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Abstract The remobilization of stored assimilates from stems to seeds plays a pivotal role in augmenting barley yield, particularly under water stress conditions. This study examines the molecular mechanisms underlying stem reserve utilization by conducting a comparative analysis of the proteome and metabolome across three barley contrasting genotypes: Yousef, Morocco, and PBYT17. Evaluations were performed at 21 and 28 days after anthesis (DAA) under both water stress and control conditions. The results indicate that the Yousef genotype exhibits superior remobilization of stem reserves, thereby demonstrating its potential to thrive even in adverse environmental conditions. Utilizing advanced quantitative proteomics and targeted metabolomics, this investigation identified a significant number of metabolites and proteins exhibiting differential accumulation across the genotypes. Specifically, 17 metabolites and 1580 proteins were catalogued, highlighting the intricate biochemical responses to water stress. Noteworthy enzymes such as sucrose synthase, inositol monophosphatase 3, and galactokinase were found to be closely associated with remobilization efficiency. In the drought-tolerant genotype, these enzymes maintained stable levels, in stark contrast to the decline observed in the susceptible genotype. This stability is crucial for promoting seed development through ascorbic acid synthesis and for mitigating oxidative stress, which is exacerbated by drought conditions. The elevated levels of certain metabolites, including glucose 6-phosphate, and UDP-glucose, in the drought-tolerant genotype suggest a robust mechanism for maintaining signalling molecules for carbon availability, which is then instrumental in regulating plant growth and seed size development. The findings from this study strongly imply that the drought-tolerant genotype, through enhanced antioxidant capacity, can effectively produce energy-rich storage compounds, thereby optimizing carbon allocation under water stress. Such insights are invaluable for future breeding strategies aimed at improving barley resilience in the face of climate variability.

Abstract Successful improvement of stable genotypes is dependent on the interaction of genotype with environment, which has a great influence on breeding new barley (Hordeum vulgare) varieties. The main objectives of this study were to (1) evaluate the effectiveness of drought tolerance indices for the selection of drought‐tolerant barley genotypes, (2) identify stable high‐yielding genotypes in variable environments, and (3) survey physiological traits of five contrasting genotypes under water deficit. In this experiment, 18 spring barley genotypes were evaluated under two moisture regimes (normal and deficit irrigations) for 2 years during the crop periods of 2022–2023 in Varamin Agriculture Experimental Station. In order to identify drought‐tolerant barley genotypes in response to water deficit, GGE (genotype and genotype by environment interaction) biplot and AMMI (additive main effects and multiplicative interaction) analysis, stability parameters, and drought indices under water deficit and normal condition were used. Also, physiological traits in three tissues (leaf, penultimate, and peduncle) were measured. Based on our results, AMMI and GGE biplot analysis revealed that the G15 genotype was superior to other genotypes under water‐deficit condition. Based on the physiological traits, the G3 and G15 had higher chlorophyll content and carotenoids than other genotypes under water deficit as compared to normal condition. Our results demonstrate the efficiency of the stability evaluation techniques to select genotypes that are high‐yielding and responsive to drought stress condition.

Abstract Nitrogen (N) is an essential element for plant growth, and its deficiency influences plants at several physiological and gene expression levels. Barley (Hordeum vulgare) is one of the most important food grains from the Poaceae family and one of the most important staple food crops. However, the seed yield is limited by a number of stresses, the most important of which is the insufficient use of N. Thus, there is a need to develop N-use effective cultivars. In this study, comparative physiological and molecular analyses were performed using leaf and root tissues from 10 locally grown barley cultivars. The expression levels of nitrate transporters, HvNRT2 genes, were analyzed in the leaf and root tissues of N-deficient (ND) treatments of barley cultivars after 7 and 14 days following ND treatment as compared to the normal condition. Based on the correlation between the traits, root length (RL) had a positive and highly significant correlation with fresh leaf weight (FLW) and ascorbate peroxidase (APX) concentration in roots, indicating a direct root and leaf relationship with the plant development under ND. From the physiological aspects, ND enhanced carotenoids, chlorophylls a/b (Chla/b), total chlorophyll (TCH), leaf antioxidant enzymes such as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT), and root antioxidant enzymes (APX and POD) in the Sahra cultivar. The expression levels of HvNRT2.1, HvNRT2.2, and HvNRT2.4 genes were up-regulated under ND conditions. For the morphological traits, ND maintained root dry weight among the cultivars, except for Sahra. Among the studied cultivars, Sahra responded well to ND stress, making it a suitable candidate for barely improvement programs. These findings may help to better understand the mechanism of ND tolerance and thus lead to the development of cultivars with improved nitrogen use efficiency (NUE) in barley.

Lake Urmia is one of the world’s most unique and hypersaline aquatic ecosystems. The aim of this study was to investigate the diversity, abundance and frequency of these microorganisms in water samples from the eastern regions of the lake over four seasons. Amplicon sequencing for the 16S rRNA gene was performed to examine bacterial communities in the samples. The study revealed significant seasonal variations in water quality parameters and their influence on the microbial communities. Majority and rarity analyses showed that winter and spring had higher core abundance and higher Gini index values, indicating a greater dominance of certain genera, while autumn and summer had a more balanced distribution. Analysis of beta diversity using the Bray–Curtis dissimilarity index emphasized that bacterial communities diverge most strongly in summer and winter, reflecting the significant changes in the environment with the season. Overall, understanding the seasonal variation in water chemistry and bacterial communities is critical for effective ecosystem management and conservation efforts.

Metal tolerance proteins (MTPs) are as metal efflux transporters, existing extensively at all plant sections and play significant roles in regulation of the metal levels in biological processes. In the current study, phylogenetic relationships, gene structures, conserved motifs, and StMTP domains were analyzed. Here, 12 MTP genes in S. tuberosum were detected and categorized in three major clusters namely Fe/Zn-MTP, Zn-MTP, and Mn-MTP and seven groups (1, 5, 6, 7, 8, 9, and 11) according to phylogenetic relationships. Based on in silico and qPCR analysis, all of StMTPs included a cation diffusion facilitator (CDF) domains and the putative Mn-MTP harbored the ZT-dimer. An evolutionary analysis indicated that StMTP genes had undergone gene duplication leading to gene loss and gene expansion events. Analysis of transcription factor binding sites (TFBS) and microRNA in promoter region and coding sequence of StMTP genes revealed the presence of 5312 putative TFBS and 13 StmiRNAs. The analysis of promoter regions of StMTP genes possess various frequencies of TFBS, illustrating various responses in different growth and developmental stages as well as under abiotic stress. Expression profile analysis revealed that the StMTP9 were up-regulated in leaves and stem, while, StMTP8 up-regulated in leaves. Both genes down-regulated in tubers, roots as well as under drought stress. These results will provide a better insight for functional characterization of StMTP genes and can be helpful to elucidate the biological structure of their genes in potato.

IntroductionPotato (Solanum tuberosum L.) is an economic crop that is grown and consumed worldwide. Potato is considered as the fourth important crop for human consumption after maize, wheat, and rice. Potato contain more carbohydrates, proteins, minerals, and vitamins per unit area than cereals. However, this crops exposed environmental stresses during growth and developmental stages particularly, drought stress. Potato is sensitive to drought condition because of narrow root system. As a result, it is necessary the investigation of molecular mechanism involved in drought stress in potato. Drought stress affected on the integrity and structure maintain of biological membrane. The actin-based myosin is necessary for the growth and organization of the endomembrane system. Given that myosin genes allow to move intercellular and intracellular providing the possibility of repair of damaged membrane areas under drought stress in plants. In eukaryotic cells, organelle movement, positioning and communications are critical for maintaining cellular functions and are highly regulated by intracellular trafficking. Directional movement of motor proteins along the cytoskeleton is one of the key regulators of such trafficking. Most plants have developed a unique actin–myosin system for intracellular trafficking. Myosins participate in a different cellular processes, endocytosis, containing cell polarization, intracellular and organellar transport, transcriptional regulation, and signal transduction. Motions are as molecular motors in biological systems. These can bind to filamentous actin and produce physical forces through hydrolyzing ATP. Myosins is one of the most diverse and largest protein families in eukaryote. Class XI and VIII motor proteins are characterized as a slow and fast motor proteins. Myosin XI possess many genes in Angiosperms. Whereas, myosin-VIII contain fewer members against class XI. Further, molecular size of myosin-VIII is smaller than myosin-XI.Materials and methodsProtein file of A.thaliana was downloaded and matrix file of hidden Markov Model (HMM) of myosin gene family was used. Here, phylogenetic analysis, gene structure, and gene expression were surveyed. Gene expression of two genes (StMyoXI-F and StMyoXI-B) was performed in different tissues (root, stem, leaves, and tuber). For analysis of expression in different tissues (leaves, stem, and root), sampling was performed 2 weeks after mother tuber growth. However, tubers were sampled 6 weeks after cultivated in Karaj. To evaluate expression under drought stress, after 6 weeks of growth, the water stress was induced by irrigation suppression in 2 weeks while, daily irrigation was maintained for control plants. Leaves and tuber sampling were performed under two conditions.Results and discussionThe seven StMyo genes were unevenly distributed in the two subgroups. The seven StMyo genes were unevenly distributed in the two subgroups. Class XI was the largest subfamily, which class VIII had the lowest subfamily. Drought treatment significantly increased expression of StMyoXI-B and StMyoXI-F genes by 80 and 8 fold compared to the control treatment, repectively. Under control conditions, StMyoXI-B and StMyoXI-F enhanced expression in root by 25 and 20 fold while, it showed low expression in leaves under control conditions. Under control conditions, StMyoXI-F gene showed the 3 and 4 fold change higher mean relative expression than the reference gene. The relative expression of StMyoXI-B gene has been increased 5 and 10 fold change in leaves and stem under non-stress conditions as compared to the reference gene. Among myosin genes, the number of exons varied from 1 to 39. Most of class-VIII proteins had fewer introns whereas, class-XI proteins possess more proteins than class VIII. This results indicated that occurred splicing process in the myosin genes.ConclusionBased on the obtained results, it is considered that these genes highly do not influenced in stem development. However, it had significantly affected in root, leaves, and tuber development. It seems this gene can be potentially a good candidate for drought tolerance breeding programs in potato.

IntroductionDrought is one of the most important factors limiting the environment for plant growth and productivity, especially in the flowering and filling stages of barley. A study was conducted to compare some statistical methods and different indicators of stress tolerance with the aim of introducing an ideal method for selecting drought tolerant lines. After wheat, barley is one of the most important crops. Barley is the fourth cereal crop in the world after wheat, corn and rice. One of the factors affecting the production of plants is water defecit, and barley has more efficient mechanisms against water shortage than other grains. Because it has higher relative drought tolerance compared to other grains. In these arid and semi-arid regions like Iran, the presence of drought stress during plant growth is a natural problem.Materials and methodsIn this study, 18 diverse barley lines at two water levels (normal conditions and water deficit stress) were examined. This experiment was performed as a randomized complete block design with three replications at the Seed and Plant Improvement Research Institute of Karaj, Iran in 2020. Drought tolerance and susceptibility indices were assessed. These indices included stress sensitivity index, mean productivity, tolerance, stress tolerance index, geometric mean productivity, harmonic mean productivity, performance under stress conditions (Ys) and normal (Yp) conditions. Correlation coefficient between yield in drought and irrigation conditions and other stress indicators was estimated according to statistical techniques. Correlation between indices and grain yield under stress and normal conditions was calculated using Minitab software. Selection based on multiple traits in breeding programs is likely to be effective in improving grain yield under drought stress conditions. The purpose of this study is to identify the most suitable indicators and compare different stress tolerance indicators to select high-yielding and drought-tolerant lines and to identify the superior barley line.Results and discussionThe highest GMP and MP were related to 4 and 13 lines. Based on tolerance index (TOL), genotype 1 had the lowest and line 7 showed the highest level of tolerance, respectively. Based on MP and GMP indices, 4, 7 and 13 lines had high drought tolerance. A high positive and significant correlation was observed between MP, GMP, Ys, Yp, which indicates that these indices are suitable for identifying drought tolerant lines. Based on the results of the principal component analysis and the bi-plot diagram, it was observed that the lines tolerant to drought stress are almost consistent with the clustering pattern of tolerant lines and the lines sensitive to drought stress are also consistent with the clustering of sensitive lines. MP and GMP indices are suitable for evaluating drought tolerance because they showed a high correlation with grain yield under normal conditions and under water stress. The closeness of 4 and 13 lines to GMP, MP, HARM, Ys indicates the tolerance of these lines to drought stress and therefore they can be suggested as drought tolerant lines.ConclusionSelection of drought tolerant lines based on a combination of tolerance indices can provide useful criteria for drought tolerance. A high positive and significant correlation was observed between MP, GMP, Ys, Yp, which indicates that these indices are suitable for identifying drought tolerant lines. These results help the modifier to select lines in different environments. Principal component analysis showed that it is important to introduce genotypes with desirable traits such as genotypes with high yield and resistance to drought stress. It is possible to speed up the improvement of new barley cultivars by using stress tolerance indicators by breeders. In general, 4, 7, and 13 lines were drought tolerant and can be used for barley improvement programs. Based on principal component analysis, drought sensitive and tolerant lines were consistent with cluster analysis. Exploiting the results of the present study can help breeders to select and identify genotypes that have relative tolerance to drought stress.

IntroductionWater deficit poses severe limitation to potato cultivation as a drought-sensitive crop plant. Selection of tolerant genotypes based on a combination of tolerance indices can provide useful criteria for breeding drought tolerant potato varieties. Water deficit affects plants at various levels and stages of their life cycle. This abiotic stress not only affects plant–water relations through the reduction of leaf water content, turgor, and total water, but it also affects stomata closure, limits gas exchange, reduces transpiration, and disturbs photosynthesis. In potato, tolerance to drought is a very complex trait. Photosynthesis is one of the basic physiological processes of plants with internal and external conditions. Any reduction of the intensity of this process causes a decrease in the amount and quality of crop plants. One of the indicators for early prediction of potato yielding can be the measurement of chlorophyll content. It is an informative tool for studying the effects of dif­ferent environmental stresses on photosynthesis. Chlorophyll content has an important role in photosynthesis and in understanding plant functions. In any research, measuring of the chlorophyll content is used for assessment of potato genotypes tolerant and/or sen­sitive to environmental stresses.Materials and methodsIn this study, 20 potato genotypes were evaluated under two water levels; normal and water deficit stress conditions. The experiment was performed as spilt-plot based on randomized complete block design with three replications at the Seed and Plant Improvement Institute, Karaj, Iran in 2018. The correlations among the different traits were measured and estimated by calculating Pearson correlation coefficients using the statistical tool in Minitab 17. Tuber yield, yield components, growth parameters, and morphological traits were measured under both well-watered and water stressed treatments. Morphological and reproductive characteristics such as plant height, leaf dry weight, chlorophyll content, yield tuber, ware yield, seed yield, non-marketable yield, and marketable yield were measured. Result and discussionAnalysis of variance showed that stem number, chlorophyll content, stem thickness, plant height, leaf dry weight (LDW), total yield, ware yield (yield>55 mm), seed yield (yield 35-55 mm), non-marketable yield (yield

ObjectiveSeed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules. Materials and methodsRaw microarray data related to the germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h, and 71h after the germination stage. Then, weighted gene co-expression network analysis (WGCNA) was utilized for the detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression patterns after 9h, 18h, and 71h after the germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR. ResultsMost of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to a stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at the germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is a lack of information on the seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism of seed germination in barley. ConclusionsThe results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular-assisted selection and breeding of fast-germinating barley genotypes.

ObjectivePotato (Solanum tuberosum) is an important food and economic crop in the world. However, potato shows susceptibility to drought stress. Thus, the investigation of the molecular mechanism of drought stress tolerance is essential considered. GF14/14-3-3 protein is one of the conserved dimeric proteins that regulate several cellular processes, ranging from metabolism to transport, growth, development, and stress response. However, only a few reports are available regarding the effect of 14-3-3 genes in response to stress in potatoes. Materials and methodsIn this study, twelve 14-3-3 genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, phylogenetic analysis, TFBS, and synteny analysis were performed on the 14-3-3 genes. In addition, the expression analysis of two genes (StGF14i and StGF14h) in four tissues (root, stem, leaf, and tuber) and their expression under drought stress in the greenhouse was investigated. ResultsBased on phylogenetic relationships, the StGF14 family members were categorized into two classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of 14-3-3 genes revealed that the highest and the lowest number of TFBs were MYB and CSD, respectively, were found in the promoters of 14-3-3 genes. Moreover, different frequencies of TFSB in 14-3-3 genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. Furthermore, the genome evolution of S. tuberosum using orthologs and paralogues identification was studied. The number of exons in 14-3-3 genes was from four to seven and most of these genes in the same subfamily had the same exon-intron patterns. The expression of two genes in leaves and tuber under drought stress as well as the gene expression of both genes in root, stem, leaf, and tuber tissues under drought were examined. Based on the expression analysis of two genes StGF14i and StGF14h in tissues and a survey of drought stress, the StGF14i gene has the maximum expression in four tissues and also, the highest expression in tubers under drought stress. Our results revealed that two orthologous gene pairs between S. tuberosum and A. thaliana as well as eight paralogous genes among potato genomes were identified. ConclusionsThe expression patterns of StGF14i and StGF14h genes in different tissues and in response to drought stress that two genes had the conserved and necessary roles in potato growth and development potato. It is hoped that the results of this study will be useful for further investigation of the functional role and molecular mechanisms of 14-3-3 genes in response to drought stresses.

Abstract Background Plants use escape strategies including premature senescence and leaf reduction to cope in response to drought stress, which in turn reduces plant leaves and photosynthesis. This strategy allows the new generation (seeds) to survive under drought but, plants experience more yield loss during stress condition. The amount of damage caused by drought stress is compensated by the expression of genes involved in regulating leaf aging. Leaf senescence alters the expression of thousands of genes and ultimately affecting grain protein content, grain yield, and nitrogen utilization efficiency. Also, under drought stress, nitrogen in the soil will not become as much available and causes the beginning and acceleration of the senescence process of leaves. The main body of the abstract This review identified proteins signaling and functional proteins involved in senescence. Further, transcription factors and cell wall degradation enzymes (proteases) related to senescence during drought stress were surveyed. We discuss the regulatory pathways of genes as a result of the degradation of proteins during senescence process. Senescence is strongly influenced by plant hormones and environmental factors including the availability of nitrogen. During maturity or drought stress, reduced nitrogen uptake can cause nitrogen to be remobilized from leaves and stems to seeds, eventually leading to leaf senescence. Under these conditions, genes involved in chloroplast degradation and proteases show increased expression. The functional (proteases) and regulatory proteins such as protein kinases and phosphatases as well as transcription factors (AP2/ERF, NAC, WRKY, MYB, and bZIP) are involved in leaf senescence and drought stress. Short conclusion In this review, senescence-associated proteins involved in leaf senescence and regulatory and functional proteins in response to drought stress during grain filling were surveyed. The present study predicts on the role of nitrogen transporters, transcription factors and regulatory genes involved in the late stages of plant growth with the aim of understanding their mechanisms of action during grain filling stage. For a better understanding, the relevant evidence for the balance between grain filling and protein breakdown during grain filling in cereals is presented.

One of the most important and effective contexts for advancing development goals in rural areas is recognizing the living conditions of households, their access to various livelihoods, and geographical factors affecting livelihoods; With this view and to evaluate the role of various livelihood assets in the sustainability of a rural area, the present study has investigated the role of livelihood capital in rural settlements in Takab area. This research is based on the mixed research method of exploratory mixed research design. According to the study, capital in the form of 3 main sections of environmental capital (mines, tourism capacity, crops, and horticultural products, livestock products (dairy), pastures, beekeeping products), human capital (level of education, desire of families to study Children and carpet weaving) and social capital (public participation and empathy, social security, ethnic diversity, and peaceful living) were categorized. The results of the research show that the study area has favorable conditions in terms of environmental, human, and social capital, and the main issue in this regard is how to use these resources. Mines as an environmental asset have not only not contributed much to the livelihood of the villagers, but have also destroyed the surrounding environment, changed land use, and destroyed infrastructure (roads). According to the findings, the reason for such consequences is mostly due to the non-participation of people in the use of environmental potential. Physical and financial capital did not have suitable conditions in the study area, the main reason for which is the distance of Takab from large and medium cities in the region, as well as the special geographical and mountainous conditions of the region.

Genetic diversity is the best way to improve available genetic resources for breeding programs in gerbera. In present study, genetic diversity of 22 gerbera cultivars was investigated using inter-simple sequence repeat (ISSR), directly amplified minisatellite DNA (DAMD), and Random Amplified Polymorphic DNA (RAPD) markers. Average polymorphism information content (PIC) for ISSR, DAMD and RAPD markers was 0.40, 0.41 and 0.40, respectively. Cluster analysis for ISSR, DAMD and RAPD divided the cultivars into three distinct clusters. The comparative analysis of the three markers (ISSR, DAMD and RAPD) showed that DAMD had superiority over RAPD and ISSR in characterization of genetic diversity in Gerbera. To our knowledge, this is the first report of a comparison of performance among DAMD, ISSR and RAPD techniques on a set of gerbera genotypes. Overall, our results showed that DAMD markers well represented different genotypes of gerbera diversity.

Abstract Background The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes. Results Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. The number of exons in U-box genes ranged from one to sixteen. For most U-box genes, the exon–intron compositions and conserved motifs composition in most proteins in each group were similar. The intron–exon patterns and the composition of conserved motifs validated the U-box genes phylogenetic classification. Based on the results of genome distribution, StU-box genes were distributed unevenly on the 12 S. tuberosum chromosomes. The results showed that gene duplication may possess a significant role in genome expansion of S. tuberosum. Furthermore, genome evolution of S. tuberosum was surveyed using identification of orthologous and paralogous. We identified 40 orthologous gene pairs between S. tuberosum with Solanum lycopersicum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Zea maize, Coriaria mytifolia, and Arabidopsis thaliana as well as eight duplicated genes (paralogous) in S. tuberosum. StU-box 51 gene is one of the important gene among other StU-boxes in S. tuberosum under drought stress which was expressed in tuber and leaf under drought stress. Furthermore, StU-box 51 gene has the highest expression levels in four tissue-specific (stem, root, leaf, and tuber) in potato as well as it had the highest number of TFBS in promoter region. Based on our results, StU-box 51 can introduce to researcher to utilize in breeding program and genetic engineering in potato. Conclusions The results of this survey will be useful for further investigation of the probable role and molecular mechanisms of U-box genes in response to different stresses.

AGC kinases are highly conserved regulators in a variety of cellular processes such as differentiation, proliferation, and growth. They are known to play important roles in stress and hormonal responses, including ROS signaling. AGC kinases are the main class of protein kinases in plants, having central functions in different stages of plant growth. In the present study, the analysis of phylogenetic relationships, gene structures, chromosomal locations, synteny analysis, gene ontology, subcellular localization, and gene expression of AGC kinase identified 28 AGC kinase genes in barley. Phylogenetic tree grouped them into seven subfamilies, as supported by exon-intron organization. Gene duplication and synteny indicated that tandom and block duplication events played an essential role in the expansion of AGC kinase gene families in barley. The Real-time quantitative reverse transcription PCR (qRT-PCR) analysis performed for HvAGC kinase gene were largely expressed in different tissues of roots, stems, and leaves in Azaran and Jolgeh cultivars under heat and cold stresses. The results of chromosomal localization showed that the AGC kinases were located on all chromosomes of barley except chromosome 1. Genome evolution of species was surveyed using identification of orthologous and paralogous genes. Identifying overlaps between orthologous clusters can enable us to study the function and evolution of proteins in different species. To our knowledge, this is the first detailed report of using AGC kinases for bioinformatics analysis in barley. Results revealed a broad understanding of the AGC kinase gene family in barley, which will be valuable for improving barley varieties’ response to heat and cold stresses. Also, HvNDR6.2 gene can utilized as molecular markers under cold stress in the three organs.

Abstract Background Potato is one of the most important food crops worldwide, contributing key nutrients to the human diet. Plant hormones act as vital switchers in the regulation of various aspects of developmental and growth stages in potato. Due to the broad impacts of hormones on many developmental processes, their role in potato growth and developmental stages has been investigated. Main body of the abstract This review presents a description of hormonal basic pathways, various interconnections between hormonal network and reciprocal relationships, and clarification of molecular events underlying potato growth. In the last decade, new findings have emerged regarding their function during sprout development, vegetative growth, tuber initiation, tuber development, and maturation in potato. Hormones can control the regulation of various aspects of growth and development in potato, either individually or in combination with other hormones. The molecular characterization of interplay between cytokinins (CKs), abscisic acid (ABA), and auxin and/or gibberellins (GAs) during tuber formation requires further undertaking. Recently, new evidences regarding the relative functions of hormones during various stages and an intricate network of several hormones controlling potato tuber formation are emerging. Although some aspects of their functions are widely covered, remarkable breaks in our knowledge and insights yet exist in the regulation of hormonal networks and their interactions during different stages of growth and various aspects of tuber formation. Short conclusion The present review focuses on the relative roles of hormones during various developmental stages with a view to recognize their mechanisms of function in potato tuber development. For better insight, relevant evidences available on hormonal interaction during tuber development in other species are also described. We predict that the present review highlights some of the conceptual developments in the interplay of hormones and their associated downstream events influencing tuber formation.

Trehalose-6-phosphate synthase is a key enzyme in trehalose biosynthesis. Trehalose has many applications in plant growth and development and in response to abiotic stresses. In this study, analysis of 11 sequences of OsTPS genes downloaded from NCBI was performed in Oryza sativa. The analysis of bioinformatics performed included co-expression network, gene expression, chromosomal map, analysis of cis element and phylogenetic relationships for the TPS gene in rice. Phylogenetic analysis showed that TPS genes were grouped into two classes. Class I and II included OsTPS1 and OsTPS2-11 genes, respectively. The gene network analysis showed that OsTPS formed the gene networks and are mostly active in nucleus and chloroplast. According to phylogeny tree, gene structure, and analysis of cis-elements, OsTPS1 gene was different from other TPS genes. Also, according to co-expressed network, OsTPS1 showed to be the central protein encoding protein trehalose-6-phosphate synthase. OsTPS1 has been suggested to play a key role in flowering initiation in rice. It has also been shown to have an important role in response to osmotic and abiotic stresses (low temperature, salinity and anoxia). Our findings can provide a better understanding of molecular mechanisms of OsTPS genes and their expression in response to various stresses.

Abstract Objective Lentil (Lens culinaris) is the third most important grain legume in the world after chickpea (Cicer arietinum L.) and pea (Pisum sativum L.). Therefore, the aim of this research was (1) to determine the genetic diversity and structure of molecular variation of genotypes and (2) to identify relationships among genotype for conservation, management, and utilization of these genotypes in crop breeding programs. Materials and methods Total genomic DNA was extracted from leaves of each genotype following a CTAB protocol. After DNA extraction, DNA samples were amplified using polymerase chain reaction (PCR). Evaluation of the genetic diversity of 90 lentil genotypes was performed using 30 SSR markers. Results A total of 145 polymorphic alleles were produced with an average of 4.06 alleles per locus. The highest number of alleles produced belonged to SSR 80 primer with eight alleles and the lowest number of alleles belonged to SSR96 primer with three alleles. Polymorphic information content (PIC) for the markers ranged between 0.35 to 0.83 with an average of 0.63. Maximum and minimum PIC have belonged for SSR80 and SSR28, respectively. Shannon index value was variable from 1.94 (for the SSR80) to 0.829 (for the SSR48). The expected heterozygosity was observed in genotypes ranged from 0.845 (SSR80) to 0.422 (SSR48). The mean of this index obtained with 0.643. Clustering analysis was performed using Neihbour-Joining algorithm and population structure analysis was performed using Bayesian method. The best number of sub-populations was identified as three. Genotypes were identified within the different sub-populations that most of genotypes in sub-populations were not separated based on their geographic origins. Conclusions Results of this study revealed that SSR marker has highly potential for evaluation. This marker could separate all of genotypes very well.

Auxin response factors (ARF) gene family plays key roles in plant development and act as transcription factors (TFs) in the regulation of gene expression. An extensive bioinformatics analysis including analysis of conserved motifs, chromosomal map, phylogenetic relationships, and expression profiles were performed for the maize ARF gene family. In this study, a set of publicly available 38 ARF maize (Zea mays) nucleotide sequences were downloaded. Using microarray data, a bioinformatics search for identification of TFBs in ARF genes using plant promoter analysis (PlantPAN) was carried out. The 38 maize ARF genes were categorized into three groups (Class I, II, and III). ARF genes have been studied by molecular methods in several different plant species however to better understand the mechanisms of these genes more studies are needed. Gene cluster analysis showed that the same set of genes on the chromosomes were positively correlated with the same number of gene clusters. Several TFBs including AP2/ERF, ERF, WRKY, bZIP, bHLH, GATA, and NAC were identified in the promoter regions. These TFBs are responsible for modulation of several biotic stress-responsive genes. The main aims of the present study were to obtain genomic information for the ZmARF gene family and their expression under abiotic and biotic stresses.

Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most critical diseases in rice. In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. Almost all responsive genes were down-regulated at around 3 h time point and up-regulated 24 h time point in response to bacterial stress in rice varieties (Oryza sativa subs. japonica ‘IR64’, ‘IRBB5’, ‘IRBB7’ and ‘Y73’). Gene ontology showed that genes are involved in different biological processes including translation and cellular protein metabolic processes. Network analysis showed that genes expressed in response to pathogen infection (Xoo) included protein translation, eukaryotic initiation factors (eIFs), ribosomal proteins, protein ubiquitin, and MAPK genes. The genes expressed in response to bacterial stress can enable plant balance between synthesis and degradation of proteins which in turn allows plants for further growth and development. TATA-box and CAAT box had the highest number of cis elements involved in bacterial stress. These genes can provide novel insights into regulatory mechanisms in biotic stress responses in rice. Identification of bacterial stress response/tolerance genes of rice can assist the molecular breeding of new rice varieties tolerant to bacterial stress.

Objective: Osteoporosis or silent disease is a major bone disorder in elderly women in current century. Estrogen has an important role in osteogenesis and prevention of bone fractures. Hormone replacement therapy (HRT) is usually accompanied by such effects as breast and ovary cancers. Thus, there is an increasing demand for replacement with plant phytoestrogens. This study is focused on determining the effects of Foeniculum vulgare extract on proliferation and osteogenesis progress in human mesenchymal stem cells. Material and Methods: Human mesenchymal stem cells were isolated and treated with different amount of plant extracts (0.5 to 100 µg/ml). Extract cytotoxicity was measured using MTT assay. The alkaline phosphatase enzyme activity was measured to evaluate the differentiation progress. Results: Results of MTT assay and alkaline phosphatase activity showed that Foeniculum vulgare extract, at range of 5 to 50 µg/ml, may positively affect cell proliferation and mineralization. The most proliferation and enzyme activity were seen with dose of 5 µg/ml. Conclusions: Foeniculum vulgare has been used in Iranian folk medicine for many years. Our in vitro study showed that Foeniculum vulgare extract has osteoprotective effects.

Mycosphaerella graminicola, the causal agent of septoria tritici blotch (STB), is a widespread and significant pathogen of wheat. To determine mating types, 89 isolates were collected randomly from wheat fields of Khuzestan, East Azerbaijan, Ardebil, Kermanshah and Golestan provinces of Iran, during 2006-7. DNA was extracted based on standard protocols. Multiplex PCR was conducted using two pairs of mating type-specific primers for MAT1-1 and MAT1-2. Sensitivity to strobilurin fungicide was determined using strobSNPrc7 and strobSNPrc1 primers. The results showed that in 35 isolates, a fragment of 340 bp amplified with MAT1-1 idiomorph specific primers and in 54 isolates a fragment of 660 bp was amplified with MAT1-2 idiomorph specific primers. While the mating type frequencies were highly unequal, the MAT1-1 was predominant. All isolates were sensitive to strobilurin and amplified a fragment of 639 bp. It is concluded that both mating types are present in Iran, although with different frequencies, which may affect genetic variation through sexual cycle. Meanwhile the studied isolates were not resistant to strobilurin fungicides which may be due to growing wheat cultivars resistant to STB rather than using strobilurin fungicides as a dominant control method.

Astragalus L. is the largest genus of flowering plants in Iran and has various complicated taxonomical difficulties in its classification. Astragalus sect. Hololeuce Bunge. with its closely related section (Sect. Onobrychoidei DC.) comprise a taxonomically complex group within bifurcate hair ones. Delimitation of mentioned sections is the most challenging issues. In this study, 9 species of Hololeuce plus 10 species of Onobrychoidei were analyzed phylogeneticaly using 38 morphologic characters. Some new morphological characters were represented as results for simple classification of the studied sections. On the other hand, it was demonstrated that the bulk of two sections constructed a monophyletic group but some taxonomic revisions were suggested.

In this research, total of 15 species belonging to Astragalus section Ornithopodium as well as its closely related ones were analyzed using morphological and molecular data. A. frigidus and A. stocksii were selected as outgroups based on previous studies. Based upon our results, species of sect. Ornithopodium along with those of sect. Onobrychoidei were placed within a single large clade with high support and are closely related taxa. Species from section Dissitiflori formed a distinct clade from the two other studied sections. Based on our molecular and morphological data, Astragalus pravitzii Podlech, which had been recently transferred to the section Ornithopodium from the section Dissitiflori, was not affiliated with that section.