مقالات رزومه علیرضا افشاری فر

Emerging plant viral diseases account for serious threats to agricultural crop yields and food security in many parts of the world. Alfalfa mosaic virus (AMV), a member of the Alfamovirus genus within the Bromoviridae family, exhibits a wide host range, infecting more than 150 plant species, including economically important crops such as alfalfa (Medicago sativa), lettuce (Lactuca sativa), potato (Solanum tuberosum), tomato (Licopersicon esculentum), pepper (Capsicum annuum) and bean (Phaseolus vulagris). AMV was initially documented infecting alfalfa in the Fars and Tehran provinces in 1968, subsequently spreading to all alfalfa-growing regions of Iran country (Zainadini et al. 2005). Serological assays have traditionally identified AMV strains, with molecular characterizations also being conducted on Iranian AMV isolates (Golnaraghi et al. 2004; Massumi & Hosseini Pour 2007; Massumi et al. 2012; Mangeli et al. 2012; Pourrahim & Farzadfar 2015). However, a number of Iranian AMV isolates have also been characterized molecularly (Mangeli et al. 2012; Pourrahim & Farzadfar 2015). Notably, based on ELISA tests and molecular examinations, Mangeli and colleagues identified AMV in various weeds, alfalfa, and vegetables such as potatoes and peppers across different Iranian regions (Mangeli et al. 2019). A greenhouse survey in Bandar Abbas, Iran, in spring 2023 revealed severe leaf chlorotic spots, yellowing symptoms, and fruit necrosis in tomato (Haji-Abad) and pepper (Bandar-Abbas) plants (Figure 1). To confirm AMV infections, total RNA was extracted from five symptomatic and one asymptomatic sample of tomato and pepper plants using TRIzol reagent (Sinaclone), followed by reverse transcription-polymerase chain reaction (RT-PCR) assays with a set of specific AMV primers (AMV-R, AMV-F) targeting a 780-nucleotide segment of the coat protein gene (Massumi et al. 2012). PCR products of the expected size (approximately 780 bp) were obtained from all of the symptomatic samples (five samples of tomato and pepper plants), while no amplified products were generated from any of the healthy leaf samples of tomato and pepper plants. Amplified fragments from one sample of each plant were gel purified using a PCR purification kit (Qiagen Co.) and sequenced directly using a paired-end sequencing strategy (Sinohe Co. Iran). Multiple alignments of the obtained nucleotide sequences (corresponding to a part of CP gene) with 15 AMV isolates obtained from GenBank showed the highest identity (97.9%. for IR-To-01 isolate and 98.3% for IR-Pep-03 isolate) with an Italian AMV strain See-1 isolated from Sechium elude and the lowest identity (95.8% for IR-To-01and 95.4% for IR-Pep-03) with an Iranian AMV isolate (IRWS2) from Wisteria sinensis. Phylogenetic analysis grouped Iranian isolates with European strains, while, the other AMV isolates (including Iranian, Asian and American isolates) were grouped into a separate clade (Figure 2), suggesting a possible introduction through seed trade. Further PCR assays targeting other viral groups, using four primer pairs, including a degenerate primer pair of potyviruses Nib1 / Nib3R (Gibbs and Mackenzie 1997); a degenerate primer pair of begomoviruses primer BC (Deng et al. 1994) / primer181V (Rojas et al. 1993) and Tobamovirus degenerate primer pair TobamodF/TobamodR (Li et al. 2018), yielded no positive results, suggesting no mixed infection of AMV with other viruses. Given the economic importance of tomatoes and related industries in southern Iran and the potential of emerging viruses which can rapidly spread and infect tomato crops, leading to reduced fruit production and quality, understanding the epidemiology and genetic variations of emerging viral diseases such as AMV is crucial for effective control measures. Ongoing research aims to elucidate genetic variations, pathogenicity, host range, and distribution of AMV in tomato and pepper plants under greenhouse and open-field conditions in Iran. Based on the results of nucleotide sequencing, based on a small part of the virus envelope protein from tomato (Haji Abad) and pepper (Bandar Abbas) under different cultivation conditions in Iran, particularly in Hormozgan province, a major center for greenhouse and outdoor tomato and pepper cultivation.

Emerging plant diseases accounts for serious treats to agricultural crop yields, and food security. Tomato torrado virus (ToTV) for the first time was reported in canary island (Spain) from greenhouse-grown tomato plants expressing yellowing areas at the base of the leaflets which later turn into necrotic spots or large necrotic area covering leaves, stem and fruit (Verbeek et al., 2007). During a field survey carried out during spring 2021, a total number of 14 tomato plant samples showing severe necrosis symptoms on tomato leaves and fruits, similar to those described for ToTV (Moodley et al., 2019), were collected from an open tomato field in vicinity of Shiraz. , Total RNA was extracted from leaf and fruit tissues of 14 symptomatic samples using Trizol reagent, and for the presence of ToTV was subjected to reverse transcription polymerase chain reaction (RT-PCR) using a set of specific primer pair (3Avp/35seq R and 3Avp/35seq F) targeting approximately a 275 nucleotide fragment in the coat protein gene (Wieczoreck et al. 2020). Eleven symptomatic tomato samples yielded an amplicon of the expected size ( about 275 bp) in RT-PCR assay, Multiple alignment of the obtained nucleotide sequences showed that the Iranian ToTV isolates have the highest similarity of 98.2% (IRSHZ1) and 97.3% (IRSHZ3) with ToTV strain TEN-03 and the lowest similarity of 96.8% (IRSHZ1) and 95.4% (IRSHZ3) with ToTV strain GNC-06, both of which were reported from Spain

During a survey in 2021 a number of pepper and tomato plant samples with the begomovirus-like symptoms such as crinkled and curling leaves were collected from pepper and tomato greenhouses in three central provinces of Iran (Yazd, Isfahan and Kerman). Some weed species occurring within proximity to the greenhouse cultivated tomato crops were also sampled. To identify the Begomovirus infection in the collected samples, total DNA samples were extracted using a CTAB-based method and subjected to polymerase chain reaction (PCR)using the begomovirus degenerate primer pair BC primer and primer181V (Anfoka et al. 2005). This primer pair produced an amplicon of about 500 bp from pepper (Yazd and Kerman), tomato (Yazd) and puppet (Yazd) samples. Multiple alignment of the resulted nucleotide sequences showed that the isolates share maximum and minimum identities of 97.8 to 88.4% respectively with nucleotide sequences of chili leaf curl virus (ChiLCV) isolates reported from Oman (97.83%), Pakistan (97.83%), and India (97.64%) while they showed less than 80.2% similarity with other geminiviruses. Furthermore, a 1351bp fragment of DNA-β satellite genome was successfully amplified from pepper and tomato isolates (collected in Molabashi and Dehaghan regions in Yazd and Isfahan provinces respectively), using specific beta-satellite primer pair Beta01 / Beta02 (Cui et al., 2004). Alignment of the obtained sequences showed a very close homology to the beta satellite (ToLCB) associated with Iranian isolate of ToLCV, (MN175237.1) (Benanej et al. 2019).

Pepper mild mottle virus (PMMoV) is a serious disease in pepper and some other plant species in the Solanaceae family, with significant damage to these crops throughout the temperate to tropical regions (Colson et al. 2010). The causative agent of the Pepper mild mottle disease single-stranded RNA virus belong to the Tobamovirus genous, family Virgaviridae, that induce (Peng et al. 2015). Mixed infection of plant viruses is a common feature in nature which may lead to more severe symptoms than their single infection. During a survey conducted in the fall and summer of 1400, capcicum plant samples showing symptoms of mild mosaic symptoms on leaves and fruit blistering and necrosis, were collected from a number of greenhouses in Isfahan. PMMoV with an another tobamovirus, Tomato brown rugose fruit virus (ToBRFV), may cause more severe symptoms on pepper or tomato plants (Lu et al. 2012). Total RNA was extracted from collected leaves and fruits tissues by using a TRIzol reagent (Sinaclone) and subjected to reverse transcription-polymerase chain reaction (RT-PCR) assay using a PMMoV specific primer pair PMMoVCP / a and PMMoVCP / s (Peng et al. 2015) a 500 bp DNA fragment was amplified from affected pepeer plants. Furthermore, To assess the presence of other viruses in mixed-infection with PPMoV, in plant samples showing severe symptoms, the extracted total RNA was used in an RT-PCR using four primer pairs including: a degenerate primer pair of potiviruses Nib1 / Nib3R (Riechmann et al. 2015);

Soybean (Glycine Max (L.) Merr), like those maize, wheat, rice and cotton crops, is an important agricultural crop traded in the global commodity markets. the production of soybean has been curtailed by numerous harsh environmental stresses, especially drought, a water deficit state of soil. The isotopic dimethyl labeling was applied to study the proteomic changes associated with the drought responses of two contrasting soybean cultivars. A total of 874 non-redundant and repeatable peptides were identified among 17787 peptides in tolerant cultivar (these peptides changed significantly to compare with sensitive cultivar) by using MS/MS analysis which corresponding to 260 of protein groups. Among these 260 protein groups, there were 142 groups being up-regulated in the drought-tolerant cultivar under drought treatment and in contrast, there were 118 groups being down-regulated by drought-tolerant cultivar. InterPro protein domain enrichment and Gene Ontology were performed for functional analysis. According to the results most of these proteins are related to photosynthesis activity, energy metabolism, ROS-scavenging activity, channel and transporter activity, gene expression and translation regulation, Carbohydrate derivative metabolic process, Organic acid and substance metabolic process and sugar alcohols catabolic process.

Autophagy is a degradation process in eukaryotes through which damaged or unwanted intracellular components are degraded. This process is also involved in plant disease resistance, although its mechanisms are not precisely known. Autophagy is regulated by multiple autophagy-related proteins (ATGs).In this study, we investigated the possible impact of two Barley yellow striate mosaic virus (BYSMV) proteins, i.e., phosphoprotein (P) and ancillary protein 3 (P3), on four important genes involved in autophagy (ATG2, ATG6, ATG7, and AGO1) in N. benthamiana. P and P3 genes were cloned in pCAMBIA-1302 vector under the control of the 2 × 35S promoter and Hemagglutinin tag. Constructs of each gene were agroinfiltrated in the abaxial side of the N. benthamiana leaves. Five days after agroinfiltration, the expression level of these genes was measured using RT- qPCR. The results showed that expression of ATG2, ATG6 and ATG7 genes increased in all treatments (P, P3, P+P3).The level of ATG2 expression was 5.57, 15.6 and 5.6 fold, in P/GFP, P3/GFP and P/P3/GFP treatments, respectively, while a 1.5-fold reduction was obtained in expression of AGO1 in all treatments. These results implied that P and P3 proteins of BYSMV can modify the expression of autophagy related genes in N. benthamiana plant. These findings suggest the involvement of AGO1, ATG6, ATG7 and ATG2 in immune responses of N. benthamiana against BYSMV, which provide a better understanding of plant host defense mechanisms against virus infections and might be an opportunity to exploit a novel antivirus approach.

Barley yellow striate mosaic virus (BYSMV) belongs to the genus Cytorhabdovirusin the family Rhabdoviridae. It causes mosaic and chlorotic striation in gramineous plants and is transmitted by Laodelphax striatellus in a propagative manner. In the present study, nucleotide sequences ofglycoprotein and phosphoprotein genes of BYSMV Zanjan isolate are reported. Following thepurification of viral nucleocapsid, the nucleotide sequence of G and P genes was determined using random-PCR method (rPCR) followed by PCR with specific primers. Putative amino acid sequences of the two proteins were aligned with other members of Rhabdoviridae using CLUSTAL W software and the phylogenetic trees were depicted. BYSMV G and P proteins showed the highest similarity to the Northern cereal mosaic virus (NCMV). In phylogenetic analysis, the viruses were grouped into two main clusters reflecting the Cytorhabdovirus and Nucleorhabdovirus genera. These results support our previous phylogenetic analysis based on polymerase gene.Analysis of transmission efficiency showed that Zanjan, Naghadeh and Sero isolates were transmitted with a higher efficiency than Mashhad isolate by the same biotype of L. striatellus.

BYDV-PAV is one of the major agents causing yellowing and dwarfing of cereals worldwide. Previous study has been report the wide distribution of BYDVs in Iran and the prevalence of BYDV-PAV in cereal fields of the country. Due to the importance of this virus, and to investigate the taxonomic position of the Iranian isolate, the full length sequence of an Iranian severe isolate of BYDV-PAV from Kerman province (KP771878) was determined. Total RNA was extracted usingRNX (-plus)TM Kit. Nucleic acid extracts were reverse transcribed and amplified using PAV specific primers. The amplified fragments were inserted into PTZ57R/T vector using Ins T/A clone PCR Product Kit (MBI Fermentas) and cloned in Escherichia coli (DH5α) and sequenced. Complete nucleotide sequence of this isolate comprises 5668 nucleotides. Sequence analysis at nucleotide level showed that the Kerman isolate has maximum homology of about 94% with two American isolates (AF235167 and EF043235) of BYDV-PAV and grouped in the same cluster, while it showed the least similarity with a Chinese isolate of BYDV-PAV (AY855920) with only 78% homology. In addition, nucleotide sequence comparison of each ORF showed that the ORF4 was the most conserved while the ORF6 was the most divergent regions.

Wheat dwarf virus (WDV) is one of the main factors causing stunting and yellowing diseases of cereals. Two strains of WDV have been reported from different parts of Iran. The barley strain (WDV-B) is only detected from naturally infected barley plants, while the wheat strain (WDV-W) infects both wheat and barley plants. Previous results regarding distribution of WDV strains have revealed the dominance of WDV-W compared to WDV-B in cereal fields of Iran. To investigate the taxonomic position of the Iranian WDV strains, the complete DNA genome of a wheat isolate of WDV-W from Shahrekord (WDV-Whe[Iran:Sh:Whe]) and of a barley isolate of WDV-W from Bavanat (WDV-Whe[Iran:Ba:Bar], with 2750 and 2749 nucleotides, respectively, were sequenced. Phylogenetic analysis of nucleotide sequences of the genome, revealed two main clusters designated WDV- W and WDV-B. Cluster WDV-W is composed of two Iranian isolates including WDV-Whe[Iran:Sh:Whe], WDV-Whe[Iran:Ba:Bar] and nine non-Iranian wheat isolates of WDW (WDV-W). An Iranian barley isolate of WDV (WDV-Bar[IR:Bar]) and seven exotic barley isolates of WDV formed the second cluster (WDV-B). Sequence comparison of different genomic regions of the two Iranian WDV-W isolates showed that the replication-associated protein was the most conserved while the movement protein and the large intergenic region were the most divergent regions.