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- ArticleAçık Erişim2025Understanding genetic diversity and population structure in forage pea (Pisum sativum var. arvense L.) using inter-primer binding site (iPBS) retrotransposon marker
Işık, Muhammet İslam; Türkoğlu, Aras; Yaman, Mehmet; Haliloğlu, Kamil; Öztürk, Halil İbrahim; Erkol, Şerife; Tan, Mustafa; Bocianowski, Jan
Forage peas are widely utilized as a source of animal feed, and their fresh shoots, fruits, and pods exhibit considerable potential for human consumption. This study aimed to assess the genetic diversity and population structure of 61 Turkish forage pea genotypes using inter-primer binding site (iPBS) retrotransposon markers. A total of 37 highly polymorphic iPBS primers were employed, producing an average of 69 bands per primer and a cumulative total of 2529 bands. The average polymorphism information content (PIC) was determined to be 0.345. The results revealed significant genetic diversity within the germplasm, as indicated by diversity indices such as the average effective number of alleles (0.704) and a Shannon’s information index (0.299). Molecular analysis of variance (AMOVA) indicated that 74% of the total genetic variation occurred within populations. Population structure analysis identified four distinct subpopulations among the genotypes, with expected heterozygosity values ranging from 0.2404 in the fourth subpopulation to 0.3094 in the second subpopulation, with an overall average of 0.2702. This study represents the first comprehensive investigation of genetic diversity and population structure in forage pea germplasm using the iPBS retrotransposon marker system. The findings highlight the effectiveness of iPBS markers in genetic diversity research and underscore their potential for broader application in the characterization of diverse forage pea collections across different geographic regions.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2024Zinc Oxide Nanoparticles: An Influential Element in Alleviating Salt Stress in Quinoa (Chenopodium quinoa L. Cv Atlas)
Türkoğlu, Aras; Haliloğlu, Kamil; Ekinci, Melek; Turan, Metin; Yildirim, Ertan; Öztürk, Halil Ibrahim; Stansluos, Atom Atanasio Ladu; Nadaroğlu, Hayrunnisa; Piekutowska, Magdalena; Niedbała, Gniewko
Climate change has intensified abiotic stresses, notably salinity, detrimentally affecting crop yield. To counter these effects, nanomaterials have emerged as a promising tool to mitigate the adverse impacts on plant growth and development. Specifically, zinc oxide nanoparticles (ZnO-NPs) have demonstrated efficacy in facilitating a gradual release of zinc, thus enhancing its bioavailability to plants. With the goal of ensuring sustainable plant production, our aim was to examine how green-synthesized ZnO-NPs influence the seedling growth of quinoa (Chenopodium quinoa L. Cv Atlas) under conditions of salinity stress. To induce salt stress, solutions with three different NaCl concentrations (0, 100, and 200 mM) were prepared. Additionally, Zn and ZnO-NPs were administered at four different concentrations (0, 50, 100, and 200 ppm). In this study, plant height (cm), plant weight (g), plant diameter (mm), chlorophyll content (SPAD), K/Na value, Ca/Na value, antioxidant enzyme activities (SOD: EU g−1 leaf; CAT: EU g−1 leaf; POD: EU g−1 leaf), H2O2 (mmol kg−1), MDA (nmol g−1 DW), proline (µg g−1 FW), and sucrose (g L−1), content parameters were measured. XRD analysis confirmed the crystalline structure of ZnO nanoparticles with identified planes. Salinity stress significantly reduced plant metrics and altered ion ratios, while increasing oxidative stress indicators and osmolytes. Conversely, Zn and ZnO-NPs mitigated these effects, reducing oxidative damage and enhancing enzyme activities. This supports Zn’s role in limiting salinity uptake and improving physiological responses in quinoa seedlings, suggesting a promising strategy for enhancing crop resilience. Overall, this study underscores nanomaterials’ potential in sustainable agriculture and stress management.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2023Effects of mammalian sex hormones on in vitro organogenesis of common bean (Phaseolus vulgaris L.)
Haliloğlu, Kamil; Türkoğlu, Aras; Balpınar, Özge; Öztürk, Halil İbrahim; Özkan, Güller; Poczai, Peter
Beans are an important plant species and are one of the most consumed legumes in human nutrition, especially as a protein, vitamin, mineral, and fiber source. Common bean (Phaseolus vulgaris L.) is a plant that also has an important role in natural nitrogen fixation. Currently, in vitro regeneration and micropropagation applications are limited in relation to genetic factors in bean Accordingly, there is great need to optimize micropropagation and tissue culture methods of the bean plant. To date, the effect of mammalian sex hormones (MSH) on in vitro conditions in P. vulgaris L. is poorly understood. This study examined the effects of different types of explants (embryo, hypocotyl, plumule, and radicle), MSH type (progesterone, 17 β-estradiol, estrone, and testosterone), and MSH concentration (10−4, 10−6, 10−8 and 10−10 mmol L−1) on the responding explants induction rate (REI), viability of plantlets rate (VPR), shoot proliferation rate (SPR), root proliferation rate (RPR), and callus induction rate (CIR). The effects of mammalian sex hormones, concentrations, explant type, and their interactions were statistically significant (p ≤ 0.01) in all examined parameters. The best explants were embryo and plumule. Our results showed that the highest REI rate (100%) was recorded when 10−10 mmol L−1 of all MSH was applied to MS medium using the plumule explant. The highest VPR (100%) was obtained when 10−10 mmol L−1 of all MSH was applied to MS medium using the plumule explant. The highest root proliferation rates (77.5%) were recorded in MS medium supplemented with 10−8 mmol L−1 17β-estradiol using embryo explant. The highest percentage of shoot-forming explants (100%) generally was obtained from embryo and plumule cultured in the MS culture medium with low MSH concentration. In addition, the highest CIR (100%) was obtained from embryo and plumule explant cultured in MS medium containing 10−10 mmol L−1 of all MSH types. In conclusion, we observed that mammalian sex hormones may be used in bean in vitro culture.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2022iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkey
Haliloğlu, Kamil; Türkoğlu, Aras; Öztürk, Halil Ibrahim; Özkan, Güller; Elkoca, Erdal; Poczai, Peter
Beans are legumes that play extremely important roles in human nutrition, serving as good sources of protein, vitamins, minerals, and antioxidants. In this study, we tried to elucidate the genetic diversity and population structure of 40 Turkish bean (Phaseolus vulgaris L.) local varieties and 5 commercial cultivars collected from 8 different locations in Erzurum-Ispir by using inter-primary binding site (iPBS) retrotransposon markers. For molecular characterization, the 26 most polymorphic iPBS primers were used; 52 bands per primer and 1350 bands in total were recorded. The mean polymorphism information content was 0.331. Various diversity indices, such as the mean effective allele number (0.706), mean Shannon’s information index (0.546), and gene diversity (0.361) revealed the presence of sufficient genetic diversity in the germplasm examined. Molecular analysis of variance (AMOVA) revealed that 67% of variation in bean germplasm was due to differ-ences within populations. In addition, population structure analysis exposed all local and commercial bean varieties from five sub-populations. Expected heterozygosity values ranged between 0.1567 (the fourth sub-population) and 0.3210 (first sub-population), with an average value of 0.2103. In contrary, population differentiation measurement (Fst) was identified as 0.0062 for the first sub-population, 0.6372 for the fourth subpopulations. This is the first study to investigate the genetic diversity and population structure of bean germplasm in Erzurum-Ispir region using the iPBS-retrotransposon marker system. Overall, the current results showed that iPBS markers could be used consistently to elucidate the genetic diversity of local and commercial bean varieties and potentially be included in future studies examining diversity in a larger collection of local and commercial bean varieties from different regions.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2022The Effect of Mammalian Sex Hormones on Polymorphism and Genomic Instability in the Common Bean (Phaseolus vulgaris L.)
Türkoğlu, Aras; Haliloğlu, Kamil; Balpinar, Özge; Öztürk, Halil Ibrahim; Özkan, Güller; Poczai, Peter
Mammalian sex hormones are steroid-structured compounds that support the growth and development of plants at low concentrations. Since they affect the physiological processes in plants, it has been thought that mammalian sex hormones may cause modifications to plant genomes and epigenetics. This study aims to determine whether different mammalian sex hormones (17 β-estradiol, estrogen, progesterone, and testosterone) in several concentrations (0, 10−4, 10−6, and 10−8 mM) affect genetic or epigenetic levels in bean plants, using in vitro tissue cultures from plumule explants. We investigated levels of DNA damage, changes in DNA methylation and DNA stability in common bean exposed to mammalian sex hormones (MSH) using inter-primer binding site (iPBS) and Coupled Restriction Enzyme Digestion-iPBS (CRED-iPBS) assays, respectively. The highest rate of polymorphism in iPBS profiles was observed when 10−4 mM of estrogen (52.2%) hormone was administered. This finding indicates that genetic stability is reduced. In the CRED-iPBS profile, which reveals the methylation level associated with the DNA cytosine nucleotide, 10−4 mM of estrogen hormone exhibited the highest hypermethylation value. Polymorphism was observed in all hormone administrations compared to the control (without hormone), and it was determined that genomic stability was decreased at high concentrations. Taken together, the results indicate that 17 β-estradiol, estrogen, progesterone, and testosterone in bean plants affect genomic instability and cause epigenetic modifications, which is an important control mechanism in gene expression.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2022Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers
Özkan, Güller; Haliloğlu, Kamil; Türkoğlu, Aras; Özturk, Halil Ibrahim; Elkoca, Erdal; Poczai, Peter
Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei’s gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei’s genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.
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