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Öğe Arbuscular mycorrhizal fungi improve the growth and phosphorus uptake of mung bean plants fertilized with composted rock phosphate fed dung in alkaline soil environment(Taylor & Francis Inc, 2019) Wahid, Fazli; Sharif, Muhammad; Fahad, Shah; Adnan, Muhammad; Khan, Imtiaz Ali; Aksoy, Emre; Ali, AmjadInoculation effect of arbuscular mycorrhizal fungi (AMF) on phosphorus (P) transfer from composted dung of cattle with a diet supplemented with powdered rock phosphate (RP) and their successive uptake by mung bean plants was assessed in alkaline soil. The efficacy of composted RP fed dung alone or/and in combination with AMF inoculums containing six different species were compared with SSP in six replicates per treatment in pots. The results showed that the association of AMF with composted RP fed dung had a positive effect on mung bean shoot (3.04 g) and root (2.62 g) biomass, chlorophyll (a, b), carotenoid contents and N (58.38 mg plant(-1)) and P (4.61 mg plant(-1)) uptake. Similarly, the percent roots colonization (56%) and nodulation of mung bean plant roots and their post-harvest soil properties were also improved by the inoculation of AMF together with composted RP fed dung. It is concluded that the combined application of AMF with composted RP fed dung has almost the same effect as SSP for improving mung bean plants growth and their nutrients uptake. Moreover, AMF inoculants can be used as a suitable biofertilizer in combination with locally available organic sources of fertilizers for improving P status and growth of plants in alkaline soils.Öğe Arpa Nikotinamin Sentaz1 (HvNAS1) Genini Yüksek Seviyede İfade Eden Arabidopsis thaliana Bitkileri Demir Eksikliğine Dayanıklılık Gösterir(2020) Aksoy, Emre; Maqbool, Amir; Abudureyimu, BuasimuhanDemir (Fe) bitki gelişimi için önemli bir eser element olup, Fe eksikliğinde yetişen bitkilerde gelişen kloroza bağlı olarak verim kayıpları yaşanır. Bu kayıpların en aza indirilebilmesi için alınabilecek agronomik önlemlere ilaveten genetik mühendisliği aracılığıyla bitkilerin özellikleri etkin bir şekilde geliştirilebilir. Rizosferde yüksek miktarda bulunan demiri köklerine alabilmek için Arabidopsis thalianagibi dikotlar indirgenme temelli bir stratejiyi kullanırlarken, arpanın (Hordeum vulgare) da yer aldığı graminelerde şelasyon stratejisi evrimleşmiştir. Bu çalışmada, arpada bulunan ve demir ile kompleks oluşturabildiği bilinen nikotinaminin üretiminden sorumlu NİKOTİNAMİN SENTAZ1(HvNAS1) geni klonlanarak, Arabidopsis bitkilerinde konstitütif olarak yüksek seviyede ifade edilmiştir. Elde edilen T3Arabidopsis bitkilerinde HvNAS1ile birlikte demir alımından sorumlu yolakta yer alan Arabidopsis genlerinin de ifade seviyelerinin arttığı belirlenmiştir. Buna bağlı olarak, bitkilerin kök uzunluklarının, kök ve gövde yaş ağırlıklarının, ferrik şelat redüktaz enzim aktivitelerinin de arttığı belirlenmiştir.Ayrıca, transgenik Arabidopsis bitkilerinin kök ve gövdelerinde biriken demir ve çinko seviyelerinde önemli artışlar belirlenmiştir. Sonuç olarak, arpa HvNAS1genini yüksek seviyede ifade eden trangenik Arabidopsis bitkilerinin rizosferden daha fazla demir alabildiği ve bu demiri daha fazla gövdeye taşıyabildiği gösterilmiştir. Bu sayede genetik mühendisliği kullanılarak HvNAS1genini yüksek seviyede ifadeeden ve demir eksikliğine dayanıklı Arabidopsis bitkileri geliştirilmiştir.Öğe Biofortification Under Climate Change: The Fight Between Quality and Quantity(Springer International Publishing, 2020) Maqbool, Amir; Abrar, Muhammad; Bakhsh, Allah; Çalişkan, Sevgi; Khan, Haroon Zaman; Aslam, Muhammad; Aksoy, EmreClimate change has been a serious problem in our industrialized world for the last century. We have faced its devastating effects on the environment, agriculture and human population. In current scenarios, around 3.8 billion people are predicted to live in areas with severe water problems by 2025. As the majority of staple crops are sensitive to environmental fluctuations, only an increase in global temperatures by 2 °C can disrupt agricultural practices and crop production periods severely. Therefore, plant breeders have canalized all the efforts to enhance the grain yield and produce more crops under adverse environmental conditions to meet the demand of the ever-increasing human population. However, the majority of current staple crop varieties produce grains with insufficient micronutrients. Moreover, climate change decreases micronutrient uptake from the soil and translocation within the plant body. In this chapter, three strategies (agronomic, breeding and transgenics) of micronutrient biofortification in various staple crops are explained with recent successful examples. © Springer Nature Switzerland AG 2020.Öğe Bitki Peptit ve Amino Asit Taşıyıcılarının Demir Taşınmasındaki Görevleri(2022) Aksoy, Emre; Maqbool, Amir; Yerlikaya, Bayram Ali; Wahid, FazliDemir (Fe) bitkiler için önemli bir mikro-besin elementi olup, eksikliği bitki büyümesi ve gelişimini engelleyerek ciddi verim kayıplarına neden olur. Toprakta bulunan yarayışlı demirin bitkiler tarafından alınması ve bitki organlarına taşınması üzerine uzun yıllara dayanan detaylı çalışmalar gerçekleştirilmiştir. Bu çalışmalar sonucunda demirin bazı organik maddeler ile şelatlanarak taşınabileceği gösterilmiştir. Bu organik maddelerin içerisinde peptitler ve amino asitler yer almaktadır. Ancak, demirin peptitler ve amino asitler ile bitki içerisine alımı veya organlar arası taşınması üzerine detaylı çalışmalar yapılmamıştır. Gerçekleştirilen az sayıdaki çalışmada oligopeptit taşıyıcı (OPT) ve İlaç/Metabolit Taşıyıcı (DMT) aileleri üzerine odaklanılmıştır. Yakın zaman önce bitkilerde keşfedilen UMAMIT amino asit taşıyıcı ailesinin demir taşınmasındaki olası rolleri ise henüz incelenmemiştir. Bu derleme kapsamında, demirin bitki içine alınması ve organlar arası taşınmasından sorumlu taşıyıcı aileleri ile OPT, DMT ve UMAMIT ailelerinin demir-peptit ve demir- amino asit komplekslerini taşımadaki rolleri özetlenmiştir.Öğe Bitkilerde Rizosferden Demir Alım Mekanizmaları(2018) Aksoy, Emre; Yerlikaya, Bayram Ali; Ayten, Sefa; Abudureyimu, BuasimuhanDemir, toprakta en çok bulunan elementlerden bir tanesi olmasına karşın çözünürlüğüalkali topraklarda düşüktür. Dolayısıyla bu tür topraklarda yetişen bitkiler sürekli demireksikliği stresine maruz kalırlar. Dünyadaki tarım arazilerin üçte biri bu tür topraklardanoluştuğundan dolayı tedavi edilemeyen demir eksikliği tarımsal üretimi kısıtlar.Bitkilerde gözlenen demir eksikliğinin tedavisinde farklı demir gübrelerikullanılmaktadır. Ancak, bu gübrelerin kullanımı üretim maliyetlerini artırmaktadır.Maliyetlerin azaltılabilmesi için bitkilerin toprakta bulunan demiri en etkin biçimdekullanabilmeleri gerekir. Bunun için de ilk olarak bitkilerin topraktaki demiri nasıl kökiçerisine aldıklarının incelenmesi gerekmektedir. Son otuz yılda yapılan çalışmalardafarklı bitki gruplarının 3 farklı demir alım mekanizması kullandıkları keşfedilmiştir. Buderlemenin amacı, demirin kök içerisine alımından sorumlu taşıyıcılar ile bu taşıyıcılarhakkındaki güncel gelişmelerden bahsetmektir.Öğe Böceklere Geniş Spektrumlu Dayanıklılık Gösteren Patates Bitkilerinin Geliştirilmesi Için Bitki Aracılığıyla Yeni Bir RNAi Stratejisi(2019) Bakhsh, Allah; Çalışkan, Mehmet Emin; Asım, Muhammad; Aksoy, Emre; Pırlak, UğurBacillus thuringiensis? den elde edilen cry genlerinin ifade edilmesiyle elde dilen transgenik bitkilerin yoğun bir şekilde tarımının yapılması, Bt bitkilerine karşı böcek ve zararlı dayanıklılığı ile sonuçlanmıştır. Etkili bir bitki zararlısı mücadelesi için, bu bitkilerin sürdürülebilirliği ve kalıcılığı sorgulanmaktadır. Son zamanlarda, RNA interferaz tekniği bitki böcek ve zararlılarına karşı bitki iyileştirme konusunda önemli bir yöntem olduğunu kanıtlamıştır. Bu proje RNA interferaz tekniğini kullanarak, patates güvesi ve Colorado patates böceğinde bulunan yüksek derecede spesifik deri değiştime ile ilgili Ecdysone Reseptör geninin (EcR) susturulmasına odaklanmştır. Patates böceği ve patates güvesinden elde edilmiş olan EcR geninin kısmi cDNA?sı özel primerler kullanılarak sens ve antisens yönlerinde aralarında bir intron içerecek şekilde pRNAi-GG vektörüne klonlanmıştır. Agria ve Lady Olympia çeşitlerininin yaprak ve internod eksplantları, pRNAi-CPB ve pRNAi-PTM plasmidleri ile EcR bölgelerine sahip LBA4404 Agrobakteri suşu ile, 35S promotör kontöründe sens ve antisens yönlerinde, transforme edilmiştir. Neomycin phosphotransferase (nptII) geni 100 mg L-1 konsantrasyonunda markör olarak kullanılmıştır. Elde edilen birincil transformantlar, standart moleküler analizler ile bitki genomunda T-DNA?ya uygun şekilde entegrasyon göstermiştir. Southern emdirme sonuçları, bitki genomunda genin entegrasyonunu gösterirken, RT-qPZR sonuçları EcR geninin transgenik bitkilerde birikme seviyelerini ortaya koydu. Çeşitlerden geliştirilen bitkiler CPB ve PTM larvalarının birincil, ikincil ve üçüncül evrelerinin etkinlikleri açısından değerlendirildi. Yaprak biyotoksisite analizleri ile iki böcek türünde de % 15-80 ölüm oranı belirlendi. Kontrol bitkilerle kıyaslandığında (1.87-6.53 X), trangenik bitkilerle beslenen böceklerde larva ağırlığında önemli derecede azalış (0.87-4.14 X) gözlendi. Ayrıca, RT-qPZR analizleri EcR geninin ifade seviyesindeki azalmayı ortaya çıkartarak, her iki böcekle muamele edilmiş EcR-dsRNA?nın işlevselliğini gösterdi. Bu çalışma, patates böcek zararlılarınının Ecdysone reseptör protein geninin ekspresyonunun susturulması için hedef zararlılara karşı dsRNA?nın patateste ifade edilmesi sonucunda RNAi teknolojisinin işlevselliğini ve entegre zararlı denetiminde etkili bir araç olduğunu gösteren ilk çalışmadır.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 Development of Insect Resistant Potato Transplastomic Lines.(Springer, 2019) Bakhsh, Allah; Joyia, Faiz Ahmad; Hossain, Md. Jakir; Aksoy, Emre; Gokce, Neslihan Zahide Ozturk; Mustafa, Ghulam; Khan, Muhammad Sarwar[Abstract Not Available]Öğe Development of Transgenic Potato Lines Expressing Ecdysone Receptor Gene of Colorado Potato Beetle(Springer, 2018) Bakhsh, Allah; Hussain, Tahira; Aasim, Muhammad; Pirlak, Ugur; Aksoy, Emre; Caliskan, Mehmet Emin[Abstract Not Available]Öğe Downregulation of imidacloprid resistant genes alters the biological parameters in Colorado potato beetle, Leptinotarsa decemlineata Say (chrysomelidae: Coleoptera)(Pergamon-Elsevier Science Ltd, 2020) Naqqash, Muhammad Nadir; Gokce, Ayhan; Aksoy, Emre; Bakhsh, AllahColorado potato beetle, Leptinotarsa decemlineata Say (coleoptera: chrysomelidae), is the important pest of potato all over the world. This insect pest is resistant to more than 50 active compounds belonging to various chemical groups. Potential of RNA interference (RNAi) was explored to knock down transcript levels of imidacloprid resistant genes in Colorado potato beetle (CPB) under laboratory conditions. Three important genes belonging to cuticular protein (CP), cytochrome P450 monoxygenases (P450) and glutathione synthetase (GSS) families encoding imidacloprid resistance were targeted. Feeding bioassays were conducted on various stages of imidacloprid resistant CPB lab population by applying HT115 expressing dsRNA on potato leaflets. Survival rate of insects exposed to CP-dsRNA decreased to 4.23%, 1532% and 47.35% in 2nd, 3rd and 4th instar larvae respectively. Larval weight and pre-adult duration were also affected due to dsRNAs feeding. Synergism of RNAi with imidacloprid conducted on the 2nd instar larvae, exhibited 100% mortality of larvae when subjected to reduced doses of GSS and CP dsRNAs along with imidacloprid. Utilization of three different dsRNAs against imidacloprid resistant CPB population reveal that dsRNAs targeting CP, P450 and GSS enzymes could be useful tool in management of imidacloprid resistant CPB populations. (C) 2019 Elsevier Ltd. All rights reserved.Öğe Editing of banana, apple, and grapevine genomes using the CRISPR-Cas9 system(Elsevier, 2024) Çelik, Selime; Deniz, Utku; Gencer, Orkun; Aksoy, EmreAmong horticultural crops, fruits have an essential place since they are key sources of nutrients such as essential vitamins and minerals, and fruit production is crucial for the economy since it has a large market globally. Apple, banana, and grapevine are highly demanded fruit crops for consumers and producers; therefore, it is no surprise that these fruits are also subjects of molecular studies. Following the publication of the apple, banana, and grapevine genomes, molecular studies in these fruits became more feasible via the utilization of next-generation sequencing (NGS), high-quality de novo assembly, transgenics, and finally, genome editing by CRISPR-Cas9. Currently, the application of advanced genome-editing techniques such as CRISPR-Cas systems pave the way for basic and applied research on apple, banana, and grapevine in a rapid and precise way. With the improvement of CRISPR technologies such as base editing, prime editing, and different types of Cas proteins, the development of new superior cultivars with desirable traits will be possible in the future. © 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.Öğe Effect of climate change on abiotic stress response gene networks in Arabidopsis thaliana(Springer International Publishing, 2022) Yerlikaya, Bayram Ali; Ates, Dilan; Abudureyimu, Buasimuhan; Aksoy, EmreClimate change leads to various abiotic stresses that the plants face within their life cycles. This leads to extensive biochemical, physiological, and morphological changes in plants. Plants have evolved several defense mechanisms to survive in abiotic stress conditions, and all of these mechanisms include the differential expression of hundreds of genes involved in tens of different biological pathways. Recent systems biology approaches have identified a core gene network that is essential in abiotic stress tolerance in plants. However, a more detailed analysis is required to understand the core transcriptional regulatory network of stress-responsive genes in the model plant Arabidopsis thaliana. Here we explain the identification of a core transcriptional regulatory network of stress-responsive genes in Arabidopsis by bioinformatic analyses under several abiotic stress conditions. Then, known functions of identified transcription factor families are discussed in detail. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2022. All rights reseverd.Öğe Effects of Natural Variations on Biofortification(Elsevier, 2021) Maqbool, Amir; Bakhsh, Allah; Aksoy, EmrePlants have evolved different strategies to uptake, translocate, and accumulate essential minerals. Genetic biofortification of staple crops has been ignored by breeders for decades in compensation of yield enhancements. Therefore, malnutrition and hidden hunger persist in developing countries. Genetic biofortification studies can benefit from the wide variation in natural wild relatives or populations of crop species. Ionomic studies have been performed in different crops as well as in Arabidopsis thaliana to determine the mineral composition of different organs in natural populations or recombinant inbred lines. Recently, quantitative trait loci (QTL) analyses and genome-wide association studies (GWAS) started to identify the molecular signatures that potentially cause the ionomic changes in natural crop populations. This chapter describes the studies in various crop species to determine the genetic variability in mineral contents and gives examples from recent advances in the identification of genetic factors controlling the variation via GWAS. © 2021 Elsevier Inc. All rights reserved.Öğe Engineering of insecticidal hybrid gene into potato chloroplast genome exhibits promising control of Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)(Springer, 2023) Hossain, Md. Jakir; Bakhsh, Allah; Joyia, Faiz Ahmad; Aksoy, Emre; Gokce, Neslihan Zahide Ozturk; Khan, Muhammad SarwarThe potato chloroplast was transformed with codon optimized synthetic hybrid cry gene (SN19) to mitigate crop losses by Colorado potato beetle (CPB). The bombarded explants (leaves and internode) were cultured on MS medium supplemented with BAP (2.0 mg/l), NAA (0.2 mg/l), TDZ (2.0 mg/l) and GA3 (0.1 mg/l); spectinomycin 50 mg/l was used as a selection agent in the medium. Leaf explants of cultivar Kuroda induced highest percentage (92%) of callus where cultivar Santae produced the highest percentage (85.7%) of transplastomic shoots. Sante and Challenger showed 9.6% shoot regeneration efficiency followed by cultivar Simply Red (8.8%). PCR amplification yielded 16 postive transplastomic plantlets out of 21 spectinomycin resistant ones. Target gene integration was confirmed by PCR and Southern blot, whereas RT-qPCR was used to assess the expression level of transgene. The localization of visual marker gene gfp was tracked by laser scanning confocal microscopy which confirmed its expression in chloroplasts of leaf cells. The transplastomic plants ensured high mortality to both larvae and adult CPB. Foliage consumption and weight gain of CPB fed on transplastomic leaves were lower compared to the control plants. Sucessful implementation of current research findings can lead to a viable solution to CPB mediated potato losses globally.Öğe Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)(Tubitak Scientific & Technological Research Council Turkey, 2023) Tariq, Haneef; Gokce, Ayhan; Aksoy, Emre; Elci, Eminur; Bakhsh, AllahRNA interference (RNAi) is a versatile genetic tool capable of selectively inhibiting the expression of any gene in a targeted organism. Its implementation holds great promise for safeguarding crops against insect pests and diseases. Vacuolar-ATPase represents an ideal target for RNAi-based pest management strategies since it is an enzyme essential for various physiological processes in insects. In this study, double-stranded RNA (dsRNA) was synthesized using an L4440 vector in Escherichia coli HT115 strain to silence the Vacuolar-ATPase proteolipid subunit mRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say). To assess the effectiveness of RNAi, L. decemlineata larvae at different developmental stages were fed potato leaflets treated with dsRNA. The feeding bioassays using dsV-ATPase resulted in significant mortality rates, ranging from 45% to 77% across all of the instar stages of L. decemlineata. Furthermore, ingestion of dsRNAs by third-and fourth-instar larvae exerted significant effects on their body weight and foliage consumption. Notably, feeding the larvae dsV-ATPase led to a significant reduction in V-ATPase gene expression, confirming the efficacy of RNAi-mediated gene silencing in controlling L. decemlineata populations. These findings highlight the potential of RNAi-mediated gene silencing as a valuable strategy for managing L. decemlineata populations by targeting essential genes.Öğe General guidelines for CRISPR/Cas-based genome editing in plants(Springer, 2022) Aksoy, Emre; Yildirim, Kubilay; Kavas, Musa; Kayihan, Ceyhun; Yerlikaya, Bayram Ali; Calik, Irmak; Sevgen, IlkayCRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T-2 generation.Öğe Genome editing for nutrient use efficiency in crops(Springer International Publishing, 2022) Yağiz, Ayten Kübra; Yavuz, Caner; Naeem, Muhammad; Dangol, Sarbesh Das; Aksoy, EmrePlant breeders have concentrated on increasing the yields, and in turn, the production in the last century to meet the increasing food demand, while ignoring the nutrition values of staple food crops. However, the malnutrition pandemic showed us that plant breeding should also focus on enhancing the nutritional quality of staple foods. Therefore, crop biofortification is one of the major goals of today's agriculture to eliminate malnutrition in the world. There are different strategies of crop biofortification, ranging from conventional to molecular breeding to transgenics. On the one hand, crop breeding seems to be a logical strategy to develop new nutritious varieties, but it takes much longer and requires manpower. On the other hand, transgenic technologies can shorten the time to develop new varieties and require less effort. Even though the obvious advantages of the transgenic technologies, transgenic crop varieties cannot be taken to the market because of strong public opposition. For this very reason, genome editing can facilitate transgene-free variety production. CRISPR/Cas-based genome editing has been used in many aspects of plant science to understand the function of the gene(s), to develop stress-tolerant varieties, and of course to develop biofortified crops. This chapter describes crop biofortification studies using conventional transgenic and genome editing technologies. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2022. All rights reseverd.Öğe Genome-wide analysis of gene expression profiling revealed that COP9 signalosome is essential for correct expression of Fe homeostasis genes in Arabidopsis(Springer, 2017) Eroglu, Seckin; Aksoy, EmreIn plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software. Induced and suppressed genes were clustered in a hierarchical way and gene ontology enrichment categories were identified. In wild-type Arabidopsis, CSN genes did not respond to iron deficiency. In csn mutant lines, under Fe-sufficient conditions, hundreds of Fe-deficiency-responsive genes were misregulated. Among the ones previously characterized for their physiological roles under Fe deficiency IRT1, NAS4, BTS, NRAMP1 were down-regulated while AHA2, MTP8, FRD3 were up-regulated. Unexpectedly, from those which were regulated in opposite ways, some had been repeatedly shown to be tightly co-regulated by the same transcription factor, FIT. Two proteins from DELLA family, which were reported to interact with FIT to repress its downstream, were found to be strikingly repressed in csn mutants. Overall, the study underlined that the absence of a functional CSN greatly impacted the regulation of Fe homeostasis-related genes, in a manner which cannot be explained simply by the induction of the master transcription factor, FIT. Correct expression of Fe deficiency-responsive genes requires an intact COP9 signalosome in Arabidopsis.Öğe Genome-wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato(John Wiley & Sons Ltd, 2024) Aksoy, Emre; Yavuz, Caner; Yagiz, Ayten Kuebra; Unel, Necdet Mehmet; Baloglu, Mehmet CengizGATA is one of the prominent transcription factor families conserved among many organisms in eukaryotes and has different biological roles in many pathways, particularly in light regulation in plants. Although GATA transcription factors (TFs) have been identified in different crop species, their roles in abiotic stress tolerance have not been studied in potato. In this study, we identified 32 GATA TFs in potato (Solanum tuberosum) by in silico analyses, and expression levels of selected six genes were investigated in drought-tolerant (Sante) and sensitive (Agria) cultivars under light, drought, and combined (light + drought) stress conditions. According to the phylogenetic results, StGATA TFs were divided into four main groups (I, II, III, and IV) and different sub-groups in I and II (eight and five, respectively). StGATA genes were uniformly localized to each chromosome with a conserved exon/intron structure. The presence of cis-elements within the StGATA family further supported the possible involvement in abiotic stress tolerance and light response, tissue-specific expression, and hormonal regulation. Additional PPI investigations showed that these networks, especially for Groups I, II, and IV, play a significant role in response to light and drought stress. Six StGATAs were chosen from these groups for expressional profiling, and their expression in both Sante and Agria was mainly downregulated under purple and red lights, drought, and combined stress (blue + drought and purple + drought). The interactomes of selected StGATAs, StGATA3, StGATA24, and StGATA29 were analyzed, and the accessions with GATA motifs were checked for expression. The results showed that the target proteins, cyclin-P3-1, SPX domain-containing protein 1, mitochondrial calcium uniporter protein 2, mitogen-activated protein kinase kinase kinase YODA, and splicing factor 3 B subunit 4-like, mainly play a role in phytochrome-mediated stomatal patterning, development, and activity. Understanding the interactions between drought stress and the light response mechanisms in potato plants is essential. It will eventually be possible to enhance potato resilience to climate change by manipulating the TFs that play a role in these pathways.Öğe Genome-wide identifiication of QTLs associated with iron defiiciency tolerance in soybean reveals GATA12 as the integrator of iron signaling in roots(Tubitak Scientific & Technological Research Council Turkey, 2023) Maqbool, Amir; Sahin, Ahmet; Bakhsh, Allah; Aksoy, EmreIron (Fe) is an essential micronutrient required for plant growth and development. However, its deficiency causes substantial yield losses, particularly in alkaline soils. Soybean (Glycine max) serves as an ideal model to study Fe deficiency chlorosis (IDC) due to its inefficient Fe uptake from the soil. Although the quantitative trait loci (QTL) associated with IDC tolerance were determined in soybean, the specific genes within these QTL regions remain unidentified. In this study, it was aimed to identify and analyze the expres-sion levels of genes present in IDC-responsive soybean QTL under Fe deficiency. Through this investigation, 6593 genes were identified within 19 QTL linked to IDC tolerance in soybean, and among these, 607 genes exhibited differential expression under Fe deficiency conditions. Notably, the orthologs of 10 selected genes, referred to as the core group, were found to be induced in Fe-signaling mutants of Arabidopsis thaliana. These core group genes were enriched in metal transport and Fe-signaling pathways. Further examination of these genes in an IDC-sensitive soybean cultivar revealed their induction under Fe deficiency and high soil pH conditions. Particularly, GATA TRANSCRIPTION FACTOR12 (GATA12) stood out with significantly increased expression levels of approximately 5 and 20 times under Fe deficiency and high pH treatments, respectively. Coexpression network analyses of the core group genes highlighted the significance of the cluster containing GATA12 as a crucial integrator of Fe signaling between the epidermis-localized FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR (FIT) and the stele-localized POPEYE (PYE) signaling networks. Overall, the findings suggest that GATA12 and its close paralogs may act in the transcriptional network linking the two Fe-signaling networks in the root stele and epidermis. This knowledge sheds light on the intricate mechanisms of Fe signaling in soybean and provides valuable insights for future studies on IDC tolerance and Fe-efficient cultivar development.
