جستجوی مقالات مرتبط با کلیدواژه « توالی یابی » در نشریات گروه « کشاورزی »

Saffron with the scientific name Crocus sativus L belongs to the lily family (Iridaceae) and is one of the most important economic and strategic products of the country, which is important to investigate its limiting factors. Saffron is an strategic plant in Razavi Khorasan that has been played an important role in economy of this area in particular in Khaf city. According to statistical methods, 89% of saffron production is produced in Iran.  Saffron has been infected by several viruses but until now there is not any report of infection with that is important species in potyviridae family and cause many symptoms on other produscts. Bean common mosaic virus is a member of potyviridae family with the positive single strand RNA genome that has rod-shaped particles caused decrease in quality and quantity in many plants, in this research, detection and molecular characterization of BCMV has been surveyed.

In order to detect and identify Bean common mosaic virus as one of the limiting factors in saffron farms, sampling of 705 samples of saffron in Khorasan Razavi province, Khaf city was carried out during the spring of 1402. The saffron samples had mosaic symptoms, dwarfism, plant deformation and zigzagging, which were transferred to the laboratory under cool conditions. Then their total RNA was extracted by Denazist Kit and RT-PCR test was carried out, using specific primers of the coat protein gene. The PCR products were electrophoresed. Results showed that in the three saffron samples, a fragment of 343 base pairs was amplified. The amplified fragments were reproduced, then extracted from gel and then 3 amplicons were sent to Macrogen Korea for sequencing. Coat protein sequences were analyzed by Blast n and aligned by Bioedit, phylogenetic tree was draw using BCMV sequences of the world and Iran, homology matrix was obtained using Sdtv.

In RT-PCR 14 saffron samples were amplified that 3 samples were chosen for sequencing. The results confirmed the infection of three saffron samples with the mentioned virus, and in the phylogeny studies of three saffron isolates in the nucleoprotein coding region of the mentioned virus, compared to the world isolates available in the gene bank, which were related to different geographical regions, five separate groups were formed, from three Iranian isolate related to saffron, two isolates (B1, B2) were placed in group 4 close to isolates from Brazil and one isolate (B3) was placed in group 5 close to two isolates from Iran (Ahvaz and Zanjan). The most similarity of the isolates in this research was between two Iranian isolates B1 and B2 with three isolates MW534342, MW534343 and MW534344 from the country of Brazil from the African continent with a similarity percentage of 100% and also the least similarity of the Iranian isolates B1, B2 and B3 with isolate KC702888 from Iran in Lorestan with a similarity level of 71%.

This is the first survey of this virus in Razavi Khorasan that showed the infection of saffron field of Khafe city as one of the major areas of production of this product. Phylogenetic analysis of this virus showed that khaf isolates were located in two different groups that could be the result of different sources for entering of this virus in this area.  The reason of separation of 3 isolates in different group should be the recombination among them. Although we detected many symptoms in the saffron fields BCMV was not detected in some of them. The reason behind of this could be related to the infection by other plant viruses that needs to be more investigated in the next scientific research.

In order to study the genetic structure and morphology of the population of the whitefin wolf herring (Chirocentrus nudus) from three regions of Abadan, Shif and Bandar Abbas on the coast of the Persian Gulf, 20 specimens from each station and a total of 60 fish were collected using gill-nets in May 2019. 29 morphometric and 5 counting traits were measured. For genetic study using mitochondrial cytochrome oxidase (COI) gene sequencing method, a piece of caudal fin of 6 fish samples from Shif, Abadan and Bandar Abbas stations were fixed in 96% ethanol and transferred to the laboratory. DNA extraction was done by phenol chloroform and polymerase chain reaction with a pair of primers. After sequencing or COI gene barcode, the sequences were aligned. The results of sequencing showed that the amplified fragment is exactly 595 bp. The COI gene in the region studied is exactly the same in all samples. Also, the results of principal component analysis (PCA) for morphometric traits showed that 9 factors with eigenvalues ​​greater than 1 were selected, which includes 84.56% of the variation of morphometric traits. The distribution diagram based on the first and second components, dendrogram of morphometric traits and phylogeny tree drawing with Maximum likelihood, Neighbor-joining and UPGMA software showed that the whitefin wolf herring has at least two populations in the north of the Persian Gulf.

The genus Malva (family Malvaceae) includes species of herbaceous plants which are often pluriannual and very common in borders and boundaries of cultivated fields, making them proper reservoirs for plant pathogens. They are most commonly used as ornamental plants, although they may be used as a food resource and remedy for various diseases. Common mallow (Malva sylvestris) is the most important Malva species which is used as garden flower as well as widely recognized for food and medicinal purposes.  Malva sylvestris are reported to be affected by several viruses from different genera including malva vein clearing virus (MVCV, Potyvirus), alfalfa mosaic virus (AMV, Alfamovirus), malva-associated soymovirus 1 (MaSV1, Soymovirus) cucumber mosaic virus (CMV, Cucumovirus), and cotton leaf curl Gezira virus (CLCuGeV, Begomovirus). In this study, we attempted to identify important viruses infecting mallow plants and compare mallow isolates with other sequences in the GenBank.

In 2022-2023, twenty samples of mallow plants with viral-like symptoms on the leaves were collected from the urban landscape of Golestan province. Total RNA was extracted by DENAzist Total RNA Isolation Kit from fresh, infected mallow leaves. All samples were analyzed by RT-PCR with specific primer pairs for the detection of CMV, AMV, and MVCV. The amplified fragments in expected size of coat protein (CP) gene of each virus were visualized under UV light in agarose gel after electrophoresis, then amplified fragment of one isolate of each virus was bi-directionally sequenced. Obtained sequences were compared to data available in GenBank. The phylogenetic trees of viruses were constructed based on the nucleotide sequences of the coat protein gene using the neighbor-joining method by MEGA11.

All three viruses were detected in some symptomatic samples collected from Golestan province. The most typical symptoms in positive samples were mosaic, vein clearing, and leaf malformation. Of a total of 20 sampled plants, MVCV, CMV and AMV were detected by RT-PCR in nine, five and two samples, respectively. An amplicon of each virus was selected and sequenced in both directions. BLASTn analysis of the sequenced data confirmed that the PCR-amplified fragments belonged to MVCV, AMV, and CMV. Phylogenetic analysis based on the nucleotide sequence of CP gene of MVCV (n=21) including Iranian and GenBank isolates showed that all isolates are divided into six groups: G1 to G6. All Iranian isolates along with the isolate from the Netherlands were placed in group G5. The phylogenetic tree placed the CMV sequences (n=51) into two distinct phylogroups I and II; the obtained isolate CMV-IR-Ma clustered together with isolates from Iran, Netherlands, South Korea, Japan, China, Hungary, Australia, France and the USA into group II. According to the results of this study, AMV isolates (n=17) can be divided into two groups, I and II. Group I which includes isolates from Canada, China, Italy, Spain, Argentina, Australia and the USA, was divided into six subgroups. The obtained isolate AMV-IR-Ma was clustered in subgroup IB with a Chinese isolate (HZ) and forms a common branch with isolates (Ir-VM, Ir-WS, and Ir-WS2) from Iran. This is the first report of mallow (Malva sylvestris) infection with CMV and AMV in Iran using RT-PCR. In addition, mixed infection with two (MVCV+CMV and MVCV+AMV) or all three viruses (MVCV+CMV+AMV) was also confirmed in some samples. The phylogenetic trees showed that most of the viral isolates were not grouped according to their geographic locations. This suggests the dissemination and spread of these viruses through infected seeds. In Iran, M. sylvestris is a common weed found in fields, waste grounds, roadside verges and gardens. Considering the potential non-persistent aphid transmission as well as mechanical transmission, virus-infected mallows can act as a natural reservoir, thereby posing a threat to other ornamental plants and crops. Since the studied viruses were not detected in the other symptomatic plants, the observed symptoms can be caused by physiological disorders such as nutrient deficiencies, the presence of different viral strains, or other unknown and undetected viral species.

This study provides new knowledge on the diversity and molecular characteristics of viruses in mallow plants (M. sylvestris) affected by the viral disease. The information obtained from this study can be helpful in improving management strategies for disease caused by these viruses in Iran. Albeit M. sylvestris is a host of these viruses, but more comprehensive research on other viral species that may infect this plant need to be conducted. Weed management could be an effective way to eliminate inoculum sources of these viruses.

Advances in next generation sequencing technologies have created the ability to efficiently and economically sequence the whole genome more than ever and provide the opportunity to discover and introduce multiple polymorphisms throughout the genome of organisms. Azeri buffalo is one of the most important breeds of Iran and it is scattered in the north to the northwest of the country and is completely adapted to the environmental conditions of this geographical region. The main purpose of this study is to introduce the genomic diversity of Iranian buffaloes and categorize them. Also, introducing the effects of these variations on different genomic regions of Azeri buffaloes have potential applications in breeding programs.

In this study, whole genome sequencing of 5 heads of Azeri buffaloes native to Iran was done by Illumina sequencing platform. Data quality was measured by FastQC software. BWA-MEM software was used for alignment with the reference genome. Finally, the variants were identified using freebayes and the SnpEff program was used to calculate the effects of the variants by mentioning their type, location and number. The alignment result of high quality reads with the reference genome showed that the alignment percentage for all 5 samples was over 97.5%, which indicates the high quality of short reads.The coverage in the sequenced samples was determined between 4x and 12.8x.

finally, 76,298,858 million variants were identified, including 57,921,822 SNPs, 6,162,328 indels, 10,534,042 MNPs, and 1,680,666 MIXEDs. Small deletions and insertions with a minimum length of 1 bp, a maximum length of 28 bp and an average of 1.39 bp were identified. From the total number of variants, the highest frequency of variants was observed in intergenic regions, 53,789,879 (62.022 percent), intron 24,003,682 (27.677 percent), respectively, and the variants detected in exons had the lowest number.

Identification of genome-level variations such as snps, small insertions and deletions, and multi-nucleotide polymorphisms in different populations are a valuable resource in genetic research and can be useful in locating genomic segments responsible for important economic traits. Also, the large volume of SNPs enables genome-wide association studies in animals. In addition, the genomic variations identified in the present study can be used to develop high-density SNP arrays in Iranian breeds for genetic and breeding applications.

Saffron (Crocus sativus L.) is a crucial crop in Iran, celebrated for its medicinal and economic value. Thriving in arid regions, it's a perennial herb with corms used in food and pharmaceuticals. As the world's priciest spice, it significantly impacts Iran's exports and industries, with a history in traditional medicine dating back 3000 years. Over 90% of global saffron comes from Iran, primarily Khorasan Razavi province (78%) and Khorasan Jonubi province (17%). Saffron is also grown in Fars, Isfahan, and Hamadan.
Boshrouyeh County in Khorasan Jonubi boasts saffron cultivation on 1,307 hectares in 2020-2021, yielding about 3.4695 tons, generating 70 billion Tomans. Regarding plant viruses, the Cucumber mosaic virus (CMV) is a significant threat, affecting various plants globally, including cucumbers, tomatoes, and more. In Iran, CMV has been reported in crops like bananas and melons, causing up to 20% yield loss.
This study focuses on CMV in saffron plants in Boshrouyeh County, using molecular methods for precise assessment due to its impact on saffron cultivation.
 
In the autumn of 2022, a survey was conducted in saffron fields to assess virus symptoms like mosaic, stunting, yellowing, wrinkling, and leaf deformities. A total of 148 samples were collected, dried, and stored for analysis. RNA was extracted from young plant leaves using a non-column RNA extraction kit. Specific viral protein coat primers were used for cDNA synthesis, followed by PCR amplification. The PCR reaction involved denaturation at 94°C for 2 minutes, followed by 40 cycles at 94°C for 40 seconds, 52°C for 30 seconds, and 72°C for 2 minutes, with a final extension at 72°C for 5 minutes. Electrophoresis confirmed three samples were infected with CMV. The amplified viral sequences were extracted and sequenced by a specialized company in South Korea. Sequence similarity was verified using BLAST tools on the NCBI database to confirm the presence of these virus strains and assess their genetic relatedness to global strains.
 
In collected plant samples, various symptoms such as curling, leaf complexity, leaf mosaic, yellowing, and discoloration were observed. To conduct phylogenetic studies, three isolates of Cucumber mosaic virus (CMV) from saffron fields in Raghe and Boshrouyeh were sequenced. Sequence comparisons using BLAST revealed all three isolates shared similarity with CMV. A phylogenetic tree based on the 657-nucleotide coat protein gene sequence was constructed. Analysis with MegaX software compared Iranian isolates with 17 gene bank isolates. The resulting tree contained twelve branches, with Iranian isolates showing the highest similarity to Syrian and Greek isolates. Specifically, Kho1 had the most significant similarity with 100% to ToCMV5-1 from Syria and 98% to PoCMV9-11, also from Syria. Kho2 had the highest similarity of 98% with CMV-GRcl1 from Greece. Kho3 showed 99% similarity to ToCMV5-1 and 99% to Kho1, both from different regions. These findings highlight the genetic diversity of CMV in saffron plants.
 
In this study, saffron fields in Boshrouyeh County were found to be infected with Cucumber mosaic virus (CMV) using a reverse transcription-polymerase chain reaction (RT-PCR) test with a specific CMV primer. Out of 148 saffron samples showing viral disease symptoms, three were confirmed to be infected with CMV, as evidenced by the successful amplification of a 657 base pair fragment using CMV-specific primers.
Genetic diversity was assessed based on the sequence of the coat protein of Iranian CMV strains and other strains available in the BLAST database. The results revealed the formation of twelve distinct branches, with Iranian strains falling within the first branch of the first group. The closest strains to Iranian ones were CMV-GRcl1 and ToCMV5-1 from Greece and Syria, respectively. The highest similarity was observed between two Iranian strains, Kho2 from Boshrouyeh and Kho3 from Raqqah, indicating geographical location did not play a significant role in viral classification.
While CMV infection in saffron had been reported using serological methods, this study emphasized the need for molecular identification and protein analysis. Notably, this research represents the first report of CMV presence in saffron fields in South Khorasan.

DNA Mitochondria is one of the most commonly molecular markers for phylogenetic studies in animals due to its simple genome structure, which presents an ideal model to study evolution and genetic similarity. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the eight species of wild and domestic goat based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.

In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes per each genome from seven wild species of goat including Markhor (C. falcoeri), Capra ibex, Capra nubiana, Capra pyrenaica, Capra sibirica, Capra caucasica, Capra aegagrus, and domesticated species of goat (Capra hircus) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software.

Based on the analysis, it was found that the highest similarity between the nucleotide sequences of the complete genome (99.50) of domestic goat (Capra hircus) and wild Capra aegagrus goat and the lowest percentage of similarity (93.79) between the nucleotide sequences of the complete genome of the breed Capra nubiana) with wild goat Capra sibirica goat. Also, based on the results of the phylogenetic tree, it was found that domestic goat breeds (Capra hircus) and wild Capra aegagrus goat are divided into one group and wild Capra ibex and Capra pyrenaica breeds are divided into another distinct cluster.

In this study, all the results obtained from complete sequences of the mitochondrial genome analysis are consistent with the results obtained from the sequence of 13 protein coding genes per each genome, which indicates the correct clustering of wild and domestic goat breeds. Therefore, mitochondrial genome sequences could be used as a suitable genetic marker for accurate phylogenetic analysis and clustering of different species of sheep.

Lactic acid bacteria (LAB) and their bacteriocins are widely used as natural and safe preservatives in food products, to control both pathogenic and spoilage microorganisms. This study aimed to isolate and identify LAB from several traditionally produced fermented fruits and vegetables from different parts of Iran, screening their potentials for producing bacteriocin-like substances production and evaluate their antimicrobial activities against various pathogens. The effect of heat treatment and different pH values on the stability of bacteriocins were also assessed and compared with commercial nisin for their possible application in the food industry as an alternative to chemical preservatives.

 Lactic acid bacteria were isolated from several fermented products like hawthorn, mixed fruit pickles containing quince and apple, mango, and medlar. pickle, and tThe isolates were identified using phenotypic (physiological and biochemical) and genotypic (16S rDNA gene sequencing) methods followed by drawing phylogenetic tree based on the neighbor-joining method. The bacteriocins were prepared from the neutralized and cell-free supernatant (CFS). To precipitate the bacteriocins, ammonium sulfate (75%), potassium phosphate buffer, and methanol-chloroform were used, and extraction was completed with a high-speed centrifugecentrifugation. After freeze-drying, the precipitate was kept as crude bacteriocin. The bacteriocin activity was measured by the critical method, and the effect of heat, storage time and pH on the stability of bacteriocins was evaluated. The minimum inhibitory concentration (MIC) and the minimum inhibitory bactericidal concentration (MBC) of the examined bacteriocins were determined on against the pathogenic strains of Escherichia coli and Staphylococcus aureus and compared with commercial nisin.

 In this research, from 162 isolated strains of LAB, four isolates (10A, S6, Sa, and Ab) were selected based on the highest amount of antimicrobial compounds and diameter of the inhibitory zone against pathogenic strains. then the isolates were identified as different strains of Lactiplantibacillus plantarum (previously classified as Lactobacillus plantarum). The phylogenetic position of the isolates was determined by drawing a phylogenetic tree. The drawn tree consists of two clusters and the first cluster consist of two sub-clusters, with two different strains of L. plantarum in each of them. In the next step, bacteriocin of the isolates was extracted using saturated ammonium sulfate and high-speed (23000g) centrifugingcentrifugation. Partially purified bacteriocins from different species showed high inhibitory effects on tested indicators, which were estimated, for L. plantarum 3360 (10A) and L. plantarum lb51 (Ab), 64000 AU/ml against Staphylococcus aureus and Escherichia coli. All selected bacteriocins indicated a stable effect at different temperatures of 60 and 121°C for 20 min and 4 and -20°C for 6 months, this effect was the examined bacteriocins were also stable against at acidic and alkaline pHs too. Also, the inhibitory property decreased under very acidic (pH < 3) and very alkaline (pH > 8) conditions, but this reduction was not significant at the 95% confidence level. Bacteriocins with 64000 AU/mL activity had higher antimicrobial properties against the pathogens compared to an equal amount of commercial NiseenNisin-S (680 AU/mL). The results of MIC and MBC showed that isolates 10A and Ab have the highest inhibitory properties compared to other extracted bacteriocins and/or nisin. Since heat and chemical preservatives are used in food preparation, the stability of bacteriocins against heat and different pH is important, therefore, after extraction and purification, the extracted bacteriocins can be used as a biological preservative in the production of various food products in the range of acidic and alkaline pH, including juices, meat products, and sauces. Encapsulation of these peptides and their application in food products needs further investigation.

In order to detection and differentiation of two complications of disorder and lack of podding in soybeans, while visiting 185 soybean fields in Golestan and Mazandaran provinces, only from the summer cultivation of 17 fields from five different places in Golestan province, plants with signs of disorder and the lack of acute podding were identified and 17 samples were selected from each field and sampling was done from the leaves or stems of the mentioned plants in order to extract RNA and DNA. Then, PCR was performed to detect nepovirus using the degenerate primer of nepovirus and to detect phytoplasma using a pair of general primers and a nested PCR test. The results of electrophoresis confirmed the amplification of the 1800 bp band in the general PCR, the 1250 bp fragment in the nested PCR related to phytoplasma, and also the amplification of the 640 bp band related to a nepovirus. Besides, no band of healthy plants was observed. at the same time, tissue grafting and mechanical inoculation were performed on GPX soybean benchmark plant using the mentioned samples and two types of symptoms appeared. From the sequencing of the disordered samples (production of a small number of seeds and small pods), Tomato ring spot virus strain ep31_63026 and from the sequencing of the samples with non-encapsulation (grassiness and no formation of pods and seeds), Aster yellows phytoplasma from the 16SrI-B group were identified, which confirmed the results of the reference plant. The phylogenetic analysis of sequencing results confirmed the presence of Phytoplasma and Nepovirus only in the summer culture of samples that had symptoms of disorder and lack of podding.

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.

Improving the quality of bread wheat is an important issue. It has attracted the attention of many researchers over the years, and in recent decades, various methods have been developed to evaluate this goal. One of the most important goals in wheat breeding programs is to improve the quality of wheat bakery. Waxy proteins that responsible for the expression of GBSS enzyme in wheat that control the ratio of amylose to amylopectin in starch, These proteins in hexaploid wheat are controlled by three genes, Wx-D1, Wx-B1, Wx-A1 and those have a key role in quality of wheat flour. The goal of this study was to investigate the nucleotide diversity of Wx-B1 gene in wild and crop cultivars and also to investigate the phylogenetic relationships between wheat and their ancestors based on waxy genes.

In the present study, the phylogenetic relationships of the waxy B gene in 34 samples including 4 species of Aegilops genus and 28 cultivars of wheat and 2 species of wild wheat were evaluated using PCR and sequencing techniques  in Ilam university.

Sequences alignment results of Wx-B-seq1 and Wx-B-seq2 genes showed there are very high conserved regions between crop and wild wheat, although in some regions there is single nucleotide diversity between crop and wild wheat. The results of similarity matrix of Wx-B-seq1 showed the highest distance was related to Sardari cultivar and the lowest distance was related to Aegilops.umbellulata sample. The similarity matrix of the Wx-B-seq2 gene showed this gene did not change much in crop cultivars except Shahi cultivar, while the two wild wheat samples T.boeticum and T.dicoccooides showed a very large genetic distance compared to the crop cultivars. The results of the substitution matrix estimation based on the maximum likelihood method for Wx-B-seq1 and Wx-B-seq2 genes showed the highest and lowest contributions of nucleotide substitution are purine and pyrimidine, respectively. Also, UPGMA clustering results for Wx-B-seq1 and Wx-B-seq2 genes divided the samples into two and three main groups, respectively.

The overall results show that the diversity observed in wild samples and The ancestors of crop wheat can be a good candidate for further studies to determine whether these changes will lead to protein content or not.

Isolation and identification of unknown microorganisms native to our country and their preservation in the collections of genetic resources in order to exploit their biological capacity are of special importance and necessity. This study aimed to identify halophyte microalgae living in the back-barrier Lipar located on the shores of the Oman Sea in Sistan and Baluchestan Province. Water and phytoplankton sampling was carried out from the back-barrier in 2019-2020. Isolation and purification of the collected microalgae were performed by serial dilution and F2 medium culture in agar and liquid media, and finally, pure single colonies were obtained. Then, the initial identification of isolates was done through microscopic observations and comparison with morphologically valid classification keys. In the next step, 18S rRNA and 16S rRNA genes were used for further verification and identification by molecular method and sequencing. Analysis of morphological data and molecular sequencing showed that two purified isolates were green microalgae Dunaliella salina and green-blue microalgae Cyanothece sp., which was identified for the first time from the back-barrier. In terms of biological and commercial capacity, these two microalgae are suitable species for mass production and are widely used in industry. The purified strains have been donated to the National Bank of Iran Genetic Resources for future research or industrial-scale exploitation.

Medicinal plants are valuable resources that have been considered by developing and developed countries considered as raw materials to become safe drugs for humans. Satureja belonging to the Lamiaceae This genus has more than 91 species with a wide distribution in the Mediterranean region. There are more than 8 species of this genus in Iran. Genetic identification and registration of different plant cultivars is one of the important stages of protecting genetic resources, which will be a difficult task for most plants in the early stages due to morphological characteristics. DNA barcoding is an emerging technology for fast and accurate species identification, and it is a molecular-based identification system that has recently been widely used, and its purpose is to identify biological samples and assign them to a specific species. Molecular DNA barcoding method is a reliable tool for identifying medicinal plants at the genus and species level. In this technique, a small part of the plant genome is sequenced and used to identify and determine the relationship between different species of a genus.

In the present study, the seeds of different species of savory plants including ( horentiss, S. bakhtiari, S. biossier, S. mutica, S. bakhtiari) were prepared from different regions of Ilam province and the National Center of Genetic and Biological Resources of Iran were investigated using DNA barcoding. Seed cultivation was done in April 2016 in the greenhouse of Ilam University. The seeds of the used species were grown in small pots. After the seeds germinated, when the seedlings grew to the stage of two to three leaves, the young leaves were sampled for DNA extraction. Genomic DNA was extracted by Doyle et al.'s method in the biotechnology laboratory of Ilam University in 1397. Quality and quantity of genomic DNA was checked using agarose gel 1/2% and nanodrop device respectively. PCR was performed using specific primers for matK, rbcL and ITS genes. Among the studied genes only matK gene was amplified in all samples.  After purification of PCR products, their product were sequenced. In order analysis of data, first, the sequence Blast in NCBI database using nucleotide Blast. Alignment of sequence was done using Clustalw method by BioEdite Sequence Alignment Editor Software. Indeed, Phylogenetic tree created using MEGA-X software.

PCR amplification show that the only matK gene well amplified in all samples, while the other genes were not amplified.  Also, the quality of the graphs shows the high quality of the sequence of the amplified fragment of the PCR product and the purity of the examined samples.  Nucleotide BLAST in NCBI show that our results have high similarity with related spices in NCBI (more than 96%). The results of the analysis of content of nucleotides in the studied samples in comparison with the sample in NCBI show that according to the changes observed in the length of the fragment amplified on the agarose gel, but there were no significant changes in the molecular percentage of nucleotides in the studied samples. Cluster analysis based on UPGMA method of matK gene showed that the samples of biossier and S. bakhtiarica of Ilam and Gilan along with the sample of S. hortensis Birjand and Yazd were in the same group and samples of s. bakhtiari Yazd and s. Khorasan mutica were in the second group.

The results of PCR amplification show that matK gene has been amplified in all samples that it can be very well way for investigating and determining of phylogenetic relationship of different savory species. The results of matK gene sequence as one of the candidate genes in plant DNA barcodes showed that the studied samples and ecotypes along with samples extracted from NCBI were classified into three groups. The results of this study showed that it is possible to use the matK gene as a part of the barcode system to identify savory species. However, due to the lack of information about the barcode library for the matK gene in the Satureja genus, it is not possible to make a definite conclusion about the species. The matK gene has two advantages, including the efficient yield of quality sequences and a high level of species discrimination. In general, re-sequencing of matK gene can be separated different samples from each other based on geographical origin.

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.

Grapevine fanleaf virus (GFLV) is a major grapevine infecting virus in the world.

Grapes showing GFLV signs were sampled from the suburbs of the city of Khorramabad in Lorestan Province of Iran in spring 2020 and RT-PCR test was performed to amplify their GFLV-CP gene and the product was sequenced.

Specific primers were able to amplify a 1515 bp fragment of the CP gene. Based on the nucleotide sequence of this fragment, GFLV was first identified in this region. The nucleotide sequence similarity of this isolate was detected at 89.14-95.64% with other isolates in the NCBI library. Also, the phylogenetic tree of these isolates, based on the genomic CP region, grouped GFLV isolates into two groups I and II. The Lorestan GFLV isolate was placed in a subgroup in Group I together with GFLV isolates from the northwestern part of Iran and the Takestan isolate, and isolates from other countries were grouped in a separate subgroup of this group. Also in the phylogenetic tree, the Northeast isolates and the Fars and Kohgiloyeh & Boyer-Ahmad province isolates were classified in Group II.

The results of this research indicate that the virus is endemic and that its likely origin was in Iran and then spread to other parts of the world. The impact of geographic segregation on the evolution of GFLV can also be deduced.

Saffron (Crocus sativus) is related to Iridaceae family and is one of the most important products in Iran. Recently, different viral diseases were detected on it. Iris severe mosaic virus is detected on some ornamental plants in Iran but has not been reported on saffron. In order to detect this virus, we collected 130 samples with yellowing, stunning, mosaic symptoms on saffron leaves and they were tested by PCR and specific primers. Finally fragments with 917 bp were amplified in 5 samples. Samples were cloned or more investigations in Macrogene company of Korea. Investigation of phylogeny according to coat protein showed that 5 Iranian isolates were separated in two groups near to Chinese isolates. Investigation in this survey showed that different groups were separated according their geographical distribution. Recombinant investigation showed that in none of Iranian isolates there is no recombination. This research is the first report of this virus and first molecular and phylogeny investigation in saffron fields of South and Razavi Khorasan.

Beet black scorch virus is one of the soil-borne sugar beet viruses in Iran. In this research work, we collected 80 samples of sugar beet farms in Razavi and Northern Khorasan Provinces. After extraction of their total RNA, the 3'UTR region of the virus genome was amplified to 315 nucleotides using reverse transcription polymerase chain reaction using specific primers. The 3'UTR of six different isolates was sequenced following cloning and then submitted to NCBI. Phylogenetic analysis based on nucleotide sequences of the 3'UTR region showed that the entire world isolates could be classified into two main groups II and I and each one was divided into two subgroups. Isolates of this study were grouped with 23 isolates from Iran in subgroup IA and Four isolates from Khorasan province were placed in the IB subgroup. Four Iranian BBSV isolates from the West were grouped in the subgroup GIIA. All Chinese isolates and the European isolates together with the USA isolate clustered in subgroup GIIB. The results of nucleotide comparison of six isolates showed that although no mutation occurred at position 3477 (uridine instead of guanine), However, in position 3398, adenine replaced guanine (similar to 60% of Iranian isolates) and in position 3393, uridine was substituted for cytosine only in Fariman isolates (MW274750). The results of comparing the average nucleotide identity of 3'UTR isolates in this study showed that they are identical to Iranian isolates in the range from 97.75% to 97.98%. Nevertheless, they had the least identity with Kermanshah isolates (92.52%).

Beans play an important role in the nutrition and health of the community due to their antioxidant properties. Recently, MYB family genes have been shown to be strongly associated with anthocyanin levels as gene-controlling seed coating. The physiological and molecular diversity of the genes involved in seed coat coating of 12 bean cultivars was conducted in the randomized complete block design. The results showed that there was a significant difference between different bean genotypes in terms of anthocyanin content, so that the highest amount of anthocyanin was observed in black beans. Molecular analysis of the MYB and AF genes showed that the this two genes were amplified in some samples, while the MYB gene was amplified in Vigna ungicolata 1, 2 and mutant and Phaseolus lunatus cultivars, while AF gene only amplification in V. ungicolata 1,2 and mutant culativars. Bioinformatics analyzes showed that the sequences from these two genes were very similar to those in the NCBI, with two new alleles being identified in the AF gene compared to the sequences used to control seed coatings in beans. Also, the phylogenetic diagram of the samples using the UPGMA method showed that the samples can be separated based on the color of the seed coat. The overall results showed that V.ungicolata mutant cultivar, due to their MYB and AF genes, as well as their high levels of anthocyanins and high performance compared to other cultivars, could be a good option for further study and introduction to farmers in the future.