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Morphological, agronomic, and quality properties of the two developed populations of alfalfa (Medicago sativa L.) under non-irrigated conditions of semiarid regions
(Soc Field Crop Sci, 2023) Ünal, Sabahaddin; Efe, Berna; Mutlu, Ziya; Işık, Şaban; Mintaş, Hacer; Oral, Hülya Hanoğlu
Alfalfa is the most important forage crop in Turkey, but no alfalfa cultivar has been developed for non-irrigated conditions in the semiarid regions of Turkey. Hence, new cultivars are needed for using in rangeland improvement, artificial pasture establishment, and hay production. The two populations (L-533, and L-1739) were compared with the three control cultivars of alfalfa (Bilensoy-80, Savas and Kayseri) in two various regions of Turkey during two years. The general results showed that there were significant differences in the plant height, but no differences in stem diameter, and stem numbers among the studied genotypes. According to combined analysis results, the L-533 and Kayseri had the highest green and hay yields, but the Savas cultivar had the lowest. Moreover, as compared to the Bilensoy-80 cultivar, the L-533 and L-1739 populations produced higher green forage yields of 22.27 and 11.57%, respectively. Also, the same increase in hay yield was 18.30% and 10.13%, respectively. Excluding crude protein contents, there were statistical differences between genotypes for the acid detergent fiber, neutral detergent fiber, and digestible dry matter yield. Moreover, higher crude protein content and digestible dry matter yield were obtained from the L-533 and L-1739, but the L-533 had also the lowest neutral detergent fiber content relative to the other population, and cultivars. The results of the current study have demonstrated that the L-533, and L-1739 had high adaptation capability, yields, and quality performance under dryland conditions of a semi-arid region and could be used as commercial cultivars.
Investigation of some basil genotypes in terms of their effect on bacterial communication system, and antimicrobial activity
(Academic Press Ltd- Elsevier Science Ltd, 2023) Yaldız, Gülsüm; Çamlıca, Mahmut; Erdönmez, Demet
The exponential growth of multiresistant bacterial strains creates the need to explore new or combined strategies to combat bacterial resistance. Medicinal plant-derived compounds against pathogenic bacteria may provide new, simple approaches to developing more environmentally friendly antimicrobial agents. Many researchers focus on exploring novel or combined strategies for combating bacterial resistance. Aromatic plants containing essential oils, such as basil, are often used as therapeutic agents in the pharmaceutical industry. Recent research has shown that basil is effective against certain harmful food phytopathogenic bacteria and has antimicrobial and anti-quorum sensing properties, which were investigated in this study. Our results have shown that the essential oil and ethanol extract of basil exhibits both antibacterial activity and anti-quorum sensing activity against some Gram-negative and Gram-positive bacterial species. It has also been found to have antifungal effects on C. albicans. Among the tested microorganisms, the genotypes of PI 531396, PI 296390, PI 414199, PI 253157, PI 296391, PI 652071, midnight, and Dino cultivars have been found to be more effective than other genotypes. The highest effect on quorum sensing system was found in Moonlight and Dino cultivars, PI 296391, PI 414199, PI 652070, PI 172997 and PI 190100 genotypes. Dendrogram analysis has shown that there is a relationship between different genotypes depending on microorganisms and anti-quorum sensing activity. Ames 29184, PI 207498, and PI 379412 genotypes were in the same group. Biplot analyses were performed to determine the relationship between the studied properties, and the results showed that more than 47% of the total variation was in all forms.
Genome-wide identification and expression analysis of MTP (Metal Ion Transport Proteins) genes in the common bean
(MDPI, 2023) Yılmaz, Hilal; Özer, Göksel; Baloch, Faheem Shehzad; Çiftçi, Vahdettin; Chung, Yong Suk; Sun, Hyeon-Jin
MTP/CDF carriers, called metal ion transport proteins, act as substrates for the transmission of micronutrients such as iron (Fe), zinc (Zn), and manganese (Mn) to membrane carriers in plants. In this study, genome-wide analysis of the MTP gene family in the common bean genome, expression analysis of the PvMTP4, PvMTP5, and PvMTP12 genes after Fe and Zn treatments, and the effects of Fe and Zn applications on iron and zinc content were investigated. This study used common bean genotypes assumed to have high or low Fe and Zn accumulation ability. PvMTP genes were defined as containing conserved catalytic domains with molecular weights and protein lengths ranging from 41.35 to 91.05 kDa and from 369 to 813 amino acids (aa), respectively. As a result of the phylogenetic analysis, three main clusters containing seven subgroups were formed. In this study, the first characterization of the MTP gene family of beans was performed, and the responses of three different PvMTP genes in the Zn-CDF group to Fe and Zn applications were revealed. The obtained findings are thought to constitute pioneering resources for future research on common bean biofortification studies, plant breeding related to Fe and Zn, and the functional characterization of the MTP gene family.
Assessing the effect of various doses of organic manures on herbage yield, essential oil, and compositions of sage grown under climate chamber and field conditions
(SpringerNature, 2023) Yaldız, Gülsüm; Çamlıca, Mahmut
Considering the importance of sage and the affirmative effects of organic sourced fertilizers on plant health and agronomic attributes, we designed to compare the effects of chemical and organic fertilizers on some quantitative and qualitative traits of sage grown under field conditions and climate chamber. This study was conducted to determine the effect of organic manures on sage quality to find the better sustainable fertilization practice for sage cultivation under pot-based experiment and field conditions. In this context, three different organic manures as sheep (SM) (5, 7.5, 10, 12.5 t ha(-1)), chicken (CM) (5, 7.5, 10, 12.5 t ha(-1)), and vermicompost (VM) (0.5, 1, 1.5, 2 t ha(-1)) with a control (no manure) and conventional fertilizer (0.15 t ha(-1) ammonium sulfate (AS) and 0.12 t ha(-1) diammonium phosphate (DAP)) were used in both experiments. Regarding the parameters considered for analysis based on the two-cuttings, we have estimated some agronomic attributes including plant height, branch number, fresh weight, and dry weight, as well as essential oil yield and compounds in sage seedlings. Accordingly, we have observed that the 1st cutting was superior in essential oil (EO) amount (0.90-2.08%), and also the 1st cutting had a high fresh and dry herb weight (61.62-226.44 and 29.78-99.67 g plant(-1)) under field condition. However, the 1st cutting was superior in EO amount (0.41-1.87%), and the 2nd cutting had also a high fresh and dry herb weight (4.94-16.78 and 1.23-3.58 g plant(-1)) in pot experiments. In addition, manool (ranging from 5.24 to 40.61%) was identified as the predominant compound whereas & alpha;-thujone and camphor were the other main compounds in both experimental conditions. Highest total fresh and dry weight were obtained from plants grown with IOF, VM3 (1.5 t ha(-1)), and VM4 (2 t ha(-1)) in pot experiments, while CM4 (12.5 t ha(-1)) application yielded the highest total fresh and dry weight under field conditions. In addition, sage plants treated with SM at a rate of 7.5 t ha(-1)and 12.5 t ha(-1) accumulated the higher content of essential oil under field condition. On the other hand, CM2 (7.5 t ha(-1)) and CM3 (10 t ha(-1)) treatments increased essential oil content in pot experiments. Also, the highest content of manool, a major compound, was observed at SM and VM applications in pot and under field conditions. Correlation and PCA analysis showed that field experiment conditions had higher correlation compared to pot experiment. The present study clearly indicated that chemical fertilizer could be replaced by organic fertilizers due to the higher positive impacts on herb and essential oil yield.
Kinetic approach to assess germination and growth parameters in 'Azkan' chickpea (Cicer arietinum L.) seeds during postharvest storage
(Pergamon-Elsevier Science Ltd, 2023) Kibar, Hakan; Soydemir, Hakkı Ekrem; Yeken, Mehmet Zahit; Çiftçi, Vahdettin
This research aimed to investigate the impact of varying storage temperature (5-, 10-, 15-and 20 degrees C) and storage duration (0-, 60-, 120-, 180-, 240-, 300-, 360-, 420-, 480-and 540-days) on moisture contents, germination parameters (germination rate, mean germination time, germination speed, seed vigor index, germination energy and electrical conductivity) and growth parameters (shoot length, root length, shoot fresh weight, shoot dry weight, root fresh weight and root dry weight) of chickpea (Cicer arietinum L.) seeds. In addition, it is aimed to determine the optimum storage temperature by applying kinetic model and multivariate analysis to these pa-rameters. During germination, the tested parameters presented differential sensitivity to both storage tempera-ture and duration. Seeds at a temperature of 20 degrees C were more affected than at 5, 10 and 15 degrees C. The storage at 20 degrees C reduced germination and growth parameters. It also caused an increase in electrical conductivity values, which decreased the viability of the seed and in the germination rate. The zero-order kinetic model was determined as the most suitable model for germination and growth parameters, and half-life and activation energy were determined accordingly. Based on the results obtained from the zero-order kinetic model, it can be suggested that the optimal storage temperature for maintaining seed quality is 5 and 10 degrees C.
Do vermicompost applications ımprove growth performance, pharmaceutically ımportant alkaloids, phenolic content, free radical scavenging potency and defense enzyme activities in summer snowflake (Leucojum aestivum L.)?
(Wiley-VCH Verlag GMBH, 2023) Çimen, Ayça; Baba, Yavuz; Yıldırım, Arzu Birinci; Türker, Arzu Uçar
Leucojum aestivum L. contains galanthamine and lycorine, which are two pharmaceutically valuable alkaloids. Vermicompost (VC), an organic waste product created by earthworms enhances soil quality and can improve the medicinal quality of the plant that is crucial to the pharmaceutical industry. The aim of this study was to determine the effects of four different VC concentrations (5 %, 10 %, 25 %, and 50 %) on L. aestivum growth parameters, alkaloid levels (galanthamine and lycorine), total phenol-flavonoid content, free radical scavenging potential, and defense enzyme activities (SOD and CAT) compared to control (no VC). The width, length, and fresh weight of the leaves were improved by 10 % VC treatment. The highest total phenolic content was found in the bulbs and leaves treated with 50 % VC. HPLC-DAD analysis of alkaloids showed that 10 % and 50 % VC treatments contained the most galanthamine in the bulb and leaf extracts, respectively. The application of 25 % VC was the most efficient in terms of lycorine content in both extracts. CAT activity was elevated at 10 %, 25 %, and 50 % VC. Based on the growth performance and galanthamine content of the bulbs and leaves, it can be concluded that a 10 % VC application was the most effective in the cultivation of L. aestivum.
Microwave-mediated approach to highly substituted nitropyrimidines via double Mannich reactions and their biological propertie
(Pergamon-Elsevier Science Ltd, 2022) Yıldırım, Muhammet; Yıldırım, Arzu; Gülbenek, Cansu
In the current study, new polysubstituted nitropyridimines were efficiently synthesized via double Mannich cyclizations of diaryl substituted b-nitroenamines with formaldehyde and aniline derivatives under microwave irradiation for 30-40 min. Furthermore, an antioxidant study showed that some of the nitropyridimines have moderate to low scavenging activity against DPPH radical. Also, in a preliminary antibacterial activity test of selected products, only one product exhibited moderate antibacterial effect against S.Epidermidis bacteria. (c) 2022 Elsevier Ltd. All rights reserved.
Long-term storage affects on the phenolic, mineral, color and cooking traits of chickpea seed
(Pergamon-Elsevier Science Ltd, 2023) Yeken, Mehmet Zahit; Soydemir, Hakkı Ekrem; Kibar, Hakan; Çiftçi, Vahdettin
This study was carried out to investigate the changes in some phenolic, mineral, color and cooking traits of chickpea seeds stored at different temperatures (5, 10, 15 and 20 degrees C) and duration (0-540 days). Significant variations in the investigated traits were found statistically before and after storage. The investigation revealed that gallic acid, protocatechuic acid, syringic acid, p-coumaric acid, chlorogenic acid, ferulic acid, quercetin, protein, phosphorus, magnesium, calcium, iron, zinc, manganese, and copper concentrations reduced at the end of the storage. Significant fluctuations in seed moisture content were observed depending on storage temperature and duration. Storage duration affected all color parameters except L* value, but storage interaction only influenced the a* value. According to correlation analysis, cooking time significantly correlated with hydration capacity and hydration index increased at the end of the storage. The eigenvalues of the first three principal components explained 80% and 75.1% of cumulative variances of mineral composition and cooking traits, respectively. In the biplot analysis, the Ca, Zn, Cu and Mg vectors revealed a high positive correlation with each other. The results of this study clearly revealed that 5 or 10 degrees C low storage temperature and 300-day storage period were the most suitable to maintain the quality of chickpea seeds. These findings could assist in providing information for the seed industry in maintaining nutritional composition for indication of storability and quality of chickpea seed, which in turn benefit the postharvest decisions for storage, distribution, and marketing.
Influence of EMS applications on fatty acids composition in safflower
(Academic Publication Council, 2023) Subaşı, İlhan; Başalma, Dilek; Arslan, Yusuf; Eryiğit, Tamer
Safflower is a valuable oil plant with 13-46% seed oil content rich in fatty acids, especially linoleic acid. In latest years, the safflower varieties with excessive oleic acid content have been started to be grown due to their high storage stability and suitability for frying. The research aimed to determine the influence of Ethyl Methane Sulfonate (EMS), which is the most commonly used chemical mutagen in experimental genetics, on the fatty acids' composition of safflower oil. In this study, seven different EMS rates were applied to 20 seeds harvested in August. As a result of the study, the primary fatty acids of the oil of the control plot plants were identified as 73% linoleic, 12% oleic, 5.8% palmitic, and 2.2% stearic acid. Compared to the control, the highest reduction among fatty acids was observed as 8.40% in oleic acid with 2 h of 0.64% EMS treatment. However, there were increases in oleic acid, stearic acid, and linoleic acid contents in some applications. In addition, lauric acid, which was not detected in the control treatments, was detected in most of the other applications, where the highest lauric acid ratio of 14.945% was determined under EMS treatment of 0.64% for 2 h. The results showed that the influence of EMS mutagenesis on safflower fatty acid composition might be affected differently by different mutation levels. Therefore, there is a need to evaluate the impact of EMS mutagenesis on fatty acids across successive generations to confirm the results of this study.
Pathogenesis-related gene (PvPR1 and PvPR2) expression involved in Meloidogyne incognita parasitism and resistance reactions of common bean genotypes in host-nematode interactions
(Canadian Science Publishing, 2022) Bozbuğa, Refik; Çiftçi, Vahdettin; Yeken, Mehmet Zahit; İmren, Mustafa
Pathogenesis-related (PR) genes are useful molecular markers, and gene expressions are activated in the reaction of plant -parasitic nematodes. Determining the PR gene expression and the resistance reaction of Phaseolus vulgaris L. genotypes against root-knot nematode are valuable for understanding plant-;nematode interactions. However, resistance reactions of P. vulgaris genotypes and the gene expression of host-nematode interactions are not fully understood. Therefore, this study aimed to determine the expression of PR genes during the infection of Meloidogyne incognita on resistant and susceptible bean varieties at 1, 3, 5, and 7 days postinfection (dpi). The results revealed that one genotype gave a reaction as "immune", and numerous genotypes were susceptible. The expression of PvPR1 and PvPR2 genes reached the highest peak at 1 dpi in nematode-infected immune plants, and the expression of PvPR1 reached 5 dpi in susceptible plants. In conclusion, PR genes involved in nematode resistance and parasitism and the immune common bean genotype have great potential in breeding programs and under-standing the exact location of resistance on the gene map would be advantageous as future work.
Mixed consortium of microbial inoculants improves yield and essential oil profile of coriander
(Society of Bioscience Bioengineering Japan, 2022) Yılmaz, Abdurrahim
Coriander (Coriandrum sativum L.), one of the oldest spice plants globally, has wide usage, mainly owing to its essential oil content. This study investigated the effects of rhizobacteria, mycorrhizae, and their combination on the yield and essential oil profile of coriander. The treatments resulted in statistically higher yield properties and essential oil values than the control. The effects of the microorganism treatments on the yield characteristics were not statisti-cally different. However, the treatments significantly affected the essential oil content and yield. While the arbuscular mycorrhizal fungi and combined application of the microorganisms were statistically equal, arbuscular mycorrhizal fungi had a higher value in essential oil content and yield by 0.75% and 11.8 L haL1, respectively. The combined appli-cation resulted in higher values of linalool (9.47%) and g-terpinene (6.75%), the components with the highest rate in the essential oil composition. The principal component analysis highlighted the importance of the combined application on the crucial components. In the light of the results, beneficial microorganism treatments were considered significant for yield and essential oil enhancement. Therefore, the wide use of these treatments will highly contribute to coriander cultivation.(c) 2022, The Society for Biotechnology, Japan. All rights reserved.
Essential oils content, composition and antioxidant activity of selected basil (Ocimum basilicum L.) genotypes
(Elseiver, 2022) Yaldız, Gülsüm; Çamlıca, Mahmut
In this study, 20 basil genotypes-3 cultivars, 1 local and 16 from the United States Department of Agriculture (USDA) were cultivated under the same conditions to determine some phenotypic properties by using the International Union for the Protection of New Varieties of Plants (UPOV) criteria; isolated essential oils and ethanol extracts were subjected to detailed chemical analyses and their biological activities were tested. According to the analysis of the essential oils, most of the examined genotypes belong to the estragole-rich chemotype. In addition, the PI 197,442, PI 211,586, PI 531,396, PI 652,070, PI 652,071, PI 414,197, Ames29184 genotypes and dino, moonlight cultivars belong to the estragol/linalool chemotype. Also, the Bolu genotype belongs to the citral chemotype, while the PI 296,391 and PI 190,100 genotypes belong to the estragole/citral chemotype. Among the 20 basil genotypes tested, the PI 174,284, PI 190,100, PI 531,396 and PI 197,442 genotypes had the highest antioxidant activity compared with the other genotypes and cultivars. The PI 652,071, PI 190,100, PI 197,442 genotypes and dino cultivar were found superior with respect to phe-nolic and flavonoid amounts as compared with other genotypes and cultivars. Variation in the main compo-nents of essential oils of basil genotypes grown under the same ecological conditions was observed. Therefore, the results we obtained are important for the selection of components with the desired properties. Also, dendrogram, correlation and biplot analyses were conducted to obtain genetic differences. Generally, genotypes and cultivars are divided into two main and two subgroups. Group B included more than 50% gen-otypes or cultivars. Correlation and biplot analyses showed relationship, and the examined properties were found related with similar. Some UPOV criteria, such as UP-1, UP-3, UP-6 and UP-7, were found similar in all genotypes and cultivars. However, other UPOV criteria showed differences among the basil genotypes and cultivars. Therefore, the dendrogram analyses were carried out to determine the relationship among the gen-otypes and cultivars depending on UPOV criteria. The dendrogram analyses divided into two main groups and two subgroups. UP-4 and UP-14 properties were the main factors for the characterization of the groups. In addition, we found antioxidant activity results showing that most of the examined genotypes are a good source of natural antioxidants with potential application in the food and pharmaceutical industries.
Self-assembly, surface, antibacterial, and solubilization properties of phenylglycine type amino acid-based cationic surfactants
(Elseiver, 2022) Olutaş, Elif Berna; Kartal, Necla Büşra; Yıldırım, Arzu Birinci
Here, synthesis and characterization of amino acid-based chiral cationic surfactants containing phenyl-glycine moiety, L-phenylglycine hydrochloride octyl ester (L-PgC8E), and L-phenylglycine hydrochloride decyl ester (L-PgC10E), and their physicochemical properties such as the micellization, surface, and volu-metric parameters have been reported. In addition, the structural analyses of the aggregates of these esters were also performed by dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques. It was found that the presence of a phenyl ring in the head group promoted the micelle formation leading to a smaller critical micelle concentration (CMC) value and enhancing the adsorption efficiency with an increased hydrocarbon chain. Besides, the antibacterial activities of the synthesized surfactants have been explored against three Gram-positive (G+) and seven Gram-negative (G-) bacteria below and above their CMC values by measuring the zone of inhibition diameter. The results showed that L-PgC8E was more active than L-PgC10E against all bacteria; this was explained by the formation of smal-ler and less stable aggregates that could interact efficiently with the bacterial membrane. Furthermore, the solubilization power (SP) of both surfactants for Methyl Red (MR) was determined, and it was found that L-PgC10E with a longer hydrocarbon chain and forming a large hydrophobic area by its large aggre-gates showed a more efficient solubilizing power.(c) 2022 Elsevier B.V. All rights reserved.
Genome-wide identification and expression analysis of DGK (Diacylglycerol Kinase) genes in common bean
(Springer, 2023) Yeken, Mehmet Zahit; Özer, Göksel; Çiftçi, Vahdettin
Diacylglycerol kinases (DGKs) are a family of enzymes that play an important functional role in various stress responses in plants by converting diacylglycerol to phosphatidic acid. In this study, genome-wide identification of DGK genes, expression analysis under non-stress in various developmental stages and under salt stress in different tissues of common bean were performed for the first time. The 6 DGK gene family members (PvDGK1, 2, 3, 5a, 5b, and 6) having conserved catalytic domains were identified by an exploration of common bean genome via multiple online databases. The protein lengths and molecular weights of PvDGKs were found between 423 and 727 amino acids (aa) and ranging from 47.31 to 81.09 kDa, respectively. Phylogenetic analysis revealed that PvDGK genes grouped into three clusters as described for known plant DGK families; cluster I (PvDGK1, 2), cluster II (PvDGK3) and cluster III (PvDGK5a, 5b, 6) genes, respectively. Quantitative real-time PCR analysis revealed that all PvDGK genes indicated divergent expression patterns in all tissues at different developmental stages under non-stress condition. Furthermore, PvDGK genes were also significantly upregulated in response to salt stress in root and leaf tissues of common bean cultivars at different time points. These results indicated the possible roles of PvDGK genes in developmental stages and salt stress in common bean. The findings herein will guide further investigations on the comprehension and functional characterization of the PvDGKs and the breeding studies to be carried out related to stress in the common bean near future.
Seasonal variation in alkaloid content, phenolic constituent and biological activities of some Leucojum aestivum L. populations in Turkey
(Elseiver, 2022) Demir, Sina Cafer; Yıldırım, Arzu Birinci; Türker, Arzu Uçar; Eker, İsmail
Summer snowflake (Leucojum aestivum L.), a bulbous plant in the Amaryllidaceae family, is a well-known source of two pharmaceutically significant alkaloids: galanthamine that is used to treat Alzheimer's disease and lycorine that has potent antiviral properties, especially against SARS-CoV-2 (COVID-19). Environmental factors such as temperature, light, soil, and so on, as well as harvest time and plant parameters such as genotype and plant parts, all have a quantitative and qualitative impact on secondary metabolite production such as alkaloids and phenols. This study hypothesized that different populations (genotype), growing seasons, environmental temperature and soil type can change the alkaloid (galanthamine and lycorine) and phenolic content, and biological activities (antioxidant and antibacterial) in the bulbs and leaves of this plant. Summer snowflakes were collected from 6 different locations in Turkey (Golcuk-Bolu, Yenicaga-Bolu, KaynarcaSakarya, Delmece-Yalova, Uluabat-Bursa and Terkos-Istanbul) at 3 different growing periods (vegetative, reproductive and ripening). Methanol extract of the plant parts were quantitatively analyzed for their alkaloid content with HPLC-DAD, and for their antioxidant capacity and total phenol-flavonoid content with spectrophotometric determination. Besides, antibacterial activity was investigated with disc diffusion assay. The locations of Delmece-Yalova and Golcuk-Bolu provided galanthamine-rich population and optimal growing conditions for the cultivation of this species. Generally, vegetative and ripening periods were the most effective in alkaloid production. But, phenolic content accumulation was unrelated to the growing seasons. Higher temperatures in the bulbs and lower temperatures in the leaves supported the galanthamine and lycorine production. It was noticeable that alkaloid and total phenol accumulation in the bulbs showed similar tendency in that the highest temperature caused the highest alkaloid levels and phenolic content. Also, neutral to slightly alkaline soils with high organic matter content were effective in enhancing the alkaloid content and phenolic constituents. Moderate antioxidant activity and no antibacterial potential were observed with L. aestivum. The results found can be a guide for revealing the best population and environmental conditions for the cultivation of this plant, as well as showing the correct harvest time for bulbs and leaves to get the best galantamine and lycorine content. (C) 2022 SAAB. Published by Elsevier B.V. All rights reserved.
Breeding improvement of fennel genotypes of different origins (Foeniculum vulgare L.) using morphological and yield parameters
(Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, 2022) Yaldız, Gülsüm; Çamlıca, Mahmut
G. Yaldiz, and M. Camlica. 2022. Breeding improvement of fennel genotypes of different origins (Foeniculum vulgare L.) using morphological and yield parameters. Int. J. Agric. Nat. Resour. 97-111. Fennel (Foeniculum vulgare L.) is a reputed spice plant and is used as an industrial medicinal plant due to its pharmaceutical and food applications, exhibiting a wide array of genetic variations depending on morphological and yield properties. Along with the current study, thirty-two different fennel genotypes and five local genotypes from Turkey were used to determine the morphological and yield properties in 2017 and 2018. A wide range of variation in plant height (39.22-129.60 cm), 1000 fruit yield (1.92-7.70 g), and fruit yield (0.12-8.68 g) was observed. As deduced from previous reports and from the current findings of the study, those relevant parameters could be considered for breeding purposes. To visualize or clarify the findings, a dendrogram was constructed to reveal the genetic variability regarding the morphological and yield properties of fennel genotypes. The dendrogram revealed that genotypes of different origins occurred in different groups, but local genotypes collected from Turkey occurred in the same group and subgroup. Additionally, correlation analysis was carried out to reveal the relationships between the relevant agronomic parameters. Of those correlation coefficients, a high correlation coefficient was noted between the number of fruits and fruit yield (r=0.849). Overall, the findings of the study revealed notable genetic variation related to fruit yield and other relevant agronomic traits for fennel genotypes, suggesting that this remarkable variation might be used for selecting superior genotypes in breeding programs. Of the genotypes analyzed, Ames30289 was the best genotype due to the highest fruit yield according to two successive years. Consequently, the findings can be considered useful information for fennel breeders, researchers and farmers in Turkey or other countries.
Assessment of genetic diversity and population structure in local alfalfa genotypes using iPBS molecular markers
(Springer, 2023) Eren, Barış; Keskin, Bilal; Demirel, Fatih; Demirel, Serap; Türkoğlu, Aras; Yılmaz, Abdurrahim
iPBS retrotransposon markers, in other words, inter-primer binding site markers based on retrotransposon, have been helpful for the determination of genetic diversity in several plants. The study was evaluated using 10 iPBS molecular markers on the level of genetic diversity and genetic structure of alfalfa genotypes. A total of 280 alleles in 50 alfalfa genotypes (48 local genotypes and 2 commercial varieties) were obtained by 267 polymorphic markers with an average of 28 per locus, ranging from 9 to 41 alleles. The rate of polymorphism of the markers ranged from 86.36 to 100% with an average of 93.71%. The average number of polymorphic bands per marker was detected as 26.7. The mean PIC value and Dice's similarity index were calculated as 0.14 and 0.50 respectively. The results of UPGMA analysis, principal coordinate analysis (PCoA), and STRUCTURE demonstrated that the 50 alfalfa genotypes could be classified into 4 subpopulations, namely the Q1, Q2, Q3, and Q4. The Nei's genetic distances ranged from 0.0121 to 0.0359. iPBS markers and alfalfa genotypes used in this study may be used in studies of alfalfa breeding and germplasm conservation.
Innovation in the breeding of common bean through a combined approach of in vitro regeneration and machine learning algorithms
(Frontiers Media SA, 2022) Aasim, Muhammad; Katırcı, Ramazan; Baloch, Faheem Shehzad; Mustafa, Zemran; Bakhsh, Allah; Çiftçi, Vahdettin
Common bean is considered a recalcitrant crop for in vitro regeneration and needs a repeatable and efficient in vitro regeneration protocol for its improvement through biotechnological approaches. In this study, the establishment of efficient and reproducible in vitro regeneration followed by predicting and optimizing through machine learning (ML) models, such as artificial neural network algorithms, was performed. Mature embryos of common bean were pretreated with 5, 10, and 20 mg/L benzylaminopurine (BAP) for 20 days followed by isolation of plumular apice for in vitro regeneration and cultured on a post-treatment medium containing 0.25, 0.50, 1.0, and 1.50 mg/L BAP for 8 weeks. Plumular apice explants pretreated with 20 mg/L BAP exerted a negative impact and resulted in minimum shoot regeneration frequency and shoot count, but produced longer shoots. All output variables (shoot regeneration frequency, shoot counts, and shoot length) increased significantly with the enhancement of BAP concentration in the post-treatment medium. Interaction of the pretreatment x post-treatment medium revealed the need for a specific combination for inducing a high shoot regeneration frequency. Higher shoot count and shoot length were achieved from the interaction of 5 mg/L BAP x 1.00 mg/L BAP followed by 10 mg/L BAP x 1.50 mg/L BAP and 20 mg/L BAP x 1.50 mg/L BAP. The evaluation of data through ML models revealed that R-2 values ranged from 0.32 to 0.58 (regeneration), 0.01 to 0.22 (shoot counts), and 0.18 to 0.48 (shoot length). On the other hand, the mean squared error values ranged from 0.0596 to 0.0965 for shoot regeneration, 0.0327 to 0.0412 for shoot count, and 0.0258 to 0.0404 for shoot length from all ML models. Among the utilized models, the multilayer perceptron model provided a better prediction and optimization for all output variables, compared to other models. The achieved results can be employed for the prediction and optimization of plant tissue culture protocols used for biotechnological approaches in a breeding program of common beans.
Magnesium- a forgotten element: Phenotypic variation and genome wide association study in Turkish common bean germplasm
(Frontiers Media SA, 2022) Baloch, Faheem Shehzad; Nadeem, Muhammad Azha; Sönmez, Ferit; Habyarimana, Ephrem; Mustafa, Zemran; Çiftçi, Vahdettin
Magnesium (Mg) is the fourth most abundant element in the human body and plays the role of cofactor for more than 300 enzymatic reactions. In plants, Mg is involved in various key physiological and biochemical processes like growth, development, photophosphorylation, chlorophyll formation, protein synthesis, and resistance to biotic and abiotic stresses. Keeping in view the importance of this element, the present investigation aimed to explore the Mg contents diversity in the seeds of Turkish common bean germplasm and to identify the genomic regions associated with this element. A total of 183 common bean accessions collected from 19 provinces of Turkey were used as plant material. Field experiments were conducted according to an augmented block design during 2018 in two provinces of Turkey, and six commercial cultivars were used as a control group. Analysis of variance depicted that Mg concentration among common bean accessions was statistically significant (p < 0.05) within each environment, however genotype x environment interaction was non-significant. A moderate level (0.60) of heritability was found in this study. Overall mean Mg contents for both environments varied from 0.33 for Nigde-Dermasyon to 1.52 mg kg(-1) for Nigde-Derinkuyu landraces, while gross mean Mg contents were 0.92 mg kg(-1). At the province level, landraces from Bolu were rich while the landraces from Bitlis were poor in seed Mg contents respectively. The cluster constellation plot divided the studied germplasm into two populations on the basis of their Mg contents. Marker-trait association was performed using a mixed linear model (Q + K) with a total of 7,900 DArTseq markers. A total of six markers present on various chromosomes (two at Pv01, and one marker at each chromosome i.e., Pv03, Pv07, Pv08, Pv11) showed statistically significant association for seed Mg contents. Among these identified markers, the DArT-3367607 marker present on chromosome Pv03 contributed to maximum phenotypic variation (7.5%). Additionally, this marker was found within a narrow region of previously reported markers. We are confident that the results of this study will contribute significantly to start common bean breeding activities using marker assisted selection regarding improved Mg contents.
Prediction of grain yield in wheat by CHAID and MARS algorithms analyses
(MDPI, 2023) Demirel, Fatih; Eren, Barış; Yılmaz, Abdurrahim; Türkoğlu, Aras; Haliloğlu, Kamil; Niedbala, Gniewko
Genetic information obtained from ancestral species of wheat and other registered wheat has brought about critical research, especially in wheat breeding, and shown great potential for the development of advanced breeding techniques. The purpose of this study was to determine correlations between some morphological traits of various wheat (Triticum spp.) species and to demonstrate the application of MARS and CHAID algorithms to wheat-derived data sets. Relationships among several morphological traits of wheat were investigated using a total of 26 different wheat genotypes. MARS and CHAID data mining methods were compared for grain yield prediction from different traits using cross-validation. In addition, an optimal CHAID tree structure with minimum RMSE was obtained and cross-validated with nine terminal nodes. Based on the smallest RMSE of the cross-validation, the eight-element MARS model was found to be the best model for grain yield prediction. The MARS algorithm proved superior to CHAID in grain yield prediction and accounted for 95.7% of the variation in grain yield among wheats. CHAID and MARS analyses on wheat grain yield were performed for the first time in this research. In this context, we showed how MARS and CHAID algorithms can help wheat breeders describe complex interaction effects more precisely. With the data mining methodology demonstrated in this study, breeders can predict which wheat traits are beneficial for increasing grain yield. The adaption of MARS and CHAID algorithms should benefit breeding research.

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