Search

Chlorophyll (Chl) is present in many plant organs and plays vital roles during growth and development. Degradation of Chl causes the loss of green colour that typically occurs during senescence, and fruit ripening. The present study addresses genome-wide identification and bioinformatics analyses of tomato (Solanum lycopersicum), SlSGR1 (Solyc08g080090.2.1) SlSGR2 (Solyc12g056480.1.1) and SlSGR-like (Solyc04g063240.2.1) genes. Multiple sequence alignment indicated that the three tomato SGR proteins have conserved domains. Motif, sequence, and protein structure analysis showed that SlSGR-like differentially evolved from SlSGR proteins. Co-expression analyses were performed for each SlSGR using transcriptomic data of two fruit ripening stages [mature green (MG) and ripe fruit (R)] of Ailsa Craig (AC) tomato cultivar. According to the co-expression network analyses, SlSGRs participate in sulphur homeostasis, fatty acid biosynthesis, and biological processes of plant development during ripening stages of tomato. Six common genes were identified in the merged co-expression network. Also, 38 transcription factor families (TFFs) were searched in the co-expression network. Only 13 transcription factors, belonging to seven TFFs, were found to be involved in regulation of these two genes. Of these TFFs, GRAS and GeBP had five and three members for SlSGR-like and SlSGR1 in the network. The expression profiles of SlSGR1/2 and SlSGR-like in different tissues and different fruit ripening stages showed that SlSGR1/2 are highly expressed in ripening fruits, whereas SlSGR-like is more involved in leaf maturation. Moreover, expression of SlSGR1/2 and SlSGR-like in the leaves of 'Ciko' and 'Black' tomato varieties under 200mM salt stress indicated that significant expression changes occurred in SlSGR2 suggesting that SlSGR genes may be involved in signalling responses to abiotic stress. The findings provide new insight into the functions of these genes in growth and salinity stress.

Mitochondrial iron transporter (MIT) genes are essential for mitochondrial acquisition/import of iron and vital to proper functioning of mitochondria. Unlike other organisms, research on the MITs in plants is limited. The present study provides comparative bioinformatics assays for the potato MIT gene (StMIT) as well as gene expression analyses. The phylogenetic analyses revealed monocots-dicot divergence in MIT proteins and it was also found clade specific motif diversity. In addition, docking analyses indicated that Asp172 and Gly100 residues to be identified as the closest residues binding to ferrous iron. The percentage of structure overlap of the StMIT 3D protein model with Arabidopsis, maize and rice MIT proteins was found between 80.18% and 85.71%. The transcript analyses exhibited that the expression of StMIT was triggered under drought and salinity stresses. The findings of the present study would provide valuable leads for further studies targeting specifically the MIT gene and generally the plant iron metabolism.

Frataxin (FH) plays a crucial role in the biogenesis of mitochondria and the regulation of iron in the cells of various organisms. However, there has been very little research on FH in plants. In this study, the potato FH gene (StFH) was identified and characterized using a genome-wide approach, and its sequence was compared to those of FH genes from Arabidopsis, rice, and maize. The FH genes were found to have a lineage-specific distribution and were more conserved in monocots than in dicots. While multiple copies of FH genes have been reported in some species, including plants, only one isoform of FH was found in potato. The expression of StFH in leaves and roots was analyzed under two different abiotic stress conditions, and the results showed that StFH was upregulated more in leaves and that its expression levels increased with the severity of the stress. This is the first study to examine the expression of an FH gene under abiotic stress conditions.

Background Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aimed to evaluate the genetic diversity of of R. pseudoacacia plants planted in urban ecosystems using R. pseudoacacia genotypes collected from Istanbul (Prince Island, Bağdat Avenue, Barbaros Boulevard and TEM highway) and Kocaeli (Dilovası District) cities. Methods and Results 15 ISSR primers were tested, nine of which gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Genetic diversity values based on Nei’s (1978) were calculated between 0.165 and 0.251. The lowest and highest PPL were found in Barbaros Boulevard and Dilovası District populations, respectively. Population structure analysis showed seven different structures for the five populations. The most genetically similar populations were found as Prince Island and Barbaros Boulevard populations, while the most diverged population was the Dilovası population. Phylogeny analysis was conducted based on ITS1 and trnL-F IGS sequences. The length of the ITS1 sequence was found as 239 bp, and the GC content ranged from 52.72% to 56.56% while the length of the trnL-F IGS sequence was found as 453 bp with GC content between 29.14-29.80%. Conclusion It is considered that the main reasons for the genetic similarities and differences is originating from either the parents of these trees or the pollution they are exposed to. In phylogenetic analysis, both region sequences showed a high discriminant value and effective discriminatory power at the family level.

Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR's probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon-helix-helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe-4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. WOS:000674224400001 2-s2.0-85110771478

Sodium azide (NaN3) is widely used as a chemical mutagen in mutation studies, especially to induce point mutations. This study was carried out to determine genetic diversity of six-rowed barley cultivar Finola and 14 mutant lines induced by sodium azide mutagenesis agent and identified by using 5 Inter Simple Sequence Repeat (ISSR) markers. According to the results, 24 bands were produced by five ISSR markers, 18 of them were found polymorphic, and the average polymorphism rate was 76.33%. The average allele number was determined as 4.8, and UBC-808 marker had the highest allele number with 6 alleles, while UBC-820 and UBC-825 markers had the lowest allele numbers with 4 alleles. The average polymorphism information content of the markers used in the study was 0.83, and ranked from 0.78 to 0.86. A dendogram was created using marker data, and according to the dendogram, genotypes were divided into two main groups. Fnl-4, Fnl-8, Fnl-10, Fnl-11 and Fnl-12 mutants existed in the first group, while the others including Finola cultivar were in the second group. Based on the principal component analysis (PCA), Finola cultivar and mutant lines Fnl-5, Fnl-13 and Fnl-14 were evaluated as they are similar to Finola although, differed for some alleles., Sodyum azid (NaN3) özellikle nokta mutasyon çalışmalarında yoğun olarak kullanılan kimyasal bir mutajendir. Bu çalışmada, Finola altı sıralı arpa çeşidi, kimyasal bir mutajen olan sodyum azid ile muamele edilerek 14 adet mutant arpa hattı elde edilmiştir. Elde edilen hatlar arasındaki genetik farklılık, 5 adet basit tekrarlı diziler arası polimorfizm (Inter Simple Sequence Repeat, ISSR) markörü yardımıyla belirlenmiştir. Elde edilen sonuçlara göre 5 ISSR marköründen 24 adet bant elde edilmiş ve bu bantlardan 18 adet polimorfik allel belirlenmiş ve ortalama polimorfizm oranı %76.33 olarak saptanmıştır. Ortalama allel sayısı 4.8 olup, 6 bant ile UBC-808 en fazla bant üreten primer olurken, en az bant üreten primerler ise 4’er bant ile UBC-820 ve UBC-825 primerleri olmuştur. Kullanılan markörlere ait ortalama polimorfizm bilgi içeriği (PIC) 0.83 olarak hesaplanmış ve PIC değeri 0.78 ile 0.86 aralığında değişmiştir. Markör verileri dendrogramda 2 ana grup oluşturmuştur. Birinci kümede Fnl-4, Fnl-8, Fnl-10, Fnl-11 ve Fnl-12 mutantları yer alırken, ikinci kümede ise Finola çeşidi ile birlikte diğer mutant hatlar yer almaktadır. Temel bileşenler analizi, Finola çeşidi ve mutant hatlardan Fnl-5, Fnl-13 ve Fnl-14 hatlarının birbirine benzemekle birlikte, bazı alleller bakımından farklı olduklarını ortaya koymuştur.

The high-affinity nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO

Boron (B) is an important nutrient, which should be provided to growth media throughout plant life. Despite the significant roles of B in plant metabolism, there is not any information about the involvement of B in enzymatic processes. However, limited studies with relation to the direct participation of B into metabolite synthesis metabolism are present. In this review the genes associated with B toxicity or deficiency and the genes linked to the metabolite synthesis under B stresses were discussed. © 2022 Elsevier Inc. All rights reserved.

As a plant-specific transcription factor, vascular plant One-Zinc-finger (VOZ) is involved in the regulation of many biological processes. VOZ genes in tomato have not been analysed comprehensively so far. In this study, two SIVOZs were identified on a genome-wide scale in tomato and analysed using various bioinformatics methods. According to Ka/Ks ratio, SlVOZ proteins are being changed by evolutionary processes to adapt to changing growth and stress conditions. Protein structure and phylogenetic analyses also indicated that transcriptional regulations of SlVOZs were controlled in a specific manner related to developmental stages and abiotic stress conditions. Digital expression results, in particular, showed that SlVOZs are not only active during different growth status of tomato but are also involved in abiotic stress response mechanism. Nonetheless, SlVOZ1 is expressed higher in both developmental stages and under salt stress conditions, confirmed by RT-qPCR. The co-expression maps constructed using RNA-seq data showed that SlVOZ2 was associated with the genes involved in hormonal regulation, formation of fruit shape, secondary wall biosynthesis and in plant development. Overall, it can be concluded that SlVOZs are not only important for plant growth and development but may also be part of the salt stress response mechanism. © 2022 Journal of Horticultural Science & Biotechnology.

High-affinity nitrate transporter 2 (NRT2) proteins have vital roles in nitrate (NO3-) uptake and translocation in plants. The gene families coding NRT2 proteins have been identified and functionally characterized in many plant species. However, no systematic identification of NRT2 family members have been reported in tomato (Solanum lycopersicum). There is also little known about their expression profiles under environmental stresses. Accordingly, the present study aimed to identify NRT2 gene family in the tomato genome; then, investigate them in detail through bioinformatics, physiological and expression analyses. As a result, four novel NRT2 genes were identified in the tomato genome, all of which contain the same domain belonging to the Major Facilitator Superfamily (PF07690). The co-expression network of SlNRT genes revealed that they were co-expressed with several other genes in many different molecular pathways including transport, photosynthesis, fatty acid metabolism and amino acid catabolism. Programming many crucial physiological and metabolic pathways, various numbers of phosphorylation sites were predicted in the NRT2 proteins.

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.

Various kinds of primary metabolisms in plants are modulated through sulfate assimilation that the uptake of this inorganic compound can be regulated via the sulfate transporters, such as sulfotransfer-ases (SOTs), engaged in the sulfur metabolism. In the current study a genome-wide approach has been utilized for recognition and characterization of SOT family genes in the significant nutritional crop po-tato (Solanum tuberosum L.). As a result, 29 StSOT genes were identified in the potato genome, which were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure demonstrated two highly conserved 5' PSB region and 3' PB motif that are essential for sulfotransferase and catalytic ac-tivities. The protein-protein interaction networks also significantly demonstrated an interesting collabo-ration between SOTs and the other genes, such as PRTase, APS-kinase, protein phosphatase and APRs, in sulfur compounds biosynthesis and regulation of the flavonoid and brassinosteroid metabolic pro-cesses, which clearly detected the importance of sulfotransferases for potato proper growth/development and stress dealing. Notably, the homology modeling of StSOT proteins and dock-ing analysis of their ligand-binding sites revealed the presence of some stress-responsive residues, such as proline, glycine, serine and lysine, in their active sites. The expression assay of StSOT genes via the potato RNA-seq data clearly suggested the engagements of these gene family members in plants growth and extension as well as responses to various hormones and biotic/abiotic stimulus circum-stances. Our predictions can be informative for the functional characterization of the SOT genes in po-tato and may the other nutritional crops.

Background Cd accumulation in plant cells results in dramatic problems including oxidative stress and inhibition of vital enzymes. It also affects mineral uptakes by disrupting membrane permeability. Interaction among Cd and other plant nutrient elements changes the nutritional contents of crops and reduces their yield. Methods and results In the present study, Cd stress in Brachypodium distachyon led to the upregulation of some heavy metal transport genes (influx or efflux) encoding cation-efflux proteins, heavy metal-associated proteins and NRAMP proteins. The Arabidopsis orthologs of the differentially expressed B. distachyon genes (DEGs) under Cd toxicity were identified, which exhibited Bradi4g26905 was an ortholog of AtALY1-2. Detailed co-expression network and gene ontology analyses found the potential involvement of the mRNA surveillance pathway in Cd tolerance in B. distachyon. These genes were shown to be downregulated by sulfur (S) deficiency. Conclusions This is the first transcriptomic study investigating the effect of Cd toxicity in B. distachyon, a model plant for genomic studies in Poaceae (Gramineae) species. The results are expected to provide valuable information for more comprehensive research related to heavy metal toxicity in plants. Akdeniz University Scientific Research Projects Coordination UnitAkdeniz University [FBA-2018-3532] The study was funded by Akdeniz University Scientific Research Projects Coordination Unit. Grant number: FBA-2018-3532. WOS:000721666100001 PubMed: 34812999

Akbudak, M. Aydin/0000-0002-1397-4678; Filiz, Ertugrul/0000-0001-9636-6389 WOS: 000475294900007 PubMed: 29550498 ATP sulfurylase (ATPS, EC: 2.7.7.4) is a crucial enzyme for sulfate assimilation pathway in both plastids and cytosol in plants. In this study, genome-wide and comparative analyses of ATPSs in 11 higher plant species, including sequence and structural analyses have been performed. Expression of ATPS genes in sorghum under cadmium (Cd) and salinity (NaCl) stresses were also investigated to provide a model experimental data for the regulation of ATPS genes under stress conditions. Thirty-one ATPS genes from 11 plant species were found. It showed that ATPSs from different species have high sequence divergences, which cause structural differences among them. Phylogenetic analysis has shown that there are two major types of ATPSs evolved in dicots while monocots were evolved to have one type of ATPs. Finally, expression analysis of ATPS genes revealed tissue and stress dependent expression pattern, which indicates expressions of ATPS genes are tightly regulated.

FIT (Fer-like iron deficiency-induced transcription factor) is one of the key regulators in uptake of iron (Fe) for plants. In this study, FIT genes from 10 plant species were identified at genome-wide scale and analyzed by computational tools. Our analyses showed that subcellular localizations of all FITs were in nucleus and FITs were generally acidic proteins. While a clear monocot–dicot divergence was observed, exon numbers were found as three and four for monocots and dicots, respectively. Arg and Leu were established as most repetitive amino acid residues in conserved regions of all FITs. All FITs had different shape and pocket numbers along with different secondary and tertiary structures despite they contained same domain structure as PF00010 (helix-loop-helix DNA-binding domain). We observed that FIT is an important target of several biological processes and a component of various metabolic pathways regulating root development and stress responses on exposure to various environmental stressors. Moreover, FITs seem to be located in heterochromatic area of chromosome and its transcription may also be upregulated on the exposure of stressors. The FITs were established to interact with Pi and Cu uptake machinery, other than iron acquisition, under Pi and Cu deficiency. Consequently, FITs can be proposed to take part in different and specific metabolic pathways together with Fe acquisition. The miRNA analyses showed that miRNAs targeting FITs take part in abiotic and biotic stress metabolism together with Pi uptake mechanism. Lastly, involvement of FIT in abiotic stress response was stimulated by phytohormones such as ABA and ethylene. © 2019, Society for Plant Biochemistry and Biotechnology.

Cinnamyl alcohol dehydrogenase (CAD) (EC 1.1.1.195) is an enzyme functioning in the reduction of variousphenylpropenyl aldehyde derivatives which are precursors in lignin and lignan production. Species-specific CADgenes have been extensively identified in recent years. In this study, we used bioinformatics tools to characterizeand classify plant CADs. The amino acid and nucleotide sequences of 16 CADs from different plant species wereused to compare their physiological properties, phylogeny, and conserved motifs. For this purpose, sequence,phylogenetical, structural analyses of proteins were conducted using various servers. All plant CADs had thecharacteristic alcohol dehydrogenase (PF08240) and zinc-binding dehydrogenase domains (PF00107). Accordingto the physicochemical analysis, it was revealed that the most of plant CADs (81.25%) were in acidic character.Sequence length (aa) and molecular weight (kDa) of CAD proteins were found in range of 356 -367 and 38.6-40.5respectively. The highest sequence similarities were found between Sorghum bicolor and Zea mays (95.3%),Panicum virgatum and Sorghum bicolor (90.9%), and Oryza sativa and Zea mays (87.1%) respectively. PlantCADs showed divergent exon-intron structures in which exon numbers were ranged from two to six. Four monocotspecies (S. bicolor, P. virgatum, Z. mays, and O. sativa) have four exons, whereas Brachypodium distachyoncontains only two exons. Phylogenetic analysis revealed that the CAD proteins mainly divided into two groups.The highest bootstrap values were found as follows: Fragaria vesca-Prunus persica clade (100%), Glycine maxMedicago truncatula (81%), and S. bicolor-Z. mays (72%). The 3D structures of plant CADs showed that Oryzaand Vitis had the most divergent structures when compared to the other plant species. Eventually, the datarepresented here contribute to studies aiming at evaluating the plant CADs extensively and at identifying new CADgenes in other plants. Sinamil alkol dehidrogenaz (CAD) (EC 1.1.1.195) lignin ve lignin üretimindeki öncül çeşitli fenil propenil aldehit türevlerinin indirgenmesinde görev alan bir enzimdir. Türlere özgü olan CAD genleri, son yıllarda önemli derecede tanımlanmıştır. Bu çalışmada CAD genlerinin (enzim veya proteinlerinin) bioinformatik araçlar kullanılarak karakterize edilip, sınıflandırılması amaçlanmıştır. 16 farklı bitki türünden elde edilen CAD nükleotit ve amino asit dizileri fizyolojik özellikler, filogenetik ve korunmuş motif bölgelerinin karşılaştırılması için kullanılmıştır. Bu amaçla CAD proteinlerinin sekans, filojenik ve yapısal analizleri çeşitli sunucular yardımıyla yapılmıştır. Bütün incelenen CAD dizilerinin alkol dehidrogenaz (PF08240) ve çinko bağlayıcı dehidrogenaz domainlerine sahip oldukları gözlenmiştir (PF00107). Fizyokimyasal analiz sonuçlarına göre, CAD’lerin önemli bir kısmının (%81,25’i) asidik karakterde olduğu gözlenmiştir. Bu proteinlerin amino asit uzunlukları (aa) ve moleküler ağırlıklarının (kDa) 356 -367 ve 38,6-40,5 arasında sırasıyla değişmekte olduğu belirlenmiştir. Dizi benzerlikleri en yüksek Sorghum bicolorile Zea mays (%95,3), Panicum virgatum ile Sorghum bicolor (%90,9) ve Oryza sativa ile Zea mays (% 87,1) arasında bulunmuştur. İncelenen CAD genlerinin intron ve ekzon yapıları birbirlerinden farklılık göstermiş olduğu ve ekzon sayılarının iki ve altı arasında değiştiği belirlenmiştir. Çalışmadaki tek çenekli türler olan S. bicolor, P. virgatum, Z. mays, ve O. sativa’nın dört ekzona sahip olduğu; Brachypodium distachyon’un ise sadece iki ekzona sahip olduğu gözlenmiştir. Filogenetik analiz neticesinde CAD proteinlerinin sadece iki ana gruba ayrıldığı saptanmış; en yüksek bootstrap değerleri sırasıyla şu şekilde bulunmuştur: Fragaria vesca-Prunus persica grubu (%100), Glycine max-Medicago truncatula (%81), and S. bicolor-Z. mays (%72). İncelenen CAD’lerin 3 boyutlu analizlerine göre, Oryza ve Vitis CAD’leri, araştırmadaki diğer bitki CAD’lerinden en fazla ayrılma göstermiştir. Son olarak bu çalışmadaki veriler, farklı bitkilerdeki CAD genleri veya proteinlerinin tanımlanması ve değerlendirmesini amaçlayan yeni çalışmalara katkı sağlayacaktır.

Ozyigit, Ibrahim Ilker/0000-0002-0825-5951 WOS: 000481746800001 Although stresses induce generation of reactive oxygen species (ROS), which are highly reactive and toxic, and cause severe damage to cellular components; plants have very efficient enzymatic ROS-scavenging mechanisms. Despite the substantial knowledge produced about these enzymes, we still have limited knowledge regarding their expression patterns in relation to the stress type, duration and strength. Thus, taking advantage of microarray data, this work evaluated the abiotic stresses (salt, cold, heat and light) induced regulation of six antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR), in 10 natural Arabidopsis ecotypes. The expression profiles of 36 genes encoding six enzymatic antioxidants including CSD1-3, FSD1-3, MSD1-2, CAT1-3, APX1-6, APXT, APXS, GPX1-8, MDAR1-5 and DHAR1-4 were investigated. In particular, FSD1, FSD2, CSD1 and CSD2 genes coding for SOD; CAT2 and CAT3 for CAT; APX3-6, APXT and APXS for APX; GPX1, GPX2, GPX5, GPX6 and GPX7 for GPX; MDAR2-4 for MDHAR; and DHAR1 and DHAR3 for DHAR families appeared to be more differentially expressed under given stress conditions. Primarily, high light as well as salt and cold stresses considerably up-regulated the gene expression, whereas cold stress significantly led to the down-regulation of genes. The overall expression pattern of ecotypes suggested that the studied Arabidopsis genotypes had different stress tolerance.

F1 kademesinde ortaya çıkan melez azmanlığıaynı zamanda F3 popülasyonlarında da önemlidir. Bu çalışma,farklı orijin ve tarımsal özelliklere sahip 8 ekmeklik buğday (Triticum aestivum L.) genotipi (Midas,As-14, Rumeli, Esperia, Gl-14, Krasunia odes’ka, Masaccio ve Lucilla) ilebunların 28 F3 melezini içeren 8x8 yarım diallel melez ekmeklikbuğday popülasyonunda, verim ile ilgili özellikler açısından; heterosis veheterobeltiosis değerlerinin saptanması amacıyla yürütülmüştür. Melezlerin veebeveynlerin yer aldığı deneme, 2016-2017 yılında Lüleburgaz/Kırklareli çiftçikoşullarında 4 tekerrürlü olarak tesadüf blokları deneme deseninde kurulmuştur.Pozitifheterosis ve heterobeltiosis değerleri, hemen hemen tüm popülasyonlardaincelenen özelleiklerin tümünde tespit edilmiştir. Başakuzunluğu için, % 28.76 heterosis ile % 22.73 heterobeltiosis; başakta başakçıksayısı için, % 10.75 heterosis ile % 5.51 heterobeltiosis; başakta tane sayısıyönünden, % 25.46 heterosis ile % 16.52 heterobeltiosis; başaktaki taneağırlığı için, % 46.66 heterosis ile % 31.61 heterobeltiosis; bitki tane verimiiçin, % 46.92 heterosis ile %32.20 heterobeltiosis değerleri bulunmuştur., Hybrid vigorwhich often observed in F1 plants is also important in F3generations. Eight bread wheat (Triticum aestivum L.) genotypes (Midas, As-14, Rumeli, Esperia, Gl-14, Krasuniaodes’ka, Masaccio and Lucilla) from both different origins and agricultural traits were crossedin a half diallel cross and evaluated for heterosis and heterobeltiosis in F3populations for some yield components. Theexperiment was conducted in a randomized complete blocks design with fourreplications in Lüleburgaz/Kırklareli under farmer conditions in 2016-2017cropping year. Positive heterosis and heterobeltiosis values wereobserved for all investigated traits in almost all crosses. The values ofheterosis and heterobeltiosis for spike length, spikelet number per spike,grain number per spike, grain weight per spike and grain yield per plant rankedbetween 28.76 and 22.73%; 10.75 and 5.51%; 25.46 and 16.52%; 46.66 and 31.61%;46.92 and 32.20%, respectively.

Assimilation of sulfur to cysteine occurs in the presence of serine acetyltransferase (SAT). In this study, SAT genes in rice (Oryza sativa) were identified and analyzed using bioinformatics approaches. Also, these genes were tested under salt stress. OsSATs have two common motifs, bacterial transferase hexapeptide and acetyltransferase and underwent purifying selection. They have more similar protein sequences compared to Arabidopsis. However, there is structural and functional divergence among OsSATs which may be driven by the segmental and tandem duplications. Purifying selection and gene duplications may also have effect leading to variation of specificity and selectivity of OsSATs. In this regard, Asp (D), His (H), Gly (G), Thr (T), Arg (R), Ala (A), and Leu (L) are identified as well-conserved residues in their active sites which have an indicator role on their functions. The OsSATs expressions in different tissues, organs and under hormones showed that jasmonic acid was main hormone inducing the expressions of OsSAT1;1, OsSAT2;1, and OsSAT2;2 whereas auxin and abscisic acid only triggered OsSAT1;1 expression. On the other hand, wet-lab expressions of OsSATs in this study indicated that OsSAT1;1, OsSAT1;2 and OsSAT1;3 genes were upregulated under different exposure times of salt stress. OsSAT1;1 is the only OsSAT induced by various situmuli. The findings can be used by plant breeders and genetic engineers to develop new rice varieties having optimal growth and stress tolerance.

Background Assimilation of sulfur to cysteine (Cys) occurs in presence of serine acetyltransferase (SAT). Drought and salt stresses are known to be regulated by abscisic acid, whose biosynthesis is limited by Cys. Cys is formed by cysteine synthase complex depending on SAT and OASTL enzymes. Functions of some SAT genes were identified in Arabidopsis; however, it is not known how SAT genes are regulated in rice (Oryza sativa) under salt stress. Methods and results Sequence, protein domain, gene structure, nucleotide, phylogenetic, selection, gene duplication, motif, synteny, digital expression and co-expression, secondary and tertiary protein structures, and binding site analyses were conducted. The wet-lab expressions of OsSAT genes were also tested under salt stress. OsSATs have underwent purifying selection. Segmental and tandem duplications may be driving force of structural and functional divergences of OsSATs. The digital expression analyses of OsSATs showed that jasmonic acid (JA) was the only hormone inducing the expressions of OsSAT1;1, OsSAT2;1, and OsSAT2;2 whereas auxin and ABA only triggered OsSAT1;1 expression. Leaf blade is the only plant organ where all OsSATs but OsSAT1;1 were expressed. Wet-lab expressions of OsSATs indicated that OsSAT1;1, OsSAT1;2 and OsSAT1;3 genes were upregulated at different exposure times of salt stress. Conclusions OsSAT1;1, expressed highly in rice roots, may be a hub gene regulated by cross-talk of JA, ABA and auxin hormones. The cross-talk of the mentioned hormones and the structural variations of OsSAT proteins may also explain the different responses of OsSATs to salt stress. WOS:000684782700001 2-s2.0-85112445896 PubMed: 34389920

Transcription factors regulate gene expression depending on environmental and extracellular stimuli and signals from other cells. WRKY, MYB, bHLH and bZIP transcription factors (TFs) are one of the most important TF families in plants. Therefore, WRKY, MYB, bHLH and bZIP TFs in potato (Solanum tuberosum, St) genome under heat, salinity and drought stresses were investigated in terms of expression, co-expression and differentially expressed genes (DEGs). A total of 26,172 genes were collectively analysed in the study and four genes were identified as common DEGs, highly expressed under each abiotic stress. The salt stress was found to induce StbHLH and StMYB TFs whereas the heat stress activated StWRKY and StbZIP TFs. Moreover, the top three highly expressed genes were identified for each TF family under each stress condition. Since some of the genes were unannotated, their functional predictions including unannotated common DEGs were made based on orthologue gene comparisons in Arabidopsis. TFs involved in gene regulation along with four common DEGs were identified in co-expression analyses. As a result, 12 bHLH, 5 bZIP, 9 MYB and 14 WRKY TFs were detected in co-expression networks of the four common DEGs. Regarding DEGs, PGSC0003DMT400040149 was generally found to be involved in sulphur metabolism. PGSC0003DMT400016360 and PGSC0003DMT400007351 gene networks were found to contain more than 400 overlapping genes, suggesting that they may have roles in similar pathways in response to abiotic stress conditions in potato. Lastly, we found that MYB-bHLH cross talking may occur in response to abiotic stresses in potato. The findings are particularly important to understand roles of TFs under the mentioned stresses in potato. WOS:000640844600001 2-s2.0-85104838080

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

Proline has various functions in plants, such as growth, development and stress response to biotic and abiotic factors. Therefore, proline accumulation and transport are vital for crop production in higher quality and quantity. The present study addresses genome-wide identification and bioinformatics analyses of tomato (Solanum lycopersicum) proline transporter (ProT) genes and their expression profiles under drought stress. The analyses indicated four novel ProT genes (SlProTs) in the tomato genome and their protein lengths ranged from 439 to 452 amino acid residues. All SlProTs contained a PF01490 (transmembrane amino acid transporter protein) domain and seven exons, and they had a basic p1. The phylogeny analysis proved that monocot-dicot divergence was not present and the SlProT proteins were distinct from the ProT proteins in monocots and Arabidopsis. Based on the digital expression analysis, SlProT1 and SlProT2 genes seemed to be more active than the others in response to abiotic stress conditions. However, detected by RT-qPCR, the expression levels of all SlProT genes under drought stress were similar. The promotor analyses of SlProT genes revealed that they contained many transcription factors binding sites in cis-elements, such as MYB, Dof, Hox, bZIP, bHLH, AP2/ERF and WRKY. Finally, our findings could contribute to the understanding of SlProT genes and proline metabolism in plants. WOS:000594130100002 2-s2.0-85092644436 PubMed: 33069977

Boron (B) is an essential plant micronutrient but studies regarding its transport are still limited to a few plants. This work identified two major B transport sequences in plants, NIP5;1 boric acid channel protein and BOR1 transporter. 80 BOR1 and 34 NIP5;1 homologs were identified in 18 different plant genomes. BOR1 homologs had a HCO3-transporter domain, 649-737 amino-acid residues with mainly basic nature, putative 8-11 transmembrane domains (TMDs) and 11-13 exons. NIP5;1 homologs had a MIP family domain, 294-311 amino-acid residues with basic nature, 5-6 putative TMDs and 3-5 exons. Tyrosine-based motif, acidic di-leucine motif and lysine residue, reported for polarity, vacuolar sorting and B-dependent degradation, were identified in BOR1 homologs. Two NPA motifs and an ar/R selectivity filter with AIGR residues, reportedly essential in B transport, were also found in NIP5;1 homologs. Two NPA motifs in AtNIP5;1 and OsNIP3;1 homologs were NPS and NPV, whereas in sequences homologous to AtNIP6;1 were NPA/V. Besides, ar/R selectivity filters were identified with A(N/S/T)IGR residues in NIP5;1 and NIP3;1 homologs. The BOR1 and NIP5;1 model structures were mainly conserved. Under different perturbations, Arabidopsis thaliana NIP5;1 and NIP6;1 genes demonstrated similar expression patterns although they act in different tissues, suggesting a common regulatory mechanism, whereas BOR1 showed a different expression pattern. BOR1 was substantially expressed in primary root, radicle and flower; NIP5;1 in primary root and roots, and NIP6;1 in petiole. NIP5;1, 6;1 and BOR1 expression in other plant organs implied their involvement in different pathways in addition to B uptake and its mobilization. WOS:000538924900001 2-s2.0-85087093473

Nitrogen (N) is an essential macronutrient for plants, and mainly taken from the soil as ammonium (NH+4). It is particularly transported into the plants by AMmonium Transporters (AMTs), which are plasma membrane proteins. In the present study, genome-wide identification, physiological and expression analyses of tomato (Solanum lycopersicum L.) ammonium transporters 1 (SlAMT1) genes under drought and salt stresses were performed. Sequence analyses revealed the presence of variations in SlAMT1s at nucleotide and protein levels. While all the SlAMT1s comprise an ammonium transporter domain (PF00909), the numbers of their transmembrane helices were found to be diverse. Digital expression analyses proved that SlAMT1-3 gene had different expression patterns compared to the others, suggesting its functional diversities. The expression analyses revealed that SlAMT1 genes were 0.16 and 5.94 -fold down-regulated under drought and salt stresses, respectively. The results suggested that expression of SlAMT1 genes were adversely affected by abiotic stress conditions. Akdeniz University Scientific Research Projects Coordination Unit grantAkdeniz University [FBG-2019-4963] This research was partially supported by Akdeniz University Scientific Research Projects Coordination Unit grant #FBG-2019-4963 to MAA. Authors thank Durmus Cetin and Sukran Yildiz for their technical assistance. WOS:000547979000009 2-s2.0-85084582218 PubMed: 32320821

2-s2.0-85079137280 WRKY transcription factor (TF) is plant specific genes and play essential roles involved in biotic and abiotic stress tolerance. Gene co-expression network (GCN) analysis is effective tool for the interpretation of transcriptomic data. In this study, a co-expression network of 152 WRKY genes using publicly available microarray data (GSE78242) was constructed under low phosphate (Pi) treatment in soybean (Glycine max). A total of 149 nodes and 641 edges were obtained from CGN and seven seed genes were identified. Particularly, Glyma.19G094100 and Glyma.16G054400 seed genes (orthologue to Arabidopsis WRKY75) were found to have a direct connection to P deficiency. Promotor analyses of seed genes revealed the variations in the number of cis-regulatory elements (CREs) ranging from 80 to 137 with a total of 835 CREs. The methylation profile of Glyma.04G218700 (orthologue to Arabidopsis WRKY51) was found higher than other seed genes. As a result, our findings can be used as a scientific basis to cope with P deficiency in soybean as well as abiotic stress tolerance. In addition, these findings of this study may prove the crop improvement studies in future, especially genetically engineered soybean plants. © 2020, Korean Society of Crop Science and Springer.

Iron (Fe) is a crucial micronutrient in plant metabolism; thus, iron homeostasis is critical for plant development. Permease in chloroplast 1 (PIC1) is the first protein determined in the chloroplast playing a role iron homeostasis. In the present study, the PIC1 gene was investigated at a genome-wide scale in four plant genomes; Arabidopsis, tomato, maize and sorghum. Based on the gene ontology database, 21 GO terms were found related to the PIC1 gene, most of which were involved in iron hemostasis and transport. The digital expression data revealed that the expression of the majority of PIC1 genes (62.5%) in Arabidopsis decreased under abiotic stress conditions. Expression profiles of tomato PIC1 (SlPIC1) and sorghum PIC1 (SbPIC1) genes were also analyzed under salt and drought stress conditions using Real Time-quantitative PCR (RT-qPCR). Our wet-lab studies demonstrated that the SbPIC1 gene was down-regulated under salt and drought stresses in all tissues, while SlPIC1 was up-regulated in all but root tissue under drought stress. Some structural variations were detected in predicted 3D structures of PIC1 proteins and the structural similarity values varied between 0.23 and 0.35. Consequently, these results may contribute to the understanding of the PIC1 gene in iron transport and homeostasis in plants. WOS:000500604000001 2-s2.0-85076043371 PubMed: 31802376

The olive tree (Olea europaeaL.) is one of the major cultivated species in the world, and Mediterranean countries produce about 90% of world cultivated olives. In this study, the genetic relationship of seven Turkish olive cultivars was investigated using non-codingtrnL-Fregions in chloroplastic genome. Cultivars demonstrated a similar sequence length of 330-340 bp with an average 35.26% G+C content. Variable (polymorphic/segregating), parsimony informative and total numbers of the insertion or the deletion of bases in the DNA (indel sites) were 4, 3, and 28, respectively. Nucleotide diversities π and θ were found as 0.00631 and 0.00644 respectively, while Tajima’s D was −0.786. cpDNAtrnL-Fregions of sequenced Turkish olive cultivars had a low level of genetic variations, and these non-coding regions were strictly conserved in all analyzed cultivars. Geographically distant shared more sequence similarities than relatively close cultivars. The phylogenetic analyses indicated that the biogeographic distribution of cultivars does not demonstrate any association inferring cultivar source. These results indicate the possibility of germplasm exchanges among countries or that some indel mutations contribute to variations of the Turkish olive gene pool. Thus, the authorities should develop the necessary programs to preserve the purity of native germplasms.

Filiz, Ertugrul/0000-0001-9636-6389; Akbudak, M. Aydin/0000-0002-1397-4678 WOS: 000423142600010 PubMed: 29236185 Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 A mu M cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4. Given names are based on phylogeny and chromosomal locations. Except SbSULTR4, all SbSULTR proteins contained Sulfate_transp (PF00916), STAS (PF01740) domains and 12 trans-membrane domains. Phylogenetic analysis revealed that four major groups were identified such as SULTR1, 2, 3, and 4 groups and SULTR4 group was separated to other SULTR groups. In promotor sequences of SbSULTR genes, many diverse cis-acting elements were found mainly related with physiological processes such as light, stress and hormone responsiveness. The expression profiles of SbSULTR genes showed that SULTR1;2, 1;3, 3;3, and 3;5 genes up-regulated in root, while expression level of SULTR4 decreased under 200 A mu M Cd exposure. The predicted 3D structures of SULTR proteins showed some conformational changes, suggesting functional diversities of SbSULTRs. Finally, results of this study may contribute towards understanding SbSULTR genes and their regulations and roles in Cd stress in sorghum.

Filiz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951 WOS: 000399687900012 PubMed: 28461726 Sulfite oxidase (SOX) is a crucial molybdenum cofactor-containing enzyme in plants that re-oxidizes the sulfite back to sulfate in sulfite assimilation pathway. However, studies of this crucial enzyme are quite limited hence this work was attempted to understand the SOXs in four plant species namely, Arabidopsis thaliana, Solanum lycopersicum, Populus trichocarpa and Brachypodium distachyon. Herein studied SOX enzyme was characterized with both oxidoreductase molybdopterin binding and Mo-co oxidoreductase dimerization domains. The alignment and motif analyses revealed the highly conserved primary structure of SOXs. The phylogeny constructed with additional species demonstrated a clear divergence of monocots, dicots and lower plants. In addition, to further understand the phylogenetic relationship and make a functional inference, a structure-based phylogeny was constructed using normalized RMSD values in five superposed models from four modelled plant SOXs herein and one previously characterized chicken SOX structure. The plant and animal SOXs showed a clear divergence and also implicated their functional divergences. Based on tree topology, monocot B. distachyon appeared to be diverged from other dicots, pointing out a possible monocot-dicot split. The expression patterns of sulfite scavengers including SOX were differentially modulated under cold, heat, salt and high light stresses. Particularly, they tend to be up-regulated under high light and heat while being down-regulated under cold and salt stresses. The presence of cis-regulatory motifs associated with different stresses in upstream regions of SOX genes was thus justified. The protein-protein interaction network of AtSOX and network enrichment with gene ontology (GO) terms showed that most predicted proteins, including sulfite reductase, ATP sulfurylases and APS reductases were among prime enzymes involved in sulfite pathway. Finally, SOX-sulfite docked structures indicated that arginine residues particularly Arg374 is crucial for SOX-sulfite binding and additional two other residues such as Arg51 and Arg103 may be important for SOX-sulfite bindings in plants.

In this work, a co-expression network-based approach was employed in analysis of basic helix-loop-helix (bHLH) transcription factor genes in soybean (Glycine max). bHLHs as regulatory agents modulate many complex associations related with regular metabolic functions and various stress factors. Co-expression networks are versatile resources to understand complex associations from functional aspects. Using a microarray data from phosphate (Pi)-starved soybean, a co-expression network of bHLH genes was constructed. A network was established with 253 nodes (bHLH genes) interconnecting 1763 edges (association) and then the network was dissected into 13 distinct clusters to extensively investigate the correlations. Each cluster was individually analyzed with emphasis on seed genes, which could be used as marker/reference genes in development of plant lines with enhanced stress tolerance. The seed genes were involved in very diverse metabolic processes, including stress modulation, metal homeostasis, hormone response and developmental roles. Our network-based clustering approach provides new insight in understanding many uncharacterized plant bHLHs. © 2016 Elsevier B.V.

Eroglu, Seckin/0000-0002-9494-7080; Filiz, Ertugrul/0000-0001-9636-6389 WOS: 000398709100007 PubMed: 28150142 Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1-8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3-7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3-7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains. Scientific and Technological Council of Turkey (Ankara, Turkey) [BIDEB-2232] We thank Benjamin Gruber for the fruitful discussion and proofreading of the article. Seckin Eroglu thanks Scientific and Technological Council of Turkey (Ankara, Turkey) for the fellowship through BIDEB-2232 program.