m. r. naghavi

An effort was made to analyze metabolome and transcriptome profiles of Ferula persica via GC-MS and RNA-seq data. The analysis of the essential oils extracted from both flower and root tissues demonstrated the prominence of monoterpene constituents, while sesquiterpene compounds were present in the lower magnitudes. Considering transcriptome analysis, 2127 differentially expressed genes were found between root and flower: 396 transcripts were up-regulated in root, while 1731 exhibited an up-regulation pattern in flower. Out of 2127 transcripts, 86 were annotated as Terpene Synthases (TPSs), of which 83 TPSs were classified subsequently into five individual sub-families of TPS-a (33), TPS-b (42), TPS-c (2), TPSe-f (3), and TPS-g (3). Several transcription factor families were recognized among the differentially expressed genes, suggesting their direct or indirect regulatory roles for the biosynthesis of terpenoids in F. persica. Finally, according to our phylogenetic results, both F. assa-foetida and F. gummosa were placed in the same clade, while F. persica was lonely settled in one monophyletic clade, with the estimated divergence time of 2.99 Million Years Ago (MYA) between F. gummosa and F. assa-foetida, and 3.87 MYA between F. persica and two other Ferula species.

miRNAs genes are regulatory elements that their main role is to downregulate gene expression at the mRNAs level. miRNAs also play important roles in several plant pathways related to important cellular activities such as growth, reproduction, differentiation, morphogenesis, apoptosis and, response to abiotic and biotic stresses. This research was conducted to identify conserved miRNAs and their target genes using next generation sequencing data in the damask rose (Rosa damascena Mill.). Although bioinformatics methods have been developed as the most efficient strategy for target miRNA identification, high-throughput experimental strategies are still in high demand. Bioinformatics tools (Cmii, psRNATarget, WEGO, Blast2GO) and laboratory method (real-time PCR) were used to identify new miRNAs, predict and determine the ontology of the target genes involved in the production of scent and color in the damask rose, respectively. Using EST and RNA-seq data based on Rosa lucieae homology, four miRNA families, including: miR5021, miR2673, miR156, and miR838, were selected as candidate miRNAs. In the next step, for the quantitative evaluation of the real-time PCR to validate the expression level of the selected miR5021 in two samples (white and hot-pink) and the biological stage (young and bud) of the damask rose, foliar spraying with the concentrations of zero (control) and 300 μM of methyl Jasmonate for 48 hours was made. Result showed the highest relative expression of miR5021 belonging to the pink sample on the young development stage. These findings accelerate future prospective studies on the regulatory mechanisms of miRNAs in Rosa damascena.

MicroRNAs are endogenous noncoding RNA that play vital roles in all plant cellular metabolic processes by mediating target gene expression. To date, miRNAs in Taraxacum spp., which is an important industrial plant, have remained largely unknown. In the present study, 970 miRNAs from 399 families were identified in Taraxacum spp by conducting computational approaches. The most frequent miRNAs in Taraxacum spp was miR5021. According to the KEGG results, miR5021, miR838, and miR1533 are related to the terpene biosynthesis pathway, while miR5015b, and miR1436 are involved in the starch and sucrose biosynthesis pathways. Quantitative real-time PCR assay was performed to validate the expression levels of five predicted miRNAs and 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase (HMGCR) and invertase as the target genes. Results indicated that the highest relative expression of miR1533 and miR1436 occurred in the flower, while the highest transcripts levels of miR5015b were observed in the stem. In addition, the higher relative expression level of the miR5021 and miR838 was consistent with the lower expression level of the HMGCR gene in all tissue, suggesting that miR5021 and miR838 are involved in regulating HMGCR gene expression. Since mevalonate pathway is the main source of isopentenyl pyrophosphate, which is used in the synthesis of rubber, miR5021 and miR838 play an important role in the production of rubber by regulating the expression of HMGCR enzyme. These findings will accelerate future perspective studies on the regulatory mechanisms of miRNAs in Taraxacum kok-saghyz.

Allium includes more than 920 species worldwide. Iran is the main habitat of many wild Allium species. In this study, onion tissue of two species A. stipitatum and A. scabriscapum from two subspecies Melanocrommyum and Reticulatobulbosa were used to evaluate and identify the expression pattern of storage proteins obtained by the SDS-PAGE method. Two-dimensional gel electrophoresis and MALDI TOF/TOF MS mass spectrometry were used to identify protein spots and to observe the expression changes of the two species. Analysis of gels by two-dimensional electrophoresis revealed 138 protein spots. The results showed a slight similarity between the gels and a different expression pattern between the samples, based on which a small number of similar spots were obtained in both gels. The results showed that there were significant differences in the expression profile of onion tissue proteins of these samples. Using the T-test, 9 protein spots with the most significant changes were identified at the 5% probability level, and among them, 3 different spots were identified using Mass spectrometry was selected for identification. The results of mass spectrometry experiments and matching of the obtained data with NCBI and Uniprot databases and bioinformatics tools showed that the tested spots were consistent with Maturasek proteins, Agmatine coumaroyltransferase-1, and a protein with the unknown function called Hypothetical Protein. The findings of this study showed that since the samples belonging to A.stipitatum and A.scabriscapum are of the same genus, but the expression pattern of their stored proteins in onion tissue is very different from each other.

To investigate the effect of irrigation volume and nutrient consumption on yield and yield components of cherry tomatoes, a greenhouse experiment was conducted as split plots in a completely randomized design. The results showed that the maximum plant height, stem diameter, number of fruits per plant, fruit yield per harvest, total fruit yield, and shoots dry weight were obtained in the treatment of 20 liters of water per square meter per day with nutrient solution application of micronutrients with concentrations of one and a half times the Hoagland solution. The highest water use efficiency obtained from the treatments of 15 and 20 liters of water per square meter per day and consumption of nutrient solution one and a half times the concentration of micronutrients in Hoagland solution with averages of 6.55 and 6.10 g final yield of fresh fruit each plant per liter of water consumption per plant, respectively. Correlation coefficients between the traits also showed a positive and significant relationship between total fruit yield with all studied traits, so that the highest correlation (r = 0.93) had with trait of number of fruits per plant and the lowest correlation (r = 0.7) had with trait of stem diameter.

Phylogenetic study of savory (Satureja spp.), which has different species and valuablecompounds such as thymol and carvacrol, is of special importance among medicinal plants. In this study, 21 accessions belonged to nine Satureja species were identified and collected from main habitats in eight provinces of Iran, including East Azarbaijan, Kurdistan, Gilan, North Khorasan, Yazd, Lorestan, Ilam, and Kermanshah. Genomic DNA extraction was performed using the modified CTAB method. In the phylogenetic study, in addition to the nine collected species, the sequences of ITS and matK genes of Satureja species registered with the NCBI were also added to the phylogeny tree as part of the group. In addition to Satureja genus, the sequences of Thymus, Ziziphora, Clinopodium genera were also used NCBI as an outgroup to root the phylogenetic tree. The results showed that in the study of Satureja. spp kinship relationships, the ITS nuclear gene was more appropriate than the matK chloroplast gene. In the native species of Iran, the maximum genetic distance was between S.mutica and S.atropatana and the minimum genetic distance was between S.rechingeri and S.khuzistanica. In the phylogenetic tree, five species of S.macrantha, S.atropatana, S.sahendica, S.edmondi, and S.bachtiarica with %100 bootstrap value, two species of S.mutica and S.spicigera with %96 bootstrap value, and two species of S.khuzistanica and S.rechingeri with %100 bootstrap value were close relatives. The results showed a significant consistency with Flora Iran and Flora Iranica in terms of morphological traits.

Savory (Satureja spp.), due to its essential oil compounds such as thymol and carvacrol, has a special place among medicinal plants. In this study, transplants of 18 accessions of six species of savory originated from five provinces of Iran, cultivated in a randomized complete block design with three replications in Tikmehdash station of East Azerbaijan, Iran. Morphological and phytochemical traits were recorded over two years. Results showed high diversity between and within the species. Among the species, S. spicigera (Ganjeh accession from Guilan)with the highest essential oil yield (20.4 kg/h) and S. sahendica (Zinjanab accession from East Azerbaijan)with the highest establishment rate early flowering date coupled the highest amount of thymol were identified as the most compatible species. Thymol content had a positive correlation with aerial floral weight and leaf area. In cluster analysis, the species were divided into three groups: S.bachtiarica from Yazd in group 1, S. mutica from North Khorasan in group 2 and species adapted to East Azerbaijan climate: S. spicigera, S. sahendica, S. atropatana and S.macrantha in group 3. In the principle components analysis, selection based on the first and second components leads to the selection of species with high essential oil yield and oil quality, respectively. Distribution of the accession/species in the biplot diagram based on the first and second components was in agreement with the results of cluster analysis. According to the results, for cold regions, early or moderate maturity species with high proportion of leaf and flower to stem and high leaf area should be selected and the performance components should be raised to a degree that does not reduce essential oil efficiency.

Cannabis (Cannabis sativa L.), commonly known as hemp, is an annual herb belongs to the family Cannabacea. The seeds of this plant have considerable content of oil and unsaturated fatty acids, and its fiber is used in the paper and textile industries. Tetrahydrocannabinol and cannabidiol are main cannabinoid compounds of this plant, which have high importance for their well-known pharmaceutical properties. Therapeutic effects of secondary metabolites of hemp on different diseases, such as cancer, Multiple Sclerosis (M.S.), and AIDS and their anxiety and palliative characteristics have been reported in several studies. Considering oil content, and therapeutic and industrial properties of the hemp as well as, its high diversity in Iran, more studies are needed to better recognize this plant and the economic production of its therapeutic compounds. In the present paper, a comprehensive review of agronomic, therapeutic and phytochemical characteristics of hemp is presented.

Rhizobacteria that benefit plants by stimulating growth and suppressing disease are called plant growth promoting rhizobacteria (PGPR) which includes rhizobia. In addition to nitrogen supply, rhizobia promote the growth of plant root system and improve nutritional uptake. In this research, for isolation and identification of rhizobacteria especially rhizobia in a symbiotic relation with non-cultivated legumes, 21 plant samples from 12 non-agricultural sites of Alborz province were collected. In order to isolate bacteria, serial dilutions were prepared from nodules, rhizosphere soil and roots. Bacteria were cultured and purified on YMA medium and morphological and biochemical characteristics of isolates were studied. In total, 16 purified strains were obtained. Bacterial DNA of all strains were extracted and 16S rRNA gene was amplified with specific primers using polymerase chain reaction (PCR). Strains were identified by sequences of this gene and using EzTaxon database. All isolated strains in this research belonged to 12 species. PCR reactions were also done for atpD, nodA and nifH genes by specific primers. Phylogenetic trees were constructed by maximum-likelihood statistical method and evolutionary distances were computed by using the Tamura-Nei model. Based on the obtained results from four strains of Ensifer meliloti which were isolated in this study, only Tal31 strain showed a higher growth with the increace of NaCl from one percent to two percent (w/v), therefore this strain is probably salt tolerant. This is the first time that Rhizobium laguerreae (Tal71) and Neorhizobium alkalisoli (Krj1) were isolated from root nodules of Trifolium pretense and Colutea buhsei respectively. These findings show that the host range of rhizobial strains are broader than it was estimated before.

For investigating mechanisms of tolerant to slat and drought stress in canola (Brassica napus L.), two spring canola cultivars such as SW5001 as tolerant cultivar and Sarigol as sensitive cultivar were evaluated at two levels of salinity and drought in factorial based on randomized complete block design with four replications using a hydroponic culture system. Sampling for proteomic analysis was performed in the rosette stage and before the stem elongation stage (two weeks after salt stress treatment ) in greenhouse. To investigate the proteome response of rapeseed to salt stress and drought stress, protein extraction from leaf was performed and subjected to first dimensional electrophoresis using IPG strips for both control and stressed plants. In the second dimension, proteins were separated by SDS-PAGE and then, staining with commassie brilliant blue, gel acquisition and quantitative analysis of protein spot by PDQuest software. Finally, 17 and 25 protein spots between control and treatment plants for salinity and drought, were detected, respectively. 10 and 15 protein spots were common between two cultivars under salt and drought stress separately. Also, four and six digit unique protein spots for tolerant cultivar under salt and drought stress respectively while for susceptible cultivars were three and four unique protein spots, respectively. The total of all proteins in response to salt stress and drought in the SW5001 and Sarigol, three proteins common in both cultivars and both the stresses that such as Oxygen-evolving enhancer protein 2-chloroplastic, Ribulose-1,5-bisphosphate carboxylase / oxygenase large subunit of ATP synthase CF1 beta subunit of the protein were identified responding to drought and salinity. This proteins are involved in cell three members of the complex in photosystem II, ATP synthase and Rubisco that seems to be the most important cell components under salinity and drought. Thus, increasing the efficiency of the three complex cause to increase the efficiency of the cells and decrease the harmful effects of salinity and drought.

In this research, considering the importance of drought and canola, an experiment was done as factorial in a Randomized Complete Block Design using ten spring canola cultivars with hydroponic method in seedling stage and with induced of drought stress by PEG6000. Two weeks after of the stress induction and at the end of the rossete stage, samples were taken. The results showed that the value of morphological and physiological traits was declined under drought stress. Also the studied cultivars were varied in response to drought stress and in general, the most tolerant and sensitive cultivars for studied traits were SW5001 and Sarigol cultivars, respectively that to graduate studies on these two cultivars proteome analysis was performed. To study the pattern of protein, extraction of protein from leaf tissue was performed and the first dimension electrophoresis using IPG strips and second dimension electrophoresis was performed by SDS-PAGE technique and after the gels staining with commassie blue, gels imaging with scanner and protein analysis with PDQuest software was done. Finally a total of 25 protein spots between control plants and under drought stress for both cultivars were detected that of these, 15 protein spots were common between two cultivars and six unique protein spots for tolerant cultivar and four unique protein spots for susceptible cultivar. After detection these proteins with mass spectrometry, overall, the most common protein groups between two cultivars were involved proteins in photo-reaction of photosynthesis, Calvin cycle and detoxifying enzymes. In total, the most important cause of the sensitivity and tolerance of canola cultivars different expression and unique expression of proteins into cultivars and finally effects of them on other were obtained.

Malaria is currently one of the most important causes of mortality in developing countries. High resistance to available antimalarial drugs has been reported frequently, thus it is crucial to focus on the discovery of new antimalarial drugs. Artemisinin, an effective antimalarial medication, is isolated from various Artemisia species. To identify the Artemisia species producing high quantity of artemisinin, eight species of Artemisia were screened with the genetic sequence characterized amplified region (SCAR) marker for higher quantity of artemisinin. The DNA band corresponding to SCAR marker was cloned into pGEM®-T Easy vector and sequenced. The content of artemisinin in tested species was also measured using high-performance liquid chromatography (HPLC) assay. The primers designed for high-artemisinin SCAR marker could amplify a specific band of approximately 1000 bp which was present in two Artemisia annua and Artemisia absinthium species. These SCAR marker sequences for two selected species were submitted into the GenBank databases under KC337116 and KC465952 accession numbers. HPLC analysis indicated that two selected Artemisia species, genetically recognized as high-artemisinin yielding plants, had higher artemisinin content in comparison to other examined species. Therefore, in this study, we propose developed SCAR marker as a complementary tool for confidently detection of high-artemisinin content in Artemisia species.

Elicitors are biotic or abiotic molecules that have effectively stimulated the production of plant secondary metabolites in plant, cell and organ cultures. Opium poppy serves as one of the particular commercial source of sanguinarine, as an anticancer and antimicrobial metabolite in the pharmaceutical industry;This study was done by the aim of increasing in expression of genes involve in the synthesis ofthisvaluablemetaboliteinplantcell suspension culture. In this study, the effects of two abiotic nano elicitors (nano TiO2 and nano-Silver), were studied on the expression of genes involve in sanguinarine biosynthesis pathway (tydc7, bbe1, DIOX2 and DBOX) at different time points (6, 24, 48, 72 and 168 hours) following treatments on shoot meristem and root suspension cell cultures using Real-time PCR. All of these genes were expressedmost abundantly6 and 24 hours after treatment with nano elicitors in both root and meristem suspension cell cultures. After time all the genes expression were significantly decreased. Comparing the results of this study with the findings of other major studies on the effect of elicitors on papaver gene expression, indicated that because of the small sizes of nano particles, they may cause the rapid induction of sanguinarine biosynthesis genes expression in the shortest possible time. Nevertheless other investigations showed the highest increasing in gene expression, 48hours after elicitation. Given that, this study was conducted on callus with dedifferentiated cells from two different organs, but remarkable distinction were observed in gene expression profile in both explant tissues. In the other words the trace of cellular memory, was seen in dedifferentiated cells regards to the origin of explants.

With regard to the significant functions of nuts in preventing cardiovascular diseases and certain kinds of cancer as well as their high consumption in our country, the present research was conducted to identify some characteristics of Iranian nut oils including walnut, almond, pistachio with cultivars Damavand, c.v.b12, Ahmad Aghaee with %4, Momtaz by measuring the total phenolic compounds using folin assay, identifying fatty acids profile by GC, oil oxidative stability at three different temperatures: / by Rancimat method and measuring other oxidative stability by Oven Test. Folin assay results showed that walnut consists the most phenolic compounds, then were pistachio and almond, respectively. Rancimat test results indicated that pistachio possessed the highest oxidative stability in each of three mentioned temperatures and then were almond and walnut, respectively. The results of the other oil oxidative stability showed the most oxidative stability among the mentioned oils and the conclusion of variation trend of peroxide index with less rate was in pistachio and then were almond and walnut, respectively. The important results of the fatty acids profile indicated that pistachio contained the most saturated fatty acids and the least saturated fatty acids belonged to walnut. Among the mentioned oils, almond oil had the least poly-unsaturated fatty acids and walnut had the most one. In addition, almond possesed higher oleic acid, then were pistachio and walnut, respectively. According to these findings and inspite of having high phenolic compounds in walnut oil compared with other mentioned oils, it is concluded that the profile of fatty acids has a more effective and crucial role in the stability of oils oxidation.

The genetic diversity of major crops, including durum wheat, has suffered an overall reduction with time. The knowledge of patterns of genetic diversity enhances the efficiency of germplasm conservation and improvement. In this study, 87 Iranian landraces of Triticum turgidum var. durum originating from different geographical areas of Iran, along with 21 durum cultivars from ten countries were evaluated using ten primer combination SSAP markers. Retrotransposons are mobile genetic elements that transpose via RNA mediation. They have wide distributions in genome because molecular markers have been designed based on them in recent years. SSAP markers BARE-1,Thv19, Tagermina and Tar1 were also used. Thv19M+ACA primer combination had the most polymorphic band in both landraces and cultivar durum wheats. Approximately 26.7 % BARE-1 bands were polymorphic in landraces.Thv19 showed a polymorphism level of 51.5%, and Tar1 and Tagermina displayed polymorphism levels of 32.8% and 27.2%, respectively. The amount of polymorphism in the studied cultivars for retrotransposons BARE1, Tagermina, Thv19 and Tar1 were 24.4%, 24.3%, 51.5%, 28.5%, respectively. This results show that Thv19 and Tar1 have more transpositional activity in the evolutionary process. Finally, Dendrogram was constructed to use algorithm UPGMA and Dice similarity coefficients.

Stripe rust is one of the most important fungal diseases of wheat that has been reported in all continents and more than 60 countries in the world. Wild emmer wheat,Triticum dicoccoides, the tetraploid progenitor of cultivated wheat, has proven to be a valuable source of novel stripe rust resistance genes for wheat breeding. G25 accession of this species has Yr15 gene that confers resistance to 31 stripe rust races and pathotypes. It has been mapped on chromosome 1BS. In the present study, as a first step towards map-based cloning of Yr15, it was fine-mapped in a F2 population with 825 individuals. According to frequency of retrotransposons in euchromatin regions of the genome and near the gene cluster, retrotransposon-based molecular markers were mostly used. Three SSR, three IRAP and seven REMAP markers were identified to be linked to the gene with a distance less than 2 cM and genetic map near the gene was saturated. Some markers were cosegragated at proximal side of the gene. One of the IRAP and two REMAP markers converted to locus specific and codominant SCAR markers. Locus specific and codominat marker, SC792, completely co-segragated with gene. Other two locus specific and codominant markers, SC1600 and SC1028, surrounded the gene in an interval of
1 cM. These markers could be used for reliable MAS and map-based cloning of Yr15. Also, it was demonstrated that retrotransposon based markers can be more useful and efficient in fine-mapping of genes controlling agronomically important traits.

In order to determine phenotypic diversity, 40 Rosa damascena accessions were evaluated in a completely randomized block design with 3 replications at the experimental field of Research Institute of Forests and Rangelands, Tehran, Iran. Several traits including flower weight, flower diameter, peduncle length, number of petals, number of stamens, leaf area, leaf dry weight and thorns intensity were recorded and analyzed for two years (2005-2006). Correlation coefficients showed that flower yield correlated positively with number of petals and negatively with peduncle length, leaf area, leaf dry weight and thorn intensity. Because of high heritability obtained for flower weight, number of petals, number of stamens and thorn intensity, selection based on these characters is recommended. Cluster and principal components analyses showed no relationship between genetic divergence and geographical origins, indicating germplasm exchange between different areas of Iran.

In order to estimate the number and inheritance of controlling genes for grain yield and some of the related traits in barley, Afzal and Radical varieties along with their F1, F2 and F3 generations were planted in a randomized complete block design with three replications. Head weight, head length, number of heads, number of spikelets, awn length, hundred grain weight, grains per head, straw yield per head , harvest index and grain yield in different generations were recorded. Analysis of variance indicated that mean squares of generations were statistically significant for all the traits. Then, generation mean analysis was performed for all the traits. Based on the results, additive and dominance effects played roles in controlling awn length. For the other traits besides the aforesaid effects, epistasis effect was also significant. Also, results indicated that dominance variance had the most important role in controlling the inheritance for traits. The average broad sense heritability for all the traits was estimated between %69 - %89. The number of genes for all traits was estimated to be between one and six.

This research was carried out to find genetic markers linked to drought tolerance in a barley doubled haploid population. In two separate experiments, 158 doubled haploid lines together with their drought tolerant parents (W i2291 and Tadmor) were evaluated in Tel Hadya and Breda (Syria) with 100 millimeter difference in rainfall. They were planted in each environment using an alpha-lattice design with two replications. Linkage map was constructed using 50 SSR and 93 AFLP markers that included 8 linkage groups for the seven chromosomes. QTL analysis was performed using composite interval mapping. Number of QTLs, their genomic location and additive effects were identified between 0.5 and 2.5 gram in Tel Hadya and Breda, respectively. Seven QTLs were determined for grain yield, one of them was common in two environments, and two separate QTLs in mean of environments in each environment. Susceptible stress index (SSI) had three QTLs which two of them were common in controlling grain yield. Bmag13 marker, which is located on third chromosome, had simultaneous linkage with QTLs which control 1000KW, grain yield.

The masculinization effects of 17α-methyltestosterone were investigated on the two developmental stages of guppy (Poecilia reticulate), namely, newly born fry and gravid females. The first group was treated with two doses of androgen, (30 and 60 mg/kg food), each for a period of 15 and 30 days and the second group (gravid females) was treated with the food doses of 400, 450 & 500 mg/kg in a 10 day duration prior to parturition. After three months, the first group masculinization ratio of 62.14% was attained only in 60 mg/kg at three-day long treatment and other treatments had no significant effect on masculinization. In this group all the treated fish developed male secondary sexual characteristics after 3 or 4 weeks. However, the above-mentioned characteristics disappeared gradually when hormone therapy was stopped. In the second group, all the treatments were significantly different from control group. 450 and 500 mg/kg treatments had the highest masculinization percentage (90.82 and 97.07, respectively) but the differences were not significant. Also there were 9.18% females in 450 mg/kg treatment and 2.93% intersex in 500 mg/kg treatment. But the so-called group mortality was higher and fecundity lower than those in the control group. Finally, it should be noted that hormonal treatment had not any significant effect on masculinization of newly born fry and with the regard to the effect of 450 mg/kg treatment on masculinization and mortality percentage, it can be introduced as the best treatment.

In order to evaluate heritability and gene action for resistance to barley powdery mildew, two resistant cultivars were crossed with a susceptible one. P1, P2, F1, F2 and F3 generations were planted in a Randomized Complete Block Design. At seedling and booting stages, susceptible cultivar was inoculated with a isolate of the pathogen. Infection type and disease severity were recorded and generation mean analysis was performed. The results showed that additive, dominance and epistasis effects were important for the two examined traits. Analysis of generation indicated that dominant variance was more important than additive variance in both traits. The approximate number of genes were estimated to be between one and two.