فرهاد نظریان فیروزآبادی

Saffron (Crocus sativus L.), a perennial plant of the Iridaceae family, is predominantly cultivated in Iran. Despite its ‎high economic value both domestically and globally as a precious spice, its cultivation faces substantial challenges from ‎numerous pathogens which significantly impact both yield and quality. Resistance genes (R-genes) encode R-proteins that ‎play a crucial role in activating plant defense mechanisms against pathogens. Nucleotide-binding site leucine-rich repeat ‎‎(NBS-LRR) genes are a family of intracellular R-genes that confer resistance to plants by initiating Effector-Triggered ‎Immunity (ETI). In this study, an in silico study was conducted on the transcriptome of saffron corms infected with ‎Fusarium oxysporum to identify NBS-LRR genes at 48 and 72 hours after inoculation using bioinformatics software and ‎databases. Arabidopsis NBS-LRR gene sequences were used to identify NBS-LRR members in the saffron corm ‎transcriptome. Then, the expression profile of NBS-LRR candidate genes was studied. Based on the results of BLASTX ‎algorithms, 63326 transcripts were documented. The results of this study revealed the presence of 30 NBS-LRR gene ‎transcripts in the transcriptome of saffron corms. The expression of the selected genes was significantly up-regulated in ‎infected corms compared to healthy control corms. Furthermore, analysis of the selected NBS-LRR genes indicated that their ‎expression levels were higher at 72 hours after inoculation compared to 48 hours. The LRR1 gene had a higher expression ‎level than the LRR2 gene at 48 and 72-hours post-inoculation. Plus, the results of this study revealed that NBS-LRR genes ‎are expressed in almost all saffron tissues, suggesting their involvement in the saffron's response to fungal infections. The ‎findings of this study suggest that NBS-LRR genes hold significant potential for utilization in future saffron breeding ‎programs. ‎

Potato (Solanum tuberosum. L.) belongs to the Solanaceae family. It is the third important crop plant as human food source after wheat and rice. Several biotic and abiotic stresses affect potato production and reduce its potential yield. In the drought stress and dehydration, the expression level of many genes changes and the accumulation of stress-related proteins is affected. Chitinases are proteins that show a basic level of expression in normal conditions, but their expression increases dramatically in disease conditions and some abiotic stresses. The existence of great diversity in plant chitinases and its induction by a wide range of biotic and abiotic factors indicates their important role in the functions related to defense and stress. According to the Economic importance and Limiting effects of drought stress for plant growght in this research, the effect of drought stress on the expression level of different classes of chitinase gene was investigated.

In this research, the members of chitinase gene family was identified in potato genome by bioinformatics and computational methods. Then, one gene was selected from each class of chitinase gene based on RNA-Seq data analysis in drought stress, and their expression level was evaluated following a water deficit treatment (50% field capacity) by Real-time PCR analysis. The expression level of genes was measured using the Livak and Schmittgen method using the 2-ΔΔct formula.

Under drought stress conditions, the majority of chitinase gene classes exhibited distinct expression patterns. Notably, among the four classes of identified chitinase genes in potato, class I exhibited up-regulation, whereas class V displayed a down-regulated trend.

In conclusion, our findings suggest a significant role for chitinases in potato's response to drought stress. The outcomes of this study offer valuable insights for screening potato cultivars/genotypes for drought tolerance and provide a foundation for molecular genetic strategies aimed at engineering drought-resistant potatoes.

Fusarium is a significant soil fungus found globally. The fungus responsible for the disease can survive as chlamydospores in infected seeds and plant debris for more than five years in the soil. When conditions are right, it can devastate entire crops. This fungus releases spores that grow when they come into contact with chemicals from the chickpea roots. The fungal threads invade the plant's roots and vascular system, which blocks the plant's ability to absorb water. As a result, the chickpea plant can die from lack of moisture. In Iran, the disease is common in many areas where chickpeas are grown, resulting in a 17% decrease in chickpea yields. In Lorestan Province, it causes root rot and wilting in chickpeas, severely impacting their production. Under suitable conditions, this disease can entirely devastate crops. To effectively manage this issue, it is crucial to identify the various Fusarium species, understand their detrimental effects, and evaluate which plants they can infect. Also, studying these species' genetic relationships can facilitate the development of improved disease control strategies.

This study focused on identifying Fusarium species that cause root rot in chickpeas in Lorestan Province. Researchers visited chickpea farms, collecting 155 samples from plants exhibiting yellowing, wilting, and root rot symptoms. The samples underwent isolation, purification, and identification in the laboratory based on their morphological traits. Pathogenicity tests were conducted on a susceptible chickpea cultivar named Arman to evaluate the pathogenic potential of the identified Fusarium species. This study focused on analyzing specific genetic markers to identify particular isolates. Researchers amplified two gene regions: the internal transcribed spacer (ITS) of ribosomal DNA and the ef1-α gene, utilizing materials from SinaGen Company. The amplified DNA fragments were sequenced by Biomegic Company in Tehran. The sequences were edited and analyzed using BioEdit 7.1 software and registered in the NCBI GenBank database. MEGA 7.0 software was employed for phylogenetic analysis to construct a phylogenetic tree, comparing the isolates with others in the gene bank. A bootstrap analysis with 1,000 repetitions was conducted to confirm the stability of the phylogenetic tree branches. The study evaluated specific isolates' harmful effects on the above-ground parts and roots of intentionally infected plants.

The phylogenetic tree presented in this study, constructed from specific gene sequences, aligns with the results of morphological analyses. The research identified Fusarium oxysporum and Fusarium solani as the most prevalent isolates. F. falciforme affects plants by causing yellowing and wilting, starting from the lower leaflets and spreading upwards. The roots also show signs of damage, with visible root rot symptoms after emerging from the soil. Additionally, there are instances of discoloration in the vascular bundles when looking at sections of the stem, both longitudinally and cross-sectionally. These findings correspond with previous studies in the field. Furthermore, the study uncovered that Fusarium falciforme is a weak pathogen for chickpea roots. Importantly, this research represents the first documented evidence of the pathogenic effects of Fusarium falciforme on chickpeas.

The phylogenetic tree presented in this study, constructed from specific gene sequences, aligns with the findings of morphological analyses. The research identified Fusarium oxysporum and Fusarium solani as the most prevalent isolates. The disease symptoms linked to most isolates from the F. oxysporum complex in this study resemble those caused by F. redolens. DNA sequencing revealed that the F. oxysporum isolates are closely related to F. redolens, with a 96% genetic similarity. All isolates of F. redolens showed symptoms similar to those of F. oxysporum f. sp. ciceris in pathogenicity tests but without any color change in the vascular tissue. Since black root rot is a localized issue, it is crucial to differentiate it from systemic diseases like wilting for effective plant pathology understanding. A combination of molecular analysis and thorough morphological examination is essential to identify these isolates correctly. These results are consistent with previous studies on the subject. Furthermore, the investigation revealed that Fusarium falciforme exhibits weak pathogenicity towards chickpea roots. Importantly, this research represents the first documentation of the pathogenic effects of Fusarium falciforme on chickpeas.

Salinity stress is a very serious threat to most agricultural products in the world. In the world, rice ranks second after wheat and is a relatively sensitive plant to salt stress. Protein kinases are an important group of kinase enzymes that phosphorylate target proteins by adding phosphate groups. These enzymes play an important role in cell communication by inducing the message of growth and reproduction. Gene expression is a process during which a useful gene product is synthesized by the information obtained from a gene. The purpose of this research was to investigate the expression level of SAPK1 gene from the protein kinase gene group in rice plants under sodium chloride salt stress by examining three different times after the stress was applied In this study, the expression pattern of SAPK1 gene in two Cultivars tolerant (Shastak Mohammadi) and sensitive (IR29) of rice plant under salt stress was investigated by factorial experiment in the form of a completely randomized design with three replications. Cultivars were planted in the research greenhouse of the Faculty of Agriculture of Lorestan University and at the seedling stage (5 to 6 leaves), salinity stress was applied to the plant at three levels of 3, 6, and 9 dS/m and the control treatment (without salt stress). Then, at three different times (6, 12, and 24 hours after applying stress), plant leaves were sampled to investigate gene expression. The leaf samples were stored in a freezer at minus 80 degrees Celsius. Then, RNA extraction and cDNA synthesis were done by special kits for each stage, and finally, The results of the analysis of SAPK1 gene expression pattern showed that in both tolerant and sensitive cultivars, the highest level of gene expression was observed at the salinity level of 9 ds/m 24 hours after applying the stress. At different times after applying the stress in the control treatment and the salinity level of 3 ds/m, the gene expression level in both tolerant and sensitive cultivars did not show any difference and was very insignificant. However, at the salinity level of 6 ds/m, 6 hours after applying the stress, the gene expression level in the tolerant cultivar increased 3 fold compared to the sensitive cultivar and control treatment. At this level, examining gene expression 12 and 24 hours after applying the stress, the amount of gene expression in the tolerant cultivar was about 7 fold higher than the sensitive cultivar and the control treatment. At the salinity level of 9 ds/m, 6 hours after applying the stress, the gene expression level in the tolerant cultivar was doubled compared to the sensitive cultivar and 4 fold higher than the control treatment. While 12 hours after applying the stress, the gene expression level in the tolerant cultivar increased by 5.5 fold compared to the sensitive cultivar and by 10 fold compared to the control treatment. Also, 24 hours after applying the stress, gene expression in tolerant cultivar was 3.5 fold higher than the sensitive cultivar and 11 fold higher than the control treatment. These results showed that the expression of SAPK1 gene increases in rice plants with increasing salinity levels. nvestigating the effect of time after applying stress on SAPK1 gene expression, it was found that in the early hours after applying stress, the amount of gene expression was low, but with increasing time up to 24 hours, gene expression in tolerant cultivar increased These results can be used in molecular studies of rice cultivars to select the most tolerant rice cultivars to salinity stress for cultivation in areas prone to salinity.

MicroRNAs (miRNAs) are a group of short non-coding RNA molecules with a length of about 18-24 nucleotides, which control target genes expression at the post-transcriptional level. There are no reports of miRNA detection in Rheum ribes plant. Therefore, in the present study, in order to predict potential conserved miRNAs and their target genes in R.ribes roots, total RNA was extracted from the root tissue and sequenced. Then, non-coding transcripts were identified in R.ribes transcriptome and considered as miRNA precursor candidate sequences. In this study, 82047 transcripts were created from R.ribes root by de novo assembly method. By searching the homology of these transcripts with mirbas database and secondary structure prediction, 4 conserved miRNAs belonging to mir396, mir164, mir319 and mir168 families were identified. 574 transcripts from R.ribes root transcriptome were targeted by these miRNAs. In general, due to the regulatory role of identified miRNAs on a wide range of genes, these miRNAs can be used to identify genes related to secondary metabolites.

MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Although thousands of miRNAs have been identified in many plant species, no studies have been reported on discovering conserved stress-related miRNAs in lentil, one of the most important staple food crops in Iran developing countries. The present study was performed to identify the conserved miRNAs and their target genes in the lentil transcriptome under salts tress. In this study, 55892 unigenes from de novo assembly process of a set of short reads derived from RNA sequencing technology of lentil under control and salt stress conditions were used for the prediction of conserved miRNAs and their target genes. Finally, six potentials miRNAsnamedlcu-miR156, lcu-miR167, lcu-miR169, lcu-miR171, lcu-miR396, and lcu-miR390 belong to six conserved families were identified. Identified miRNAs showed differential expression under salt stress. The results showed that the target genes of the identified miRNAs play an important role in most biological processes such as differentiation, growth, signaling and response to biotic and abiotic stresses. In addition, the results showed that some transcription factors belonging to SBP, C2H2, GRAS, M-type_MADS and MYB families are widely affected by the regulatory process of identified miRNAs. In general, the set of miRNA and their target genes identified in the present study can be used as a useful basis for more in-depth and accurate research on the role of miRNAs in response of lentil to salt stress.

Plant diseases, particularly diseases caused by fungi and oomycetes pose significant challenges in modern agriculture worldwide. Pathogen associated molecular pattern (PAMP) like chitin found in the cell walls of fungi and oomycetes, trigger defence signalling, leading to expression of R-genes and the production of reactive oxygen species (ROS), and accumulation of a wide range of metabolites. Chitin elicitors prompt the expression of defence-related genes such as chitinases, ultimately the resulting in the breakdown of chitin in the pathogen's cell wall. To assess the expression level of certain chitinases in potatoes and the activity of antioxidant enzymes, leaves of a tolerant potato genotype (jelly) was challenged with chitin oligomers in vitro. Result of this study revealed that 48 hours post chitin induction, the expression of different classes of chitinase genes were significantly increased. Class I chitinase (Soltu.DM.10G017450) and class III chitinase (Soltu.DM.11G026160) genes, had respectively the highest (5.5-fold relative to control) and the lowest (1.1-fold relative to control) expression level after 48 hours post chitin inoculation. However, the activities of antioxidant enzymes catalase and ascorbate peroxidase did not change significantly compared to the control. These findings suggest that the application of chitin does not activate the signaling pathways involved in the biosynthesis of antioxidant enzymes 48 hours after chitin treatment. In addition, results of this study may imply that chitinase genes can be cloned by genetic engineering approaches to generate transgenic plants resistant to pathogens.

Kelussia odoratissima Mozaff, is one of the most important medicinal plants in Iran and is facing the risk of extinction. Keluss is not only used as a valuable herb in its raw form but also possesses numerous therapeutic properties in traditional medicine and modern herbal drug combinations from a pharmacological perspective. However, the lack of information on its genetic diversity and the mechanisms of important metabolite production in this plant pose challenges for genetic research on this species. In the present study, with the aim of developing high-throughput EST-SSR markers, the assembly process of short reads obtained through next generation sequencing technology was employed. A total of 7575 microsatellite loci were identified in 6388 unigenes. Among these markers, dinucleotide motifs followed by trinucleotide and mononucleotide motifs exhibited the highest abundance. Blast analysis of the sequences containing microsatellites revealed that 79.74% of the transcripts had at least one record in the non-redundant protein database. Further investigations involving transcription factors and functional annotations indicated that most of the microsatellite-containing unigenes are involved in metabolic pathways and the biosynthesis of secondary metabolites. The results showed that these markers assist in the analysis of genetic diversity and metabolic pathways of this plant, information that can be crucially important for the conservation and sustainable utilization of this valuable plant.

Kelus (Kelussia odoratissima Mozaff.) is one of the medicinal, spicy, aromatic and endemic herb that grows in restricted regions of Iran,. Due to the importance of its pharmaceutical compounds in traditional medicine, the excessive harvesting of kelus has put it at the risk of extinction. To protect kelus from extinction, plant tissue culture can be used to produce useful compounds and secondary metabolites. The hairy root culture is an efficient system for the production of medicinal compounds and valuable secondary metabolites in plants. For this purpose, two pathogenic strains of Agrobacterium rhizogenes (A4 and ATCC15834), two types of explants (cotyledon and hypocotyl), three levels of acetosringon (a1= 0 µmol, a2=50 µmol, and a3= 100 µmol), and three levels of glucose (b1=0, b2=0.5%, b3=1%) were applied using a factorial experiment based on a completely randomized design with three replications. The effect of such different factors on the induction and production of hairy roots in kelus was investigated. The results showed that both Agrobacterium strains were able to induce hairy roots in kelus. Also, ATCC15834 strain in MS medium with 100 µmol of acetosringon in the presence of 0.5% glucose had the highest efficiency in the production of hairy roots in cotyledon explants. The lowest amount of hairy roots was observed for A4 strain in MS medium without both acetosringon and glucose in both explants. PCR analysis was performed with rolC specific primers to ensure hairy root induction has occurred by A. rizhogenes. The results of this research showed that for the first time in Iran, it was possible to induce hairy roots in kelus explants.

Due to the increasing concern about the growing resistance of pathogenic bacteria to a variety of common antibiotics, it is vital to find and introduce new drugs to treat bacterial infections. To this end, intensive efforts need to be taken to find novel antimicrobial agents with diverse antimicrobial modes of action, preventing pathogen growth. Combination therapy using current antibiotics and other biological or chemical molecules might be efficient as an exciting new approach.

In the present study, the synergistic antibacterial activity of Dermastin B1 recombinant peptides isolated from transgenic T1 tobacco plants either alone or in combination with peppermint essential oils were evaluated against Xanthomonas translucen, Xanthomonas perforans, Xanthomonas citri, Xanthomonas gardneri and Pseudomonas syringae by measuring the Fractional Inhibitory Concentration (FIC) index at different concentrations.

The results of this study showed that the MIC of Dermaseptin B1 peptides and the peppermint essential oils against bacteria were 50 µg/ml and 4.6 µg/ml, respectively. FIC index showed a synergistic effect of peppermint essential oils with Dermaseptin B1 recombinant peptide with FIC=0.49.

The results of this study suggest that Dermasptin B1 recombinant peptides can be effective either alone or in combination with the peppermint essential oils to control bacterial infections. However, it seems that there is a synergistic effect between recombinant peptides and peppermint essential oils in combat against phytopathogens.

Hairy and adventitious roots are efficient systems for expressing recombinant proteins. In the present study, the amount of DrsB1-CBDAvr4 recombinant protein in hairy and adventitious root systems was compared. To this end, the effect of different factors on the optimization of culture conditions to obtain adventitious and hairy roots was evaluated in three separate experiments by assessment of biomass production in T1 transgenic plants expressing DrsB1-CBDAvr4 recombinant protein. The efficacy of Agrobacterium rhizogenesis in producing hairy roots was ensured using rolC gene specific primers. The insertion of DrsB1-CBDAvr4 recombinant peptide transgene in the genome of hairy and adventitious roots was confirmed by PCR analysis. Also, the level of DrsB1-CBDAvr4 protein was measured in hairy and adventitious roots by ELISA analysis. Analysis of the variance of data showed that the highest number of roots and the longest roots were obtained in MS media supplemented with 1 mg/L NAA and 0.5 mg/L IBA. The results of adventitious root biomass showed that liquid MS medium containing 1 mg/L of NAA hormone had a significant effect (P <0.01) on biomass production. More biomass was obtained in MS medium supplemented with 1mg/L NAA, whereas a lower fresh and dry weight was obtained in a 1/4 MS medium with no NAA. The results also showed that ATCC15834 strain with MS media supplemented with 3% sucrose, 10 minutes inoculation time was high efficiency to induce hairy roots in tobacco plants. The results of ELISA analysis showed that clones obtained from both roots showed a significant difference in terms of total protein content. The amount of recombinant protein from hairy roots was much higher than that of adventitious roots.

Mitogen activated protein kinase (MAPK) cascades are key players in plant immune signalling pathways. MAP kinase singling consists of a number of associated proteins where MAPKKKs are located upstream of MAPK cascade activating multiple MAPKs. MAPKKKε, a positive regulator of cell death, is associated with plant immunity. Phytophthora infestans is a pathogenic oomycete that inflicts potato late blight disease, delivering RXLR effector proteins to plant cells to modulate host immune signalling and colonization incident. The RXLR effector PexRD2 interacts with the kinase domain of MAPKKKε. Using a CRISPR/Cas9 system, a construct was made to introduce four guide RNAs (gRNAs) in potato cultivar, Agria. Thirty-five mutant lines were regenerated, in which three and two transgenic lines with deletions and insertions were analysed, respectively. A mutant line with a three-allelic knock down of MAPKKKε was obtained, showing ~70% reduction in MAPKKKε expression level resulting in enhanced susceptibility to P. infestans. The results of this study provide evidences that editing MAPKKKε to modulate PexRD2 interaction, enhances susceptibility to P. infestans, suggesting that MAPKKKε plays a key role in resistance to P. infestans in potato. Therefore, it can be anticipated that MAPKKKε gene can be used in future potato breeding programs to generate biotic stress resistance plants.

The high nutritional value has made potato the fourth most important food source after wheat, rice and corn worldwide. In this study, in order to identify and investigate the expression pattern of the most significant genes involved in the synthesis of flavonoids at different potato tuber developmental stages, the RNA sequencing data was obtained from three different potato tuber development stages, namely; initiation of stolon formation, stolon swallowing and initiation of tuber formation. In order to validate the expression of identified genes involved in the biosynthesis of flavonoids in potato tuber (62 genes), the expression of significant genes were evaluated by using qRT-PCR method. The results of this study showed that at the stolon swallowing stage, 10 and 11 genes had a significant increase and decrease in expression, respectively. Comparing the stolon swallowing stage with initiation of stolon formation, 7 and 20 genes showed a significant increase and decrease in expression. At the initiation of tuber formation, it was found that 14 genes had a significant decrease in expression. In total, 4 key genes CYP98A3, ACT, SAT and BEAT were identified with significant changes among developmental stages. The amount of flavonoid in the three developmental stages was also significantly increased with the transition of developmental stages. The average of flavonoid content was 1.9, 7.2 and 24.8 mg/gFW for tree developmental stages, respectively. Since CYP98A3, ACT, SAT and BEAT are key genes involved in the biosynthesis of secondary metabolites in the potato tuber, they can be considered as possible candidate genes for alteration of flavonoids content in potato.

Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds biosynthesis pathways. MicroRNAs (miRNAs) play an important role in different processes such as growth and development, cell proliferation, response to stresses and biosynthesis metabolite. As far as the bioinformatic data are concern, the genome/transcriptome of kelus has not been sequenced. The present study was performed to identify the conserved miRNAs and their target genes in the kelus leaf transcriptome. After pair-end sequencing with the Illumina HiSeq 2500 platform, clean reads were assembled. In total, 4658 unigenes were found to contain potential miRNAs sequences. Following strict filtering criteria, five miRNAs belonging to five conserved miRNA families (miR156-3P, miR408, miR169, miR171 and miR398) were identified among candidate sequences. Results of this study revealed that the target genes of the identified miRNAs were involved in various metabolic pathways, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, peroxisome degradation, and fatty acid degradation. By affecting genes associated with six metabolic pathways, miR408 was identified as the most influential conserved microRNA in the kelus leaf transcriptome. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of kelus, these miRNAs can be used as candidate genes for breeding kelus quantitative and qualitative traits.

miRNA genes consider as an important class of gene expression regulators that have diverse responses to environmental stresses and play a key role in regulating gene expression during post-transcriptional regulation. Hypericum perforatum, is well-known medicinal plant for its application in the treatment of depression due to the effects of its bioactive compounds named hypericin and hyperforin. The present study was performed to identify the conserved miRNAs and their target genes in the transcriptome of H. perforatum. First, RNA-seq data were obtained from the European Nucleotide Archive (ENA) of EMBL-EBI database and then the transcriptome (RNA) sequences were assembled. The non-coding transcripts were identified and considered as miRNA precursors candidate sequences. Finally, six miRNAs named Hp-miR395, Hp-miR845d, Hp-miR414, Hp-miR159, Hp-miR159e, and Hp-miR156c were identified from the candidate sequences using of C-mii software after applying strict filters.  Investigation of the protein-protein interaction network determined the relationships between the target genes and target proteins especially in transcription factors. In the next step, to confirm the target genes for the identified miRNAs, the foliar application of Methyl Jasmonate (MJ) with concentrations of 0 (control) and 200 μM was performed on H. perforatum plants and the expression pattern of two target genes was investigated. In the analysis of qRT-PCR expression changes at 12, 24, 48 and 72 hours after applying MJ, the relative expression level of Hyp-1 (DN121523_c1_g4_i2) and HD-Zip (DN121003_c0_g1_i1) transcripts increased after 72 hours of application of MJ. In general, regarding to the regulatory role of the identified miRNAs in the present study, these genes could be used to better and more accurately identify the biosynthetic pathway of hypercin and hyperforin.

Saffron (Crocus sativus L.) is the most valuable spice in the world. Due to the lack of genomic information, saffron breeding has encountered many problems. To this end, generating and collecting genetic data using Next Generation Sequencing (NGS) techniques is crucial for saffron traditional and molecular breeding programs. Molecular markers, especially powerful co-dominance markers such as simple sequence repeats (SSRs) markers play an important role in breeding projects. In the present study for the first time, SSR markers related to genes associated with F. oxysporum disease of corms were identified following a RNA-Seq based transcriptomic approach. To this end, total RNA was extracted from mature corms and RNA-Seq was performed based on the Novaseq6000 platform. The De-novo assembly was performed with Trinity software and the MISA search tool was used to identify SSRs. Based on the results of this study, 357028 transcripts were identified. A total of 70060 transcripts were identified to contain SSR sequences. BLAST algorithm analysis revealed that the highest similarity between saffron SSRs was found with that of rice and Arabidopsis. Among the identified unigenes, 18846, 23988 and 10969 genes were identified in UNIPROT, Nr and GO databases, respectively, in which 10375 unigenes were common to all databases. Due to the high priority of saffron in Iran as a strategic crop plant, any genetic information, including mining SSRs, is of great importance in studying genetic diversity, constructing genetic maps, linkage and QTLs analysis in saffron future breeding programs.

The aim of this study was to evaluate the effect of reducing nitrogen fertilizer application as well as foliar spray of zinc sulfat on the quality characteristics of two sugar beet cultivars in autumn cultivation. The study was conducted in a factorial design based on randomized complete block design with three replications at the Faculty of Agriculture in Lorestan University during two crop seasons (2017-19). The Experimental treatments included two autumn-sown sugar beet cultivars (Chimene and Rosagold) and four fertilizer levels including F1: 138 kg ha-1 nitrogen (control), F2: 124 kg ha-1 nitrogen and foliar spray of zinc sulfate, F3: application of 110 kg ha-1 nitrogen and foliar spray of zinc sulfate, F4: 96.6 kg ha-1 nitrogen and foliar spray of zinc sulfate at a rate of 5/1000. The highest root yield (90.15 t ha-1) belonged to Rosagold cultivar and among the treatments, the highest root yield was related to F2 treatment. The highest sugar content (16.15%) was obtained in 20% reduction in nitrogen application and foliar spray of zinc sulfate. Also, the highest white sugar content (15.57%) was obtained from Rosagold cultivar in 20% reduction in N fertilizer application and foliar spray of zinc sulfate, which showed 26.17% increase compared with control treatment (F1). The highest molasses sugar and Na, K and α- N as 2.7, 2.61, 7.90 and 2.90 meq 100 gr beet-1, respectively was observed in Chimene. Also, the highest bolting percentage was obtained in Chimene and the application of 300 kg ha-1 nitrogen. According to the results of this study, it can be concluded that autumn cultivation of sugar beet using Rosagold cultivar is possible in Khorramabad region and foliar spray of zinc sulfate can compensate the reduction of nitrogen consumption by 20% without reducing the quantity and quality of autumn sugar beet.

Satureja genus, from the Lamiaceae family, is a medicinal plant that is widely distributed in the southern regions of Iran. Different species of this plant have many medicinal properties such as antioxidant properties and medical applications. However, lack of molecular markers, especially microsatellite markers, has severely limited the development of Satureja genetic researches. Therefore, in this study, 271907 and 225534 transcripts were obtained with average lengths of 1079 and 1018 bp and N50 values equal to 1802 and 1740 for S. khuzistanica and S. rechengeri, respectively. The assembly process of short reads of transcriptome sequences of S. khuzistanica and S. rechengeri was used to identify microsatellite markers. In the present study, 44624 and 34546 SSR loci were identified in S. khuzistanica and S. rechengeri, respectively. Among these markers, dinucleotide repeat motifs were the most abundant, followed by mononucleotide and trinucleotide. In S. khuzistanica and S. rechengeri, the results of blast of transcripts containing SSR showed that 72.27% and 75.32% of the transcripts had at least one record in the non-redundant protein database, respectively. Functional annotation was performed through the search for homology and gene ontology (GO). In total, 14792 (33.4%) transcripts with SSR markers for S. khuzistanica and 12480 (36.12%) transcripts with SSR markers for S. rechengeri were classified into three groups of GO. Gene ontology analysis reported that most of the assembled transcripts are related to the Molecular Function (MF) group. 45% of the total transcripts containing microsatellites were allocated to 401 pathways, in which the biosynthesis of secondary metabolites was identified as the second pathway with the maximum number of members after the metabolic pathways. This is the first report about the identification of microsatellite markers from the transcriptome sequence of Satureja and this information could be an effective source for breeding programs of this medicinal plant.

MicroRNAs (miRNAs) are one of the small and non-coding regulatory molecules, which regulate gene expression by transcriptional cleavage or translational suppression. miRNAs are involved in regulating a wide range of metabolic and physiological processes in plants.The mint family plants, especially Satureja khuzistanica, are well known herbs for its flavor, fragrance and medicinal properties. To date, no miRNAs have been identified in Satureja species. In present study, a computational approach based on homology search was used to identify miRNAs and their targets of Satureja khuzistanica. Non-coding unigenes were identified and considered for candidates of miRNAs precursor. After evaluating the general parameters such as GC percentage, minimum folding free energy (MFE), minimum free energy index (MFEI) and secondary structure, 58 miRNAs were identified, which among them, by applying plant specific parameters and filtring the miRNAs from several transcripts, overall ten miRNAs were identified. Then, 930 target transcripts were predicted using psRNATarget website and the annotation of them was performed by using BLASTx tools of NCBI Blast+ software (v2.6.0). Examination of target genes showed that auxin-responsive genes, GRAS, AGO2 and LAC family genes are the main targets of the identified miRNAs in S. khuzistanica. Pathway enrichment analysis of the target genes revealed that the secondary metabolic pathway is significantly among the targets of the identified miRNAs. This is the first study describing miRNAs and their role in the regulation of target genes in S. khuzistanica.

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.

Every year new cultivars of Chrysanthemums modified with a high economic value. In order to study the genetic variation of some chrysanthemum cultivars using morphological markers, 17 quantitative trait were evaluated 20 varieties of chrysanthemums accordance with standard methods. The results of the data analysis for morphological traits showed that studied cultivars in most traits were significant differences in the level of one percent. The average comparison showed that "Elika" cultivar had a highest plant high, "Ramtin" cultivar had a highest number of flowers and "Gol-Giss" cultivar had a highest flower head diameter. Principal component analysis showed five main factors that had Eigen values greater than one, could be 77/10% of the total variation. Cluster analysis to determine how far and near these were drawn that into two main groups were divided, the "Farid", "Nadia 2" and "bolur" and "Ramtin" highest genetic similarity in the first group and also the "Fariba 2" and " kimia 3" in the second group had the highest genetic similarity. The results of this study showed that the number of lateral branches, number of flowers and leaves during the length of the petiole highest diversity was observed. The results showed that cultivars diversity of these figures are very high and can be used in programs of breeding chrysanthemums in the future.

Autumn planting of sugar beet has more water use efficiency and agricultural advantages than spring planting. In order to investigate the possibility of autumn planting of two sugar beet cultivars and compare their root yield, a study was conducted in the Faculty of Agriculture of Lorestan University during two cropping years (2017-2018 and 2018-2019). This study was conducted in the form of a split factorial design with three replications. The main factor has two levels and includes planting method 50-50 (P1), 25-50 (P2), and the sub-factors including two varieties of autumn sugar beet (Rosagold and Chimene) and four levels of fertilizer (F1: application of 300 kg.ha-1 nitrogen (Control), F2: application of 270 kg.ha-1 nitrogen and foliar application of zinc sulfate, F3: application of 240 kg.ha-1 nitrogen and foliar application of zinc sulfate, F4: application of 210 kg.ha-1 nitrogen and foliar application of zinc sulfate in the amount of 5 per thousand. Rosagold cultivar with F2 treatment significantly (p<0.01) increased the photosynthesis active rate. The highest amount of stomatal conductance was observed in P1 planting arrangement with Rosagold cultivar. The highest CGR (16 g.m-2.day-1) and root yield (98.70 t.ha-1) were obtained from P1 planting arrangement, Rosagold cultivar and F2 fertilizer level. According to the obtained results, it can be stated that zinc sulfate foliar application has the ability to compensate for the reduction of nitrogen consumption by 10%, without reducing the yield and quality of autumn sugar beet.

Hairy root culture obtained via Agrobacterium rhizogenes-mediated genetic transformation is considered an essential strategy for in planta enhancement of secondary metabolites/or recombinant protein production. High growth rates and genetic stability characterize hair roots compared to ordinary plant root systems. Low root biomass is one of the significant challenges in any hairy root establishment. To this end, the hairy root culture medium was supplemented with various nitrogen and phosphorus sources and combinations to increase the total biomass production.

Sterile leaf explants were excised from 10-day old tobacco plants and inoculated with Agrobacterium rhizogenes to induce hairy roots formation. Inoculated leaf explants were kept in dark conditions for two days at 25±2 ˚C. Leaf explants were washed and transferred to the MS culture medium supplemented with cefotaxime at sterile conditions. The inoculated explants were kept in the tissue culture room at 25±2 ˚C until hairy roots appeared. Different ratios of nitrate to ammonium (5.1/5.1, 19/20, and 30/5.1 mM) and three potassium dihydrogen phosphate (KH2PO4) as a source of phosphorus (3, 6, and 12 mM) in two types of solid and liquid culture media were used to optimize hairy roots formation and compared in a factorial experiment based on a completely randomized design with three replications, each containing ten explants. The fresh and dry weight of hairy root was recorded 30 days after hairy root formation.

Transgenic hairy roots were confirmed by PCR analysis using the rolC gene-specific primers. No bacteria contamination was found following PCR analysis of transgenic hairy roots. Analysis of the variance of hairy roots dry and fresh weight data showed that nitrogen, phosphorus, and culture media had a significant (P<0.05) effect on hairy roots biomass production. The highest biomass accumulation (11.66 gr/FW and 0.47 gr/DW) was recorded in the media containing 30/5.1mM ratio of NO3/NH4 ratio and 12 mM of KH2PO4, respectively. The lowest dry and fresh weight were obtained when 5.1/5.1 mM of NO3/NH4 and 3 mM KH2PO4 were used.

This study suggested that a higher NO3/NH4 ratio and KH2PO4 can lead to the highest hairy roots biomass production. Therefore, it is recommended to use a higher proportion of NO3/NH4 to produce more in planta biomass needed for pharmaceutical and industrial products. Furthermore, it can be concluded that it is possible to optimize the hairy root production if hairy roots are used to scale up the amount of metabolite/recombinant proteins production in tobacco.

Reduction in crops yield due to global warming threatens food security. Response of plants to heat stress is a complex prosses. MicroRNAs play an essential role in heat stress response regulatory network with post-translational modification of transcript, specially transcription factors. Lentil is one of the most important legumes cultivated in Iran. The role of microRNAs, in response to biotic and abiotic stresses in lentil plant, has not been studied so far. In this study, in order to identify conserved miRNAs and their target genes in lentil under heat stress, the total RNA was extracted using Trizol reagent and the RNA samples were sequenced. Then, transcripts which did not code any protein were examined to identification of miRNA precursors. Finally, seven miRNAs were identified which belonged to six conserved miRNA families including miR408, miR172, miR169, miR167, miR166 and miR156 that miR408, miR169 and miR166 were downregulated and miR156 was upregulated in response to heat stress. Study of these miRNAs targets showed that, most of these miRNAs involved in regulation of heat stress-responsive transcription factors including of HSF, NF-Y subunits, ARR-B, WRKY, MYB, AP2 and C3H. This result can help to better understanding of gene expression regulatory network in response to heat stress.

Catharanthus roseus is an ornamental and evergreen plant, which is used in cancer treatment due to production of important alkaloids, Vinblastine and vincristin. C.  roseus is also of great importance for pharmaceutical industry. Vinblastine and vincristine in the terpenoid indole-alkaloid pathway (TIAs) synthesis in Low level. Difficulties with chemical synthetic production and low production level in plant lead to find practical solutions to increase the amount of these two economically important alkaloids. It seems plant growth regulators such as salicylic acid (SA) induce expression of major genes involved in vinblastine and vincristine production. In addition to increasing in the alkaloid content, especially vinblastine and vincristine, application of SA activates the plant defense system and under normal condition and in dealing with stresses, improve C.  roseus yeild. To this end, the relative expression of terpenoid indole alkaloids (TIAs) pathway genes in all three Indole, Terpenoid and Alkaloid pathways studied following foliar application of SA at a concentration of 0.01 mM by using qRT-PCR analysis. The results of this experiment showed that the mRNA transcript level of the first gene in the phenolic pathway reduced, although the down-regulation was not statistically significant. The transcript level of TIAs pathway genes were also increased after SA foliar application. The highest 4-O-acetyltransferase (Dat) gene transcription level observed at 24 and 48 h after treatment, suggesting Dat could be a primary responsive gene to SA treatment.