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Öğe Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system(Cambridge Univ Press, 2018) Demirel, Ufuk; Tindas, IlKnur; Yavuz, Caner; Baloch, Faheem Shehzad; Caliskan, Mehmet EminHaving knowledge on genetic similarity and DNA profile of potato genotypes facilitates a breeder's decision for parent selection and provides accurate variety identification. Fingerprinting and identification of genetic similarity among 151 potato genotypes were achieved using an inter-primer-binding sites (iPBS) retrotransposon marker system. Our study is the first application of iPBS markers for fingerprinting and distinguishing large numbers of Solanum tuberosum genotypes. Initially, 16 potato genotypes were screened using 45 iPBS retrotransposon markers to identify polymorphisms. Seventeen of these primers were selected for fingerprinting the whole set of accessions due to strong, reproducible and polymorphic bands. The 17 iPBS primers produced 290 scorable bands of which 224 were polymorphic. The number of bands per primer ranged from 10 to 26 with an average of 17.1. The number of polymorphic bands per primer was between 6 and 21. The polymorphism percentage per primer ranged from 46.2 to 100.0% with an average of 77.2% per primer. The mean polymorphism information content (PIC) values of iPBS primers varied from 0.12 to 0.31 per primer. Genetic similarity based on Jaccard's coefficient of potato genotypes ranged from 0.61 to 0.93 with an average of 0.73. The data produced herein may be used for selection of appropriate parents and variety description in the future. The findings of the present study suggest that iPBS retrotransposons are powerful and easy DNA markers for fingerprinting the large samples of potato germplasm.Öğe Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.)(Springer Heidelberg, 2021) Yousaf, Muhammad Farhan; Demirel, Ufuk; Naeem, Muhammad; Caliskan, Mehmet EminTuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software WinRHIZO (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r(2) = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases StPP1), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production.Öğe Bazı Macar ileri patates hatlarının adaptasyon yetenekleri ile yüksek sıcaklığa toleranslarının belirlenmesi ve yüksek sıcaklığa toleranslı yeni patates ıslah hatlarının geliştirilmesi(2014) Çalışkan, Mehmet Emin; Çalışkan, Sevgi; Demirel, Ufuk; Polgar, Zsolt; Cernak, Istvan; Vaszıly, Zsolt; Karaat, Ege Fırat[Abstract Not Available]Öğe Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars(Springer Heidelberg, 2021) Gokce, Zahide Neslihan Ozturk; Aksoy, Emre; Bakhsh, Allah; Demirel, Ufuk; Caliskan, Sevgi; Caliskan, Mehmet EminMicroRNAs are small, non-coding RNAs that are responsible for regulation of gene expression during plant growth and development. Although there are many studies on miRNAs in other plants, little work has been done to understand the role of miRNAs in abiotic stress tolerance in potatoes. This study investigates changes in miRNA profiles of two different potato cultivars (tolerant, Unica and susceptible, Russet Burbank) in response to heat, drought and their combination. Transcriptomic studies revealed that miRNA profiles depend on the susceptibility and tolerance of the cultivar and also the stress conditions. Large number of miRNAs were expressed in Unica, whereas Russet Burbank indicated lesser number of changes in miRNA expression. Physiological and transcriptional results clearly supported that Unica cultivar is tolerant to combined drought and heat stress compared to Russet Burbank. Moreover, psRNATarget analysis predicted that major miRNAs identified were targeting genes playing important roles in response to drought and heat stress and their important roles in genetic and post-transcriptional regulation, root development, auxin responses and embryogenesis were also observed. This study focused on eight miRNAs (Novel_8, Novel_9, Novel_105, miR156d-3p, miR160a-5p, miR162a-3p, miR172b-3p and miR398a-5p) and their putative targets where results indicate that they may play a vital role at different post-transcriptional levels against drought and heat stresses. We suggest that miRNA overexpression in plants can lead to increased tolerance against abiotic stresses; furthermore, there should be more emphasis on the studies to investigate the role of miRNAs in combined abiotic stress in plants.Öğe Comparison of Aeroponics and Conventional Potato Mini Tuber Production Systems at Different Plant Densities(Springer, 2021) Caliskan, Mehmet Emin; Yavuz, Caner; Yagiz, Ayten Kubra; Demirel, Ufuk; Caliskan, SevgiMini tubers are the starting materials of a disease-free seed potato production scheme. Low multiplication rates as well as non-homogenous tuber size distribution are considered the main constraints of a conventional mini tuber production system. In recent years, an aeroponics production system has been developed to overcome the aforementioned problems. It has previously been observed that this system allows multiple harvests with an average yield of 20-50 mini tubers per plant. Several factors, such as cultivar, planting density, nutrient composition of the mist solution, spraying interval and duration and lighting also affect both tuber number and tuber size. However, less attention has been paid to the association of these factors with the aeroponics system. This paper highlights the importance of planting density effect on conventional and aeroponics system. The mini tuber production performances of three potato cultivars (Hermes, Marabel and Sante) were compared at four different planting densities (25, 50, 100 and 200 plants/m(2)) under both conventional and aeroponics systems in two production cycles. The number of tubers per plant increased with decreasing planting density, being highest at 25 plants/m(2)and lowest at 200 plants/m(2)for both cycles. Mean tuber number in the aeroponic system was 19.85 tubers per plant at 25 plants/m(2)and 13.20 tubers per plant at 200 plants/m(2). As the number of tubers per plant decreased, so did their size. As planting density increased, tuber yield per plant both in aeroponics and conventional system decreased, but in general, tuber yield per plant was higher in aeroponics than in the conventional system. In the 1st cycle, the number of tubers per m(2)for Hermes, Sante and Marabel was 290, 364 and 334, respectively, in the conventional system and 787, 1021 and 1168, respectively, in the aeroponics system. Similar numbers were recorded in the 2nd cycle. The average tuber weight was higher in the conventional than in the aeroponics system. Tuber yield/m(2)in this study varied from 5.9 to 9.3 kg/m(2)in the aeroponics system, about twice as high as in the conventional system.Öğe Determination of the Optimum Seed Amount and Inter-row Spacing for the Seed and Essential Oil Yield of Aniseed (Pimpinella anisum L.)(TAYLOR & FRANCIS LTD, 2014) Ozel, Abdulhabip; Kosar, Islim Guler; Erden, Kaan; Demirel, UfukThis study aimed to determine the optimum seed amount and inter-row spacing in aniseed (Pimpinella anisum L.) cultivation. The study was conducted at the research field of Faculty of Agriculture at Harran University for two seasons (2001 and 2002). The treatments consisted of two row spacing (15 and 30 cm) and four seed amounts (10, 20, 30 and 40 kg ha(-1)). The following results were obtained from both years: seed yield varied between 958.0 and 1470.0 kg ha(-1), essential oil yield varied between 27.5 and 46.4 l ha(-1), 1000-seed weight varied between 3.2 and 3.9 g, seed number per umbel varied between 124.8 and 203.6, number of branch per plant varied between 4.3 and 8.2, and number of umbels per plant varied between 5.1 and 12.2. The highest seed yield was obtained from interaction of 15 cm row spacing and 20 kg ha(-1) seed amount applications. Overall applications were found to be ineffective on (E)-anethole rates.Öğe Düşük Akrilamid Potansiyeline Sahip Patates Genotiplerinin Tanımlanması İçin Özgün Tarama Araçlarının Geliştirilmesi(2020) Çalışkan, Mehmet Emin; Demirel, Ufuk; Çalışkan, Sevgi; Gökçe, Zahide Neslihan Öztürk; Bakhsh, AllahBu proje sanayilik patates ıslahında seleksiyon aracı olarak kullanılabilecek özgün tarama araçlarının gelistirilmesi amacıyla Türkiye ve Almanya'dan birer arastırma ve sanayi kurulusunun katılımıyla 2017-2019 yılları arasında yürütülmüstür. Projede Türk ve Alman ıslah programlarından gelen 90'ar adet ıslah hattı ile iki ülkede yetistirilen 20 adet tescilli çesit olmak üzere toplam 200 genotipten olusan deneme popülasyonu Türkiye'de iki (Konya ve Hatay), Almanya'da iki (Stormstorf ve Mehringen veya Zarnewanz) lokasyonda iki yıl denemeye alınmıstır. Denemelerde verim ve bazı verim unsurları yanında yumru özgül agırlıgı, kuru madde oranı, nisasta oranı, indirgen seker oranı gibi yumrunun sanayilik kalite özellikleri belirlenmistir. Popülasyon içinden seçilen 192 genotipte 21K SolCap dizini kullanılarak SNP analizleri yapılmıs ve kalite özellikleri ile iliskili SNP'ler belirlenmistir. Tarla denemeleri sonucunda incelenen tüm özellikler açısından genotipler arasında önemli farklılıkların oldugu tespit edilmistir. Tüm çevreler içerisinde en yüksek ortalama yumru verimi (8.2 t/da) 2017 yılında Almanya'nın Mehringen sehrinde yapılan denemede elde edilirken aynı yıl Almanya'nın Stromstorf lokasyonunda yapılan deneme en yüksek ikinci verim degerini (6.4 t/da) vermistir. Türkiye'de Konya lokasyonunda Hatay'a göre daha yüksek verim elde edilirken, Konya'da kısıtlı sulamaya baglı olarak 2017 yılında %39, 2018 yılında ise %42 düzeyinde verim azalması görülmüstür. Iliskilendirme haritalaması sonucunda özgül agırlıkla iliskili 6, kuru madde oranıyla iliskili 12, nisasta oranıyla iliskili 6 ve indirgen seker içerigiyle iliskili 61 adet SNP markörü tespit edilmistir. Özgül agırlık, kuru madde oranı ve nisasta oranı karakterleri ile iliskili 6 tane ortak SNP belirlenmistir. Böylece, dört farklı sanayilik kalite karakteriyle iliskili toplam 73 SNP markörü belirlenmistir. Incelenen karakterlerle önemli düzeyde iliskili oldugu bulunan SNP?lerin yer aldıgı 55 farklı gen tespit edilmistir. Bunlardan sakkaroz sentaz geninin incelenen tüm kalite özellikleri ile önemli düzeyde baglantılı olması nedeniyle bu genin ve genle baglantılı PotVar0031068, solcap_snp_c1_8574 ve solcap_snp_c2_27764 SNP markörlerinin patates genotiplerinin sanayilik kalite özelliklerini belirlemek için güçlü bir aday seleksiyon markörü niteliginde oldugu belirlenmistir.Öğe Early-stage screening for heat tolerance in cotton(WILEY, 2016) Demirel, Ufuk; Copur, Osman; Gur, AtillaThe study aimed to identify early-stage traits of cotton for heat tolerance using multitrait approach reflecting field yield performance. Seedling growth and physiological response of 16 cultivars to high temperature were investigated at three different developmental stages and four heat stress conditions in a climate chamber. Some traits such as hypocotyl dry weight, leaf pigment contents and cellular respiration were significantly correlated with previously known yield of ten cultivars grown in the hot field conditions. Sixteen cotton cultivars were classified for their heat tolerance by principle component analysis (PCA) using yield-correlated physiological traits. As a result, we showed that heat tolerance classification of cultivars based on PCA significantly coincided with the yield results of cultivars grown in hot field. As a conclusion, yield-correlated physiological traits determined in the study may facilitate selection of heat-tolerant cotton genotypes at early stage. In addition, yield-correlated early-stage traits can be used in phenotyping for QTL and association mapping studies to develop selection markers for heat tolerance.Öğe Effects of Growth Regulators, Media and Explant Types on Microtuberization of Potato(Springer, 2020) Yagiz, Ayten Kubra; Yavuz, Caner; Tarim, Cehibe; Demirel, Ufuk; Caliskan, Mehmet EminMicrotubers (MT) are an innovative approach for nuclear seed production in potato (Solanum tuberosumL.). They are produced under in vitro conditions using different protocols. However, content and type of growth media as well as explant types significantly affect the MT production efficiency. This study was conducted to develop an efficient protocol for MT production by evaluating different growth regulators at different concentrations, types of growth media and explants in two separate experiments. In Experiment 1, the effects of six different growth regulators, and their three application rates on MT formation were compared. The effects of two growth media and three explant types on MT production were compared in Experiment 2. As a result, our studies indicated that cotton based liquid MS medium containing 0.1 mg L(-1)Thidiazuron, and using whole plants as explant can be used for efficient MT production in potato.Öğe Elucidating the genetic diversity and population structure of international cotton germplasm using inter-primer binding site (iPBS) retrotransposon marker system(Springer, 2024) Yesil Bayril, Binnur; Bakhsh, Allah; Nadeem, Muhammad Azhar; Demirel, UfukCotton (Gossypium hirsutum L.) is an important crop throughout the world and is one of the most important industrial raw materials. It is very important to characterize the available cotton germplasm aiming to identify novel genetic and genomic resources that can be used for future cotton breeding. Keeping this in view, a total of 179 cotton genotypes were characterized with the inter-primer binding site (iPBS) retrotransposon marker system. Seven iPBSretrotransposon primers yielded a total of 134 scoreable bands and among these, 128 bands were polymorphic. The mean polymorphic bands per primer were 18.28, with values ranging between 16 and 21. The mean polymorphism rate of 7 iPBS retrotransposon primers was calculated as 96.28%. The polymorphism information content value varied between 0.31 and 0.46 with an average of 0.395. Genetic similarity was calculated using the POPGENE software and values ranged between 0.320 and 0.955. Population structure and neighbor-joining analysis divided the evaluated germplasm into two populations. The analysis of molecular variance revealed that maximum variations (96%) are due to differences within the populations. The information presented here has comprehensively demonstrated the potential of iPBSretrotransposon markers in detecting genetic diversity and phylogenetic association analyses of cotton. This knowledge will be helpful for future cotton breeding.Öğe Environmental requirements of potato and abiotic stress factors(Elsevier, 2022) Demirel, UfukGrowth, development, and yield of potato are seriously affected by the environmental conditions. Globally, more than 50% of total potato is cultivated under drought and heat-prone countries. Potato tuber yield is dramatically reduced under restricted environmental conditions such as drought, heat, and high salinity. Because of the abiotic stresses, the loss in total potato yield is expected to reach up to 32% by 2050. Since potato has high tuber yield and is nutritious, it is considered as an important crop to fight against hunger. Therefore increasing the potato yield under abiotic stress conditions can help feeding the growing human population. The importance of increasing the tuber yield in the regions having extreme environmental conditions has been understood. Accordingly, researchers have been making efforts to deeply understand the response mechanism of potato to abiotic stress factors. Recently, the studies on abiotic stress response of potato have increased and the knowledge obtained from the studies has been used for developing new potato cultivars having higher yield under extreme conditions. Therefore the focus of this chapter is to discuss: (1) environmental requirements of potato such as temperature, water, and soil, (2) the deviation from the optimum of these factors, (3) the physiological, biochemical, and molecular responses of potato to environmental conditions, and (4) improvement approaches. © 2023 Elsevier Inc. All rights reserved.Öğe Establishment of highly efficient and reproducible Agrobacterium-mediated transformation system for tomato (Solanum lycopersicum L.)(Springer, 2022) Hashmi, Muneeb Hassan; Saeed, Faisal; Demirel, Ufuk; Bakhsh, AllahA simple and improved Agrobacterium-mediated transformation protocol of tomato (Solanum lycopersicum) cultivar Rio Grande was developed to inspect the potential of producing transgenic tomatoes. In this study, regeneration and transformation efficiency as assessed in response to the seedling age, explant type, co-infection, co-cultivation duration, selection pressure (kanamycin), and the optimal concentration of plant growth regulators (PGR) 6-benzylaminopurine (BAP), gibberellic acid (GA3), and indolebutyric acid (IBA) in a Murashige and Skoog (MS) basal medium. To accomplish this goal, 2- to 4-wk-old tomato explant cotyledons, hypocotyl, and cotyledonary nodes were excised and transformed with the EHA105 Agrobacterium tumefaciens strain harboring pBIN19 binary vector containing uidA reporter gene and nptII as a selectable marker. Results revealed that 14-d-old cotyledonary nodes and leaves inoculated for 15 min with A. tumefaciens strain EHA105 following 48-h co-cultivation were optimal for the highest percent transformation efficiency 27.31. Antibiotic kanamycin (Kan) at 25 mg L-1 in the regeneration selection medium was found to be effective. MS medium containing optimal concentrations of 1.5 mg L-1 of BAP, 0.2 mg L-1 GA(3), and IBA 1.5 mg L-1 showed a significant level of percent regeneration, shoot elongation, and rooting efficiency of transformed plantlets. Molecular analysis of T-0 transgenic tomato plants showed integration and a higher relative expression level of the uidA gene. The optimized A. tumefaciens-mediated transformation method for tomato cultivar Rio Grande showed the highest percent transformation efficiency (TE) and regeneration efficiency (RE) and is likely to give consistent results with different tomato cultivars.Öğe Evaluation of miRNA Mediated Networking and Feedback Against Drought, Heat and Combined Stress Tolerance in Potato (Solanum tuberosum L.)(Springer, 2020) Asim, Arslan; Demirel, Ufuk; Bakhsh, Allah; Gokce, Zahide Neslihan Ozturk[Abstract Not Available]Öğe Farklı Patates Çeşitlerinin Kuraklığa Tepkilerinin Transkriptom Seviyesinde Karşılaştırılması ve Ümitvar Genlerin Islah Programlarında Kullanımının Değerlendirilmesi(2017) Öztürk, Neslihan Zahide Gökçe; Azimi, Mohammad Hussain; Demirel, Ufuk[Abstract Not Available]Öğe Genome-wide association studies (GWAS) revealed a genetic basis associated with floral traits in potato germplasm(Tubitak Scientific & Technological Research Council Turkey, 2022) Zia, Muhammad Abu Bakar; Demirel, Ufuk; Nadeem, Muhammad Azhar; Ali, Fawad; Dawood, Ahmad; Ijaz, Muhammad; Caliskan, Mehmet EminPotato is an important noncereal staple crop serving as a source of food for a large number of the world's population. Genomewide association study (GWAS) analysis has become a useful tool to uncover the genetic basis of important plant traits by revealing significant association with the trait of interest. The present study aimed to explore the phenotypic diversity and to identify the genetic basis associated with important floral traits. A total of 237 tetraploid potato genotypes were used as plant material, and field experiments were conducted according to augmented block design for two consecutive years (2016, 2017). Analysis of variance for the studied floral traits reflected highly significant genotypic effects. Mean data for both years revealed the significant variation for pistil length (5.53 to 9.92 mm), stamen length (6.04 to 9.26 mm), and pistil length above stamen (1.31 to 4.47 mm). Pearson's correlation analysis reflected a highly significant and positive correlation of pistil length with stamen length (r = 0.42) and pistil length above stamen (r = 0.28). Principal component analysis was performed, and the first two PCs were considered accounting for a total of 81.2% variation. Constellation plot divided the studied potato panel into two main populations on the basis of stamen and pistil length. A total of 12,720SNP markers were used for the marker-trait association, and a total of 15 markers were found significantly associated with studied traits across both years. Identifying the same markers across both years helped in the validation of the obtained marker-trait associations. The identified significant markers reflected some of the putative candidate genes that might be beneficial in potato breeding programs. To the best of our knowledge, this is the first study identifying the genetic basis of important floral traits and might be helpful to the scientific community interested in potato marker-assisted breeding in these traits.Öğe Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel(Springer, 2020) Zia, Muhammad Abu Bakar; Demirel, Ufuk; Nadeem, Muhammad Azhar; Caliskan, Mehmet EminPotato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Nigde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r(2) value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.Öğe Harnessing plant-mediated RNAi for effective management of Phthorimaea absoluta by targeting AChE1 and SEC23 genes(Elsevier, 2024) Hashmi, Muneeb Hassan; Tariq, Haneef; Saeed, Faisal; Demirel, Ufuk; Gokce, Ayhan; Merzendorfer, Hans; Aksoy, EmreTomato production on a global scale is under persistent pressure due to the devastating impact of Phthorimaea absoluta Meyrick (Lepidoptera: Gelechiidae), the South American tomato leaf miner. To combat this devastating pest, we explored the potential of plant-mediated RNA interference (RNAi) as a novel strategy for its management. Using transgenic techniques, we developed RNAi constructs (p35SÖğe Herbisite Dayanıklılık Geni (CP4-EPSP Sentez) Içeren Transgenik Patates Hatlarının Geliştirilmesi(2019) Sümer, Safa; Rahamkulov, İlhom; Demirel, Ufuk; Çalışkan, Mehmet Emin; Bakhsh, AllahAmaç: Yabancı otlar diğer bitkilerde olduğu gibi patates bitkisinde de önemli kayıplara yol açmaktadır.Bu çalışmada herbisite dayanıklılık karakterinin Agrobacterium aracılığıyla iki farklı patateseaktarılması amaçlanmıştır.Materyal ve Metot: Bu amaçla, genetik aktarımı için “Lady Olympia” ve “Desiree” patates (Solanumtuberasum L.) çeşitlerinin yaprak ve boğumarası doku parçaları eksplant olarak kullanılmıştır. Genaktarımı yapmak için pCAMHE-EPSPS plazmidini içeren Agrobacterium tumefaciens bakterisininLBA4404 izolatları kullanılmıştır. Gen aktarım amacıyla kullanılan pCAMHE-EPSPS plazmidinde 35Spromotoru kontrolü altında CP4-EPSPS geni bulunmaktadır. Çalışmada, T-DNA bölgesinde bulunangusA geninin varlığı aday transgenik bitkilerin erken dönemde tespit edilmesini kolaylaştırmıştır.Bulgular: In vitro besi ortamında transgenik hücrelerin seçimi için 1.5 mM’lik Glifosat N-(fosfonometil)glisin en uygun konsantrasyon olarak bulunmuştur. Lady Olympia ve Desiree çeşitlerindetransformasyon etkinliği sırasıyla % 0,7 ve % 0,3 olarak hesaplanmıştır. Aday transgenik bitkilerdeyapılan GUS histokimyasal analizi, PCR deneyleri, kantitatif gerçek zamanlı PCR ve yatay akışlı ölçümçubuğu analizleri sonucunda CP4-EPSPS geninin transgenik patates hatlarında işlevsel olarakyer aldığı tespit edilmiştir.Sonuç: Yapılan glifosat herbisit uygulaması sonucunda da CP4-EPSPS geninin patatese karşı etkinliğiniortaya koymuştur. Geliştirilmiş transgenik patates hatları ıslah programında gen kaynağıolarak kullanılabilirler.Öğe Herbisite Toleranslı Patates Hatlarının Geliştirilmesi(2017) Bakhsh, Allah; Çalışkan, Mehmet Emin; Demirel, UfukMoleküler genetikteki modern teknikler, arastırmacılara ekonomik önemi olan karakterlerin kültür bitkilerine aktarılmasına imkan tanımaktadır. Tek bir karakter olarak veya böceklere dirençlilik karakteriyle birlikte olsun, 2016 yılında herbisite dirençli kültür bitkilerinin tarımı toplam 161,9 milyon ha alanda yapılmıstır. Herbisite dirençlilik özelligi tasıyan kültür bitkilerin büyük bir çogunluguna EPSPS genini aktarılmıstır ve bu gen total bir herbisit olan Glifosata direnci saglamaktadır. Bu proje kapsamında, bes farklı patates çesidine (Lady Olympia, Desiree, Agria, Granola ve Innovator) herbisite dirençlilik özelligi kazandırmak için yaprak ve bogum arasının eksplant olarak kullanıldıgı etkili, düsük maliyetli, tekrar edilebilir bir Agrobacterium yardımlı gen aktarım protokolü gelistirilmistir. Ardından, 35S promotörünün idare ettigi EPSPS genini içeren ve proje kapsamında yeni gelistirilen rekombinant pCAMHEEPSPS isimli ikili vektör, LBA4404 Agrobacterium susuna yerlestirilmis ve bu sus 5 patates patates çesidine ait yaprak ve bogum arası eksplantlarını enfekte etmek için kullanılmıstır. Gen aktarım çalısmaları sonucunda toplam 300 adet aday transgenik bitki gelistirilerek seraya aktarılmıstır. Aday transgenik bitkilerde yapılan PCR analizleri sunucunda 300 aday transgenik bitkinin 76 tanesinde aktarılan EPSPS genin varlıgı belirlenmistir. Böylece projedeki genel gen aktarım etkinligi %25,3 olmustur. Bunun yanında uygulanan GUS, Southern emdirme, qRT-PCR ve LFD analizleri ile Glifosat uygulamaları sonucunda transgenik bitkilerde EPSPS geninin entegrasyonu ve ifadesi dogrulanmıstır. Özellikle Lady Olympia, Granola, Agria ve Desiree çesitlerinden gelistirilen bazı T1 transgenik bitkiler Glifosat uygulamasına diger transgeniklere göre daha yüksek tolerans sergilemislerdir. Proje kapsamında gelistirilen herbisite toleranslı transgenik patates hatlarının, ıslah programlarında kullanılabilecak iyi birer gen kaynakları olacakları tahmin edilmektedir.Öğe Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress(Springer, 2023) Saeed, Faisal; Hashmi, Muneeb Hassan; Aksoy, Emre; Demirel, Ufuk; Bakhsh, AllahBackgroundBacterial diseases are a huge threat to the production of tomatoes. During infection intervals, pathogens affect biochemical, oxidant and molecular properties of tomato. Therefore, it is necessary to study the antioxidant enzymes, oxidation state and genes involved during bacterial infection in tomato.Methods and resultsDifferent bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and H2O2 response was measured in Falcon, Rio grande and Sazlica tomato cultivars. In this study, RNA Polymerase II (RNAP) C-Terminal Domain Phosphatase-like 3 (SlCPL-3) gene was identified and characterized. It contained 11 exons, and encoded for two protein domains i.e., CPDCs and BRCT. SOPMA and Phyre2, online bioinformatic tools were used to predict secondary structure. For the identification of protein pockets CASTp web-based tool was used. Netphos and Pondr was used for prediction of phosphorylation sites and protein disordered regions. Promoter analysis revealed that the SlCPL-3 is involved in defense-related mechanisms. We further amplified two different regions of SlCPL-3 and sequenced them. It showed homology respective to the reference tomato genome. Our results showed that SlCPL-3 gene was triggered during bacterial stress. SlCPL-3 expression was upregulated in response to bacterial stress during different time intervals. Rio grande showed a high level of SICPL-3 gene expression after 72 hpi. Biochemical and gene expression analysis showed that under biotic stress Rio grande cultivar is more sensitive to Pst DC 3000 bacteria.ConclusionThis study lays a solid foundation for the functional characterization of SlCPL-3 gene in tomato cultivars. All these findings would be beneficial for further analysis of SlCPL-3 gene and may be helpful for the development of resilient tomato cultivars.
