul; Kahraman, Abdullah; Esiyok, Dursun; Tanyolac, BahattinBACKGROUNDThe common bean is the most important grain legume and a major source of protein in many developing countries. We analysed the following traits: pod fibre (PF), seeds per pod (SPP), plant type (PT), growth habit (GH), and days to flowering (DF) for a set of diverse common bean accessions and determined whether such traits were associated with amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. RESULTSIn this study, 66 common bean genotypes were used and genotyped with 233 AFLP, 105 SNP and 80 SSR markers. The association analysis between markers and five traits was performed using a General Linear Model (GLM) in Trait Analysis by aSSociation, Evolution and Linkage (TASSEL). The population structure was determined using the STRUCTURE software, and seven groups (K = 7) were identified among genotypes. The associations for such traits were identified and quantified; 62 markers were associated with the five traits. CONCLUSIONThis study demonstrated that association mapping using a reasonable number of markers, distributed across the genome and with the appropriate number of individuals harboured to detect DNA markers linked to the traits of PF, SPP, PT, GH and DF in common bean. (c) 2014 Society of Chemical IndustryÖğe Association mapping of days to flowering in common bean (Phaseolus vulgaris L.) revealed by DArT markers(Springer, 2018) Ates, Duygu; Asciogul, Tansel Kaygisiz; Nemli, Seda; Erdogmus, Semih; Esiyok, Dursun; Tanyolac, Muhammed BahattinIn the current study, 173 common bean genotypes from several geographic regions were studied. Days to flowering (DF) was evaluated in two experimental locations in Izmir, Turkey (Bornova and Menemen) in 2 years (2015 and 2016) and was found to range from 30 to 62.7 days with a mean value of 41.5 days. A total of 22,848 SNPs based on diversity array technology were developed, and after filtering, the remaining 20,766 SNP markers were used for calculating linkage disequilibrium. Chromosomes 1-11 contained 1846, 2342, 2184, 1153, 1351, 1520, 1953, 2080, 2065, 1199, and 1511 SNPs, respectively. A total of 1562 SNPs were identified as scaffold markers. The PIC value was 0.25, ranging from 0.005 to 0.500. Common bean accessions were divided into two main subpopulations, namely POP1 (Mesoamerican) and POP2 (Andean). Mixed linear model using the Q + K model showed that three SNPs had a significant association (p < 0.01) in Bornova in 2015 and seven SNPs had a significant association (p < 0.01) in the same location in 2016. Five significant associations (p < 0.01) were identified in 2015 while six (p < 0.01) were identified in Menemen in 2016. When the data from both locations and both years was combined, six SNPs were significant (p < 0.01). For DF, 11 putative candidate genes were predicted from the sequences representing homology to linked SNPs. We conclude that the markers, which were significantly associated with the DF of the common bean genotypes in the current study, can be used for marker-assisted selection in plant breeding program of common bean.Öğe Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey(Tubitak Scientific & Technical Research Council Turkey, 2017) Nemli, Seda; Asciogul, Tansel Kaygisiz; Ates, Duygu; Esiyok, Dursun; Tanyolac, Muhammed BahattinThe common bean (Phaseolus vulgaris L.) is the most consumed food legume in the world and is a major source of dietary protein, carbohydrates, and valuable micronutrients, especially in developing countries. Diversity Arrays Technology (DArTseq), based on genome reduction with restriction enzymes, provides a rapid, high-throughput, and cost-effective tool capable of generating thousands of genotyped single nucleotide polymorphisms (SNPs) for a genome-wide analysis of genetic diversity. In this study, we aimed to characterize common bean accessions using SNPs detected by a DArTseq approach. A total of 43,018 SNPs were identified from 173 common bean accessions, including Andean and Mesoamerican genotypes. After filtering raw and redundant data, a total of 16,366 SNPs were considered for further analyses. According to population structure analysis, the genotypes were roughly divided into 2 gene pools of Andean and Mesoamerican types. Pairwise fixation index (Fst) values were calculated to resolve the differentiation between populations. This study demonstrated that discovering SNPs from the whole genome is a potential resource for identifying naturally diverse accessions and also the information could be used in breeding programs to develop new common bean varieties.Öğe Diversity in nutritional composition of Swiss chard (Beta vulgaris subsp L. var. cicla) accessions revealed by multivariate analysis(Cambridge Univ Press, 2011) Bozokalfa, M. K.; Yagmur, Bulent; Asciogul, Tansel Kaygisiz; Esiyok, DursunMineral concentration levels in cultivated vegetables have received very little concern in the context of biodiversity despite the fact that most vegetables have a rich micronutrient composition. Swiss chard is an important salad crop which is high yielding and rich in minerals, vitamins and phenolic compounds. It is also extremely easy to grow. However, there is a lack of information on the genetic variability of mineral concentration of Swiss chard. Mineral composition diversity of 54 genetically diverse Swiss chard accessions, representative of all Turkish Swiss chard genetic resources, was investigated using multivariate analysis. These traits are useful in evaluating germplasm diversity in the nutritional concentration context and for use in further breeding programmes which will focus on improving mineral concentrations in Swiss chard cultivars. The results displayed significant differences among accessions and remarkably high nutrient contents. The data gathered were analyzed using principal components (PCs) and cluster analysis and revealed five major groupings. The data also observed 74.39% of total variation. The first three PCs accounted for 49.86% of the total variation in the population. Present values provided great variability among accessions and the results demonstrate that it is possible to identify genetic differentiation among Swiss chard accession for some nutritional elements. The genetic resources that exist indicate that potentially important accessions could be used as a gene source due to their high levels of K, Ca, Cu and Zn in breeding programmes.Öğe Effects of tomato-based rotations with diversified pre-planting on soil health in the Mediterranean soils of Western Turkey(Elsevier, 2020) Kayikcioglu, Huseyin Husnu; Duman, Ibrahim; Asciogul, Tansel Kaygisiz; Bozokalfa, Mehmet Kadri; Elmaci, Omer LutfuTurkey ranks fourth among the tomato (Lycopersicon lycopersicum L.) producers in the world and the tomato varieties extend to 40 % of the total vegetable yield of the country. Farmers have continued to cultivate tomato due to the economic potential of this crop in the main vegetable growing regions of Turkey. Intensive agriculture without employing crop rotations and the inclusion of the excessive and the same type of chemical fertilizers continuously regardless of the soil properties reduces the productive capacity of the soil and adversely affects its ecosystem functions. A three-year (2016-18) diversified cropping system combined with field experiments and employing reduced tillage was conducted in Izmir, a semiarid region in Western Turkey, adopting the randomized complete block design with three replications. Six different tomato-based rotations with diversified preplanting comprising two, three and four different plant species [CR1 (tomato / corn / mustard); CR2 (tomato / bean / mustard); CR3 (tomato/corn/wheat/mustard); CR4 (tomato / bean / wheat / mustard); CR5 (tomato / corn / fallow); CR6 (tomato / bean / fallow)] were employed to evaluate the impact on the parameters of soil health such as basal soil respiration, nitrogen mineralization, and the activities of the enzymes dehydrogenase and beta-glucosidase. in the tomato phases, soil samples were drawn on the 16th day after planting of the seedlings at 0-20 cm depth in April 2016 and April 2018. the multivariate analysis of variance revealed that different crop rotations (Treatment: CRs), and their interaction (TreatmentxYear) on the soil microbial characteristics were significantly different in terms of the dependent variables (P < 0.01). on analysis, the microbial parameters in the experimental soils soared by 36 % with the CR2, followed by a 29 % increase with the CR6 compared to the initial levels in both treatments. the average results at the completion of the experiment revealed that design CR4, which included legumes and experienced the greatest variety of plants in the rotation, encouraged 18-30 % more microbial activity than did the other treatments. Our results suggest that two diverse cropping systems CR4 and CR2 managed with reduced tillage could benefit soil health by improving soil respiration, N-mineralization, and the actions of the dehydrogenase and beta-glucosidase enzymes. As both the fertilizer and irrigation inputs in CR4 were lower than in the other rotations, it could be recommended as a sustainable ecological and feasible crop rotation model for processing the tomato production under the Mediterranean climatic conditions.Öğe Evaluation of phenotypic diversity and geographical variation of cultivated (Eruca sativa L.) and wild (Diplotaxis tenuifolia L.) rocket plant(Cambridge Univ Press, 2011) Bozokalfa, M. Kadri; Esiyok, Dursun; Ilbi, Hulya; Kavak, Suleyman; Asciogul, Tansel KaygisizRocket (Eruca spp. and Diplotaxis spp.) is widely cultivated as a green vegetable in Mediterranean countries, Europe, United States and Brazil, but few rocket cultivars are available and limited variety selection has taken place. Plant genetic resources and germplasm are fundamental sources for plant breeding, and the assessment of the genetic diversity among germplasm accessions is useful to facilitate the more efficient use of plant genetic resources. The objective of this study was to characterize phenotypic diversity and relationships among genotypes of Eruca and Diplotaxis originating from 11 countries across three regions (Europe, Africa and Asia). Principal component analyses explained over 85% of total variation for 51 qualitative and quantitative agromorphological traits. Cluster analyses divided the accessions into five major clusters according to plant traits, siliqua properties and geographical origin of genotype with a few exceptions. These findings indicate a number of useful traits in the gene pool and a wide range of phenotypic variation that provides a good source of diversity for use in modern Eruca breeding programmes.Öğe GENETIC VARIABILITY AND ASSOCIATION PATTERN AMONG QUANTITATIVE NUTRITIONAL TRAITS IN SWISS CHARD (Beta vulgaris subsp L. var. cicla) ACCESSIONS AND ITS IMPLICATION FOR BREEDING(Serbian Genetics Soc, 2014) Bozokalfa, M. Kadri; Yagmur, Bulent; Esiyok, Dursun; Asciogul, Tansel KaygisizIn addition to improving agronomic traits, enriched cultivar such as nutritional elements and health promoting compounds are new demands for today's and the future's perspectives of crop breeding. In this respect, among leafy vegetables Swiss chard is a good source of nutritional elements and supplies large amounts of health promoting compounds. The existing knowledge of genetic variability for mineral composition both at the phenotype and genotype level, heritability of characters and also relationships among investigated minerals is fundamental for variety selection in Swiss chard. This also applies for the assurance of desirable agronomic traits with optimum mineral concentrations. This research analysis of variance indicated highly significant differences among Swiss chard accessions for all investigated mineral concentrations and the accessions display higher phenotype coefficient variation than genotype coefficient variation for all traits. The results revealed that phosphorus, magnesium, sodium, iron, copper, zinc, manganese, nitrate and nitrite exhibited high genetic advance accompanied with high heritability (>60%). The remaining mineral content demonstrated high heritability with moderate genetic advance. Genotype correlations were higher than the phenotype correlation for significant mineral concentrations. Genotype and phenotype correlations followed similar trends in all significant cases indicating the high heritable nature of the characters and the results showed that Swiss chard accessions should allow for the selection of individuals for enriched mineral concentration in edible parts of the plant.Öğe Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)(Academic Press Inc Elsevier Science, 2020) Erdogmus, Semih; Ates, Duygu; Nemli, Seda; Yagmur, Bulent; Asciogul, Tansel Kaygisiz; Ozkuru, Esin; Tanyolac, Muhammed BahattinSNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg(-1) with an average of 1,280.9 mg kg(-1) and the Mn concentration ranged from 4.87 to 27.54 mg kg(-1) with a mean of 11.76 mg kg(-1). A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of Delta K was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. in 2016, six SNPs (on Pv1-4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1-4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. in Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively.Öğe Molecular cytogenetic characterization of common bean (Phaseolus vulgaris L.) accessions(Tubitak Scientific & Technical Research Council Turkey, 2020) Tuna, Gulsemin Savas; Yucel, Gulru; Asciogul, Tansel Kaygisiz; Ates, Duygu; Esiyok, Dursun; Tanyolac, Muhammed Bahattin; Tuna, MetinWith an annual global production of approximately 25 million tons, the common bean (Phaseolus vulgaris L), a member of the genus Phaseolus, is one of the major protein sources used as food for humans. in this study, it was aimed to investigate the genome size of the common bean genetic resource collection (154 common bean accessions) in Turkey by flow cytometry (FCM) and determine whether geographical variables affected the genome size. in addition, the number and distribution of 5S and 45S ribosomal DNA loci were designated by performing a fluorescence in situ hybridization (FISH) analysis in some of the accessions. The FCM analyses revealed that the mean nuclear DNA content of the accessions varied from 1.28 pg2C-1 to 1.55 pg2G1 (mean 1.35 pg2C-1), and the differences between these accessions were statistically significant (P < 0.01). Intraspecific variation in the genome size was determined, and a positive correlation was found between the altitude and genome size. However, latitude and longitude did not have any statistically significant effect on the genome size. in the principal coordinate analysis, the accessions were divided into 3groups. Based on the results of the FISH analysis performed on 5 different accessions with varying genome sizes, using 5S and 45S rDNA genes as probes, the number of 5S rDNA loci was 4 in the common bean and stable among the common bean accessions, while the number of 45S rDNA loci was highly polymorphic, varying between 6 and 16. Consequently, it was determined in the present study that the genetic resource collection of common bean had a wide variation in terms of genome size and genome organization.Öğe VARIABILITY, HERITABILITY AND ASSOCIATION ANALYSIS IN PLANT TRAITS OF SWISS CHARD (Beta vulgaris subsp cicla)(Serbian Genetics Soc, 2011) Esiyok, Dursun; Bozokalfa, M. Kadri; Asciogul, Tansel KaygisizEsiyok D., M. Kadri Bozokalfa and T. Kaygisiz Asciogul (2011): Variability, heritability and association analysis in plant traits of swiss chard (Beta vulgaris subsp. cicla) - Genetika, Vol 43, No. 2, 239-252. Plant breeders mainly interested in improvement agronomic properties of desirable trait accompanied with genetic architecture of major characters and their interrelationship. Genetic variability and character association are prime importance and provide essential contribution for successful breeding programme. In the present research genetic variability, heritability, phenotypic and genotypic correlations of several agronomic characters were studied in fifty-four swiss chard accessions and cultivars. Analysis of variance observed highly significant variations among accessions, and phenotypic coefficient of variation (PCV) was higher magnitude of genotypic coefficient of variation (GCV) for all agronomic characters. The lamina length, lamina width, petiole thickness, petiole width, lightness, chroma and leaf dry matter observed high magnitude broad sense heritable characters accompanied with high genetic advance. Genotypic correlation coefficient showed higher than phenotypic correlation coefficient which could be explained by low environmental effect on investigated agronomic traits. Positive correlation was revealed between petiole length, lamina length, lamina width, petiole thickness and petiole width which comprise total yield in swiss chard.
