Soybean Mosaic Virus Isolates Research Articles

First report of Soybean mosaic virus of sword bean in South Korea.

Soybean mosaic virus (SMV) is a member of the genus Potyvirus in the family Potyviridae. Legume crops are often infected by SMV. SMV has not been naturally isolated from sword bean (Canavalia gladiata) in South Korea. In July 2021, 30 samples of sword bean were collected at the field located in Hwasun and Muan, Jeonnam, Korea to investigate viruses infecting sword bean. The samples exhibited symptoms typical of viral infection such as mosaic pattern and, mottling of leaves. Reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) techniques were employed to identify the agent of viral infection in sword bean samples. Total RNA was extracted from the samples using the Easy-SpinTM Total RNA Extraction Kit (Intron, Seongnam, Korea). Out of the 30 samples, seven were found to be infected by the SMV. RT-PCR was performed using RT-PCR Premix (GeNet Bio, Daejeon, Korea) with SMV-specific primer set, forward primer (SM-N40, 5'-CATATCAGTTTGTTGGGCA-3') and the reverse primer (SM-C20, 5'-TGCCTATACCCTCAACAT-3'), yielding a product of 492 bp (Lim et al., 2014). RT-LAMP was performed using RT-LAMP Premix (EIKEN Chemical, Tokyo, Japan) with SMV-specific primer set, the forward primer (SML-F3, 5'-GACGATGAACAGATGGGC-3', SML-FIP, 5'-GCATCTGGAGATGTGCTTTTGTGGTTATGAATGGTTTCATGG-3') and reverse primer (SML-B3, 5'-TCTCAGAGTTGGTTTTGCA-3', SML-BIP, 5'-GCGTGTGGGTGATGATGGATTTTTTCGACAATGGGTTTCAGC-3') for diagnosis of viral infection (Lee et al., 2015). The full coat protein genes of seven isolates were amplified using RT-PCR to determine their nucleotide sequence. The standard nucleotide BLAST (blastn suite) showed that the seven isolates had approximately 98.2-100% homology with SMV isolates (FJ640966, MT603833, MW079200, and MK561002) in NCBI GenBank. The sequences of seven isolates were deposited in the GenBank database under the accession numbers: OP046403-9. For the pathogenicity assay of the isolate, the crude saps from SMV-infected samples were mechanically inoculated into sword bean. Fourteen days after inoculation, the mosaic symptoms were observed on the upper leaves of sword bean. As a result of the RT-PCR diagnosis in the upper leaves, SMV was reconfirmed in sword bean. This is the first report of natural SMV infection in sword bean. As sword beans are increasingly consumed for teas, transmitted seeds are resulting in a decrease in pod production and quality. It is necessary to develop efficient methods of seed processing and management strategies to control SMV infection in sword bean.

First report of Passion fruit green spot virus in yellow Passion fruit (Passiflora edulis f. flavicarpa) in Casanare, Colombia.

Passiflora edulis, commonly known as passion fruit, is a vine species of passionflower native to South America. In Colombia, yellow passion fruit (P. edulis f. flavicarpa) is the most important species in terms of net production and local consumption. Recently two brevipalpus transmitted cileviruses, (i) passion fruit green spot virus (PfGSV) and (ii) hibiscus strain of citrus leprosis virus C2 (CiLV-C2H) were detected in passion fruit in Brazil and Hawaii, respectively (Ramos-González et al., 2020, Olmedo-Velarde et al., 2022). CiLV-C2H infects both citrus and hibiscus in Colombia (Roy et al., 2015, 2018) but there was no report of PfGSV elsewhere apart from Brazil and Paraguay (Costa-Rodrigues et al., 2022). Apart from emerging begomovirus diseases, five major viruses are known to infect passion fruit in Colombia: soybean mosaic virus (SMV), cowpea aphid-borne mosaic virus, passion fruit yellow mosaic virus, cucumber mosaic virus, and a tentative Gulupa bacilliform badnavirus A (Cardona et al., 2022). Current findings of CiLV-C2H in passion fruit and PfGSV in hibiscus motivated us to investigate the possibilities of cilevirus infection in passion fruit in Colombia. During surveys, along with healthy yellow passion fruit leaves, five symptomatic plant samples from Meta and three from Casanare were collected before sent to the Molecular Plant Pathology Laboratory at Beltsville, MD under APHIS permit. Passion fruit samples from Meta showed leaf mottling, rugose mosaic, and leaf distortion, whereas leaf variegation, chlorotic spots, yellowing, green spots in senescent leaves and green vein banding were observed in the Casanare samples (Supp. Fig. 1). Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, USA). To know the potential cilevirus infection in these samples, three PfGSV specific (Ramos-González et al. 2020) and a CiLV-C2 generic primer pairs (Olmedo-Velarde et al. 2021) were used in the RT-PCR assays. All five passion fruit samples from Meta failed to produce either CiLV-C2 or CiLV-C2H or PfGSV amplicon whereas all three Casanare samples successfully amplified 321, 244 and 299 nts of PfGSV-RNA1 and -RNA2 amplicons using C13F/C13R, C6F/C6R and C8F/C8R primers, respectively. Bi-directional amplicon sequencing followed by BlastN analysis revealed ≥99% nt identity with the PfGSV-RNA1 (MK804173) and -RNA2 (MK804174) genome sequences. An optimized ribo-depleted library preparation protocol was utilized to prepare two cDNA libraries using the RNA extracts of a PfGSV suspected positive (Casanare) and a negative (Meta) samples (Chellappan et al., 2022). HTS libraries of Casanare and Meta samples resulted in 22.7 to 29.5 million raw reads, respectively. After adapter trimming and filtering, clean reads were mapped to the Arabidopsis thaliana reference genome and unmapped reads were de novo assembled (Chellappan et al., 2022). BlastN analysis from the assembled contigs identified 1-3 contigs corresponding to PfGSV-RNA1 and -RNA2, respectively, from Casanare sample whereas 3 contigs of SMV were identified in Meta passion fruit sample. No other virus sequence was obtained from either of the libraries. Assembled contigs covered 99.33% of the RNA1 and 94.42% of the RNA2 genome, with read depths of 64,474 and 119,549, respectively. Meta sample contigs (OP564897) covered >99% of the SMV genome, which shared >99% nt identity with the Colombian SMV isolates (KY249378, MW655827). Both RNA-1 (OP564895) and -2 (OP564896) segments of the Casanare isolate shared 99% nt identity with PfGSV isolate (MK804173-74). Our discovery identified PfGSV in Colombia, for the first-time outside Brazil and Paraguay. The findings of PfGSV in yellow passion fruit increases the potential threat and possibility of PfGSV movement via Brevipalpus sp. from passion fruit to other hosts.

Molekularna identifikacija i karakterizacija izolata virusa mozaika soje poreklom iz Srbije

Certified and non-certified seed of the soybean cultivar Dukat showing symptoms of mottling were collected at the preharvest stage from soybean fields in the location Tamiš (South Banat District, Serbia) in 2021. To identify the presence of soybean mosaic virus (SMV), a total of 10 samples, five of each type of seed, were selected and tested by RT-PCR using primers SMVCPF/SMVCPR, which amplify a fragment of the coat protein (CP) gene. The molecular assay confirmed the presence of SMV in all tested seed samples. For further analyses, the CP and P1 genome regions of two selected isolates (DS-21 and NDS-21, representing certified and noncertified seed, respectively) were partially sequenced. The Serbian SMV isolates shared very low nucleotide diversity and were mutually closely related based on the CP (99.8% nt/99.2% aa identities) and P1 (99.7% nt/ 99.6% aa identities) regions. Phylogenetic analyses based on both genomic regions showed that the two Serbian SMV isolates originating from certified and noncertified seed belonged to one cluster, and consequently to the same SMV subpopulation. Since this is the first molecular characterization of SMV in Serbia, further research should be focused on collecting samples from different locations and of different varieties, and on determining the variability of SMV population in Serbia based on whole-genome analysis. This research will contribute to better understanding of the epidemiology of this pathogen with the ultimate goal of developing and implementing appropriate control measures.

Evolution and Phylogeny of Soybean Mosaic Virus Based on 143 Complete Genomes.

Soybean mosaic virus (SMV) of the genus Potyvirus is an important virus in cultivated soybeans. Here, we obtained 7 SMV genomes from soybean germplasms using RNA sequencing and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes derived from 10 plant species and 12 countries. The phylogenetic tree we constructed using coding DNA sequences revealed the existence of nine clades of SMV isolates/strains. Recombination analysis revealed 76 recombinant events and 141 recombinants in total. Clades 1 and 3 contain the most common SMV pathotypes, including G1 through G7, which are distributed worldwide. Clade 2 includes several Chinese SMV pathotypes. The SMV isolates were further divided into two groups. The SMV isolates in the first group, including clades 8 and 9, were identified from Pinellia and Atractylodes species, whereas those in the second group (clades 1 through 7) were mostly found in cultivated soybeans. The SMV polyprotein undergoes positive selection, whereas most mature proteins, except for the P1 protein, undergo negative selection. The P1 protein of SMV isolates in group 1 may be highly correlated with host adaptation. This study provides strong evidence that recombination and plant hosts are powerful forces driving the genetic diversity of the SMV genome.

Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences.

Soybean mosaic virus (SMV) of the family Potyviridae is the most devastating virus that infects soybean plants. In this study, we obtained 83 SMV coat protein (CP) sequences from seven provinces in Korea using RT-PCR and Sanger sequencing. Phylogenetic and haplotype analyses revealed eight groups of 83 SMV isolates and a network of 50 SMV haplotypes in Korea. The phylogenetic tree using 305 SMV CP sequences available worldwide revealed 12 clades that were further divided into two groups according to the plant hosts. Recombination rarely occurred in the CP sequences, while negative selection was dominant in the SMV CP sequences. Genetic diversity analyses revealed that plant species had a greater impact on the genetic diversity of SMV CP sequences than geographical origin or location. SMV isolates identified from Pinellia species in China showed the highest genetic diversity. Phylodynamic analysis showed that the SMV isolates between the two Pinellia species diverged in the year 1248. Since the divergence of the first SMV isolate from Glycine max in 1486, major clades for SMV isolates infecting Glycine species seem to have diverged from 1791 to 1886. Taken together, we provide a comprehensive overview of the genetic diversity and divergence of SMV CP sequences.

Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus

Soybean mosaic virus (SMV) has threatened the global yield of Leguminosae crops, but the mechanism of its infection, spread, and evolution remains unknown. A systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern. The overall nucleotide composition and correlation analysis revealed that the preferred synonymous codons mostly end with A/U. Clustering by RSCU value of each strain and phylogenetic tree analysis showed that the SMV isolates studied were divided into four clades, with a low overall extent of codon usage bias (CUB) in SMV. According to the ENC, PR2, neutrality plot, and correspondence analysis, natural selection of geographical diversity may play a critical role in the CUB. Higher adaptability was shown in Glycine with SMV and more pressure was received by clade III. These findings could not only provide valuable information about the overall codon usage pattern of the SMV genome, but could also aid in the clarification of the involved mechanisms that dominate the codon usage patterns and genetic evolution of the SMV genome.

Strongylodon macrobotrys: new host of soybean mosaic virus in Brazil.

Strongylodon macrobotrys, commonly known as the jade vine, emerald vine, or turquoise jade vine, is a species of Fabaceae native to the Philippines. The plants have blue-green color inflorescences, which makinge them one of the most admired ornamental plants in Brazil (Muniz et al. 2015). In addition, the plants contain compounds with anticancer properties (Ragasa et al. (2014) isolated compounds from S. macrobotrys with anticancer properties. In March 2019, an adult jade plant, grown under the trellis system in an experimental area at the campus of the University of São Paulo (USP), Piracicaba, state of São Paulo, was found showing mosaic symptoms typical of a virus infection. Preliminary examination of negatively stained leaf extracts by transmission electron microscopy detected elongated, flexuous particles similar tolike thoseat of a potyviruses. Further observations of thin sections of symptomatic leaf tissues revealed the presence of cylindrical inclusions, as well as bundles of thin, elongated, and filamentous particles, typical of potyvirus infection in epidermal, parenchymalparenchymal, and vascular regions, as well as bundles of thin, elongated and filamentous particles. Subsequent molecular and biological assays confirmed the presence of a potyvirusTo identify the species of the virus, .Presence of a potyvirus was confirmed by subsequent molecular and biological assays. Ttotal RNA was extracted from a pool of symptomatic leaves from the plant using the Purelink viral RNA/DNA kit (Thermo Fisher Scientific), and analyzed by one- step RT-PCR using potyviruses universal primers PV1/SP6 and WCIEN-sense (Mackenzie et al. 1998; Maciel et al. 2011), which amplify a 750-bp fragment. Total RNA extracted from an asymptomatic jade vine, obtained from a florist shop, was used as a negative controlincluded in the assay. PCR products at the expected size (~750-bp) were observed in the symptomatic plant but not in the asymptomatic plant. BLASTn analysis of the Nnucleotide sequence of the amplicon obtained only from total RNA of the symptomatic plant (GenBank accession no. MN970030) showed that it shares 90.82% to 97.859% identity with corresponding nucleotide sequences of the Korean isolate WS162 of soybean mosaic virus (SMV) deposited at the GenBank (, accession no. FJ640973, FJ640956, D88616). Extracts from symptomatic leaves of the jade plant wereas mechanically inoculated onto leaves of healthy plants of jade vine, Jack bean (Canavalia ensiformis), soybean cv. NA 5909 (Glycine max), cowpea (Vigna unguiculata), and passion fruit (Passiflora edulis f. flavicarpa). One plant of jade plant and four plants of each other species were inoculated , and infection was assessed based and monitored for symptom expression on symptom expression, and RT-PCR. The jade vine and Jack bean plants were infected by SMV, showingdeveloped mild mosaic symptoms approximately 60 and 15 days after inoculation, respectively , whereas the plants of other species were absent of any visible symptoms . To confirm the potyvirus identity, the jade vine samples were also tested by cConventional RT-PCR with SMV-specific primers pairs CP-F-SMV/CP-R-SMV (Jaramillo Mesa et al., 2018) and SMV-CPf/SMV-CPr (Wang and Ghabrial, 2002), thawhicht amplify fragments of 1000 990-bp and 469-bp90, respectively, nucleotides offrom the CP geneome region of SMV was performed, respectively. Amplicons of expected sizes were obtained from the total RNA of the leaves of field-infected and the mechanically inoculated plant of jade plantsvine as well as the Jack bean plants, but not from the asymptomatic jade plantvine and plants of other species the negative control. The viral nucleotide sequences obtained with the above pairs of primersBLASTn analysis of nucleotide sequences of the amplicons showed that they share 96.81% and 97.63% identity, respectively, with the same Korean SMV isolate WS162. These results demonstrate that… the field-symptomatic jade vine was infected with SMV, which is naturally transmitted by aphids speciess in a non-persistent manner and via soybean infected seeds (Hajimorad et al. 2018)( ). The virus appears to have has a restricted narrow natural host range., Aapart from soybean, and to date, it has only been reported the natural infection has been documented only in soybean, Lagenaria siceraria, Passiflora spp., Pinellia ternata, Senna occidentalis, and Vigna angularis (Almeida et al., 2002; Chakraborty et al. 2016; Hajimorad et al. 2018). To our knowledge, this is the first report of SMV in S. macrobotrys in the world. Further surveys are necessary to determine the incidence of the virus in ornamental jade plants vines and its importance as virus reservoirs for commercial soybean crops.

Construction and characterization of an infectious clone of Soybean mosaic virus isolate from Pinellia ternata

Soybean mosaic virus (SMV), one of the major viral diseases of Pinellia ternata (Thunb.) Breit., has had a serious impact on its yield and quality. The construction of viral infectious clones is a powerful tool for reverse genetics research on viral gene function and interaction between virus and host. To clarify the molecular mechanism of SMV infection in Pinellia ternata, it is particularly important to construct the SMV full-length cDNA infectious clone. Therefore, the infectious clone of Soybean mosaic virus Shanxi Pinellia ternata isolate (SMV-SXBX) was constructed in this study by Gibson in vitro recombination system, and the healthy Pinellia ternata leaves were inoculated by Agrobacterium infiltration, further through mechanical passage and RT-PCR, confirming that the 3' end of the SMV-SXBX infectious clone had a stable infectivity when it contained 56-nt of poly(A) tail. This method is not only convenient and efficient, but also avoids the instability of SMV infectious clones in Escherichia coli. The construction of SMV full-length infectious cDNA clones laid the foundation for further study on the molecular mechanism of SMV replication and pathogenesis.

Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes

Soybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about the genetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolates were obtainedfrom Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP) were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic and molecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombination had occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of the non-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow of the SMV-NI populations was found between the southeastern and northeastern populations, the southwestern population was relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI) and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identical recombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RI might be in an expanding state, while the SMV-NI population is relatively stable.

Вплив вірусу мозаїки сої на урожайність трансгенної сої та дослідження його молекулярно-генетичних властивостей

Вперше в Україні показано, що трансгенні сорти сої уражуються вірусом мозаїки сої. Встановлено, що, не зважаючи на генетичні модифікації, урожайність ВМС-інфікованих рослин суттєво знижена. При ураженні вірусною інфекцією (ВМС) врожайність сої зменшувалась у обох господарствах Київської і Полтавської областей на 35,0 – 65,7 % відповідно. Більш значне зниження урожаю (в 2,6 рази) при вірусній інфекції відмічено у Полтавській обл. в умовах дуже посушливого клімату 2017 року (ГТК = 0,53) порівняно із 2016 (ГТК=0,99). Відмічено, що ВМС-інфекція негативно впливає на продуктивність і структуру урожаю рослин ГМ-сої. ВМС-інфекція зменшує на 21,9% кількість бобів і на 22,5% кількість зерен на одній рослині, масу зерен з однієї рослини – на 27,1% та масу 1000 зерен – на 29,7% порівняно зі здоровими рослинами. Визначено, що досліджуваний ізолят ВМС SGP–17 має спільне походження з іранськими, американськими ізолятами, а також польським та українським. Аналіз нуклеотидних та амінокислотних послідовностей гену капсидного білка виявив високий рівень дивергенції нуклеотидів порівняно з ізолятами з інших країн та чотири унікальні амінокислотні заміни, що можуть бути залучені до здатності цього ізоляту інфікувати трансгенні рослини сої. Отримані результати свідчать на користь вирощування вітчизняних сортів сої, створених класичними методами селекції та які містять детермінанти природної генетичної стійкості до ВМС.

ВІРУСНІ ІНФЕКЦІЇ ПШЕНИЦІ ОЗИМОЇ І СОЇ ТА ЇХ ВПЛИВ НА УРОЖАЙНІСТЬ КУЛЬТУР ЗА УМОВ ЗМІН КЛІМАТУ

Climate changes affect the level of damage from plant diseases, because the environment has a significant impact not only on plants, but also on pathogens and their vectors. Therefore, studying of the viruses, crop yield and productivity, agroclimatic changes should be in the complex. The aim of the study was to investigate the viruses affecting winter wheat and soybean plants, their yield in conditions of infection with viruses and changes in the climatic conditions of the Poltava region. Methods: biometric; crop and its structure; DAS-ELISA, RNA extraction from plant material, RT-PCR, sequencing, phylogenetic analysis, statistical methods. Results. It is established that Wheat streak mosaic virus (WSMV) is the most widespread and harmful for wheat crop and Soybean mosaic virus (SMV) – for soybean. For the first time in Ukraine, the yield of winter wheat and soybean plants under conditions of virus damage and changes of climatic conditions in the Poltava region was studied. Correlation between the HTC (the hydrothermal coefficient of Selyaninov), the damage caused by viral diseases and the productivity of winter wheat and soybean plants is revealed. It is shown that transgenic soybean Grimo is affected with SMV, which reduce grain yield twice. The molecular genetic properties of the SMV isolate GRP-17 were studied and it is determined that it has a common origin with Iranian, American, Chinese isolates and isolate from Ukraine. It has been determined that, the amino acid substitutions in CP gene of GRP-17 are unique compared to sequences of all SMV isolates taken for the analysis. Conclusions. Analysis of the meteorological data in the agrocenosis was carried out and it was established that the yield of wheat and soybean crops is closely related to the ratio of precipitation and air temperature (HTC). From these parameters also depended the frequency of WSMV and SMV detection, because they have a direct impact on insects – vectors of the viruses. The changes in the molecular genetic level in CP gene of GRP-17 can be involved in the it's harmfulness and ability to infect transgenic soybean plants.

FIRST REPORT OF SOYBEAN MOSAIC VIRUS INFECTING PASSION FRUIT IN ECUADOR

Passion fruit (Passilora edulis, family Passifloarceae) is widely cultivated in Ecuador. In September 2015, mottling and downward curling of the leaves were observed in Quevedo (Los Rios, Ecuador). Based on the type of symptoms, infection by a potyvirus was suspected. Six symptomatic and symptomless passion fruit samples were screened by DAS-ELISA using specific antibodies (Agdia, USA) to soybean mosaic virus (SMV), a member of the genus Potyvirus, family Potyviridae. All symptomatic samples were ELISA-positive. Total RNA was isolated from a single plant with Triazol (Sigma, USA) and used in RT-PCR to amplify a DNA fragment of ca. 350 bp with universal primers designed in the potyviral NIb domain (Zheng et al., 2008). The amplicon was sequenced and the 322 bp sequence (GenBank accession No. MF370353) was analysed by BLAST and compared with the corresponding sequence of SMV isolates from different countries. The partial NIb gene sequence of isolate SMV-Ecuador showed a 98.1% and 95% maximum identity at the nucleotide and amino acid levels with a SMV isolate from China (KP710874). A phylogenetic tree constructed with MEGA version 4.1 showed that the SMV isolate from Ecuador was closely related to and clustered with the Chinese isolate KP710874, whereas isolates from Canada (HQ166265), South Korea (FJ807700 and FJ640955), China (KX834323) and Iran (KF297335) formed a separate cluster. To the best of our knowledge, this is the first report of SMV on passion fruit in Ecuador.

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data.

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

Characterization of a soybean mosaic virus variant causing different diseases in Glycine max and Nicotiana benthamiana.

We discovered a soybean mosaic virus (SMV) variant (4278-1) that caused systemic infections in Nicotiana benthamiana plants, resulting in stem stunting and leaf shriveling. The virus had a particle morphology and incubation period similar to those of other SMV isolates but differed from them in the leaf symptoms it caused when infecting soybean and N. benthamiana. The genome of this variant consisted of a 9994-nt single-stranded RNA, which was different from most of the other known SMV isolates (approximately 9600 nt). Interestingly, we found evidence that two recombination events (nt 1-476 and nt 1145-1349) had occurred between 4278-1 and a watermelon mosaic virus analogue (WMV analogue), in the 5' untranslated region and the P1 cistron.

First molecular evidence of Soybean mosaic virus (SMV) infection in soybean from India

The occurrence of Soybean mosaic virus (SMV) in soybean grown in mid-hill condition of Meghalaya, India was confirmed by symptomatology, transmission electron microscopy, reverse transcription-polymerase chain reaction (RT-PCR) and partial characterization of cytoplasmic inclusion protein (CI), nuclear inclusion protein and coat protein (NIb-CP) domains. Sequence analysis showed 99.0 % nucleotide and amino acid identities for both domains with previously reported SMV (isolate Ar13) from Iran. This is the first molecular evidence of SMV infection in soybean from India.

Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences

Soybean mosaic virus (SMV), a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1 041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide (NT) sequence identities and 95.1-100% amino acid (AA) sequence identities. The P3 coding regions of the 16 SMV isolates share high identities (92.4-98.9% NT and 96.0-100% AA) with the reported Korean isolates, followed by the USA isolates (88.5-97.9% NT and 91.4-98.6% AA), and share low identities (80.5-85.2% NT and 82.1-84.7% AA) with the reported HZ1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus (WMV), with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.

Identification of strains and screening of resistance resources to soybean mosaic virus in Anhui Province

In order to clarify the local constitution,distribution,and population dynamics of soybean mosaic virus( SMV) in Anhui Province and to screen resistant accessions to epidemic SMV strains,461 potential SMV samples of soybean leaves have been collected from main soybean regions in Anhui Province during 2009-2010. Of those,83 SMV isolates were identified through expanding propagation,single lesion isolation purification,serological determination. They were grouped into the 14 SMV strains including SC3-SC9,SC11,SC13-SC15,SC17,SC19 and SC22,based on their response to 10 unified national soybean differentials. Of the 14 SMV strains,7strains were found for the first time in this study,encompassing SC5,SC11,SC14,SC15,SC17,SC19 and SC22.The comparison between present and previous identification results of SMV strains showed that SC3 and SC7 strains were still predominant in Anhui Province with 16. 9% and 25. 3% of the total number of isolates,and SC15 was lower with 12. 1%. In terms of soybean accessions resistant to popular strains of SC3 and SC7,5 of 149 accessions,Zhongzuo J8023,Zhonghuang 45,L85-2308,Zhongguo 47 and Suike 13 showed high resistance to SC3strain and 9 accessions to SC7,including Zhonghuang 45,Su03-4-1-4 and Lu06-7 etc. 13 accessions displayed resistant to SC15,account for 13. 7% of the 95 tested soybean accessions. In this paper,we clarified the SMV predominant strains and their variation trend in the main soybean producing regions of Anhui Province,providing the basis for the breeding and layout of resistant soybean accessions to the disease.

Sequence variability in the HC-Pro coding regions of Korean soybean mosaic virus isolates is associated with differences in RNA silencing suppression

Soybean mosaic virus (SMV), a member of the family Potyviridae, is an important viral pathogen affecting soybean production in Korea. Variations in helper component proteinase (HC-Pro) sequences and the pathogenicity of SMV samples from seven Korean provinces were compared with those of previously characterized SMV isolates from China, Korea and the United States. Phylogenetic analysis separated 16 new Korean SMV isolates into two groups. Fourteen of the new Korean SMV samples belonged to group II and were very similar to U.S. strain SMV G7 and Chinese isolate C14. One isolate in group II, A297-13, differed at three amino acid positions (L54F, N286D, D369N) in the HC-Pro coding sequence from severe isolates and SMV 413, showed very weak silencing suppressor activity, and produced only mild symptoms in soybean. To test the role of each amino acid substitution in RNA silencing and viral RNA accumulation, a series of point mutations was constructed. Substitution of N for D at position 286 in HC-Pro of SMV A297-12 significantly reduced silencing suppression activity. When the mutant HC-Pro of A297-13 was introduced into an infectious clone of SMV 413, accumulation of viral RNA was reduced to less than 3% of the level of SMV 413 containing HC-Pro of A297-12 at 10days post-inoculation (dpi) but increased to 40% of SMV 413(HC-Pro A297-12) at 40dpi. At 50dpi RNA accumulation of SMV 413(HC-Pro A297-13) was similar to that of SMV 413(HC-Pro A297-12). However, at 50 dpi, the D at position 286 of HC-Pro in SMV 413(HC-Pro A297-13) was found to have reverted to N. The results showed that 1) a naturally occurring mutation in HC-Pro significantly reduced silencing suppression activity and accumulation of transgene and viral RNAs, and 2) that there was strong selection for revision to wild type when the mutation was introduced into an infectious clone of SMV.

Role of Soybean mosaic virus–Encoded Proteins in Seed and Aphid Transmission in Soybean

Soybean mosaic virus (SMV) is seed and aphid transmitted and can cause significant reductions in yield and seed quality in soybean (Glycine max). The roles in seed and aphid transmission of selected SMV-encoded proteins were investigated by constructing mutants in and chimeric recombinants between SMV 413 (efficiently aphid and seed transmitted) and an isolate of SMV G2 (not aphid or seed transmitted). As previously reported, the DAG amino acid sequence motif near the amino terminus of the coat protein (CP) was the major determinant in differences in aphid transmissibility of the two SMV isolates, and helper component proteinase (HC-Pro) played a secondary role. Seed transmission of SMV was influenced by P1, HC-Pro, and CP. Replacement of the P1 coding region of SMV 413 with that of SMV G2 significantly enhanced seed transmissibility of SMV 413. Substitution in SMV 413 of the two amino acids that varied in the CPs of the two isolates with those from SMV G2, G to D in the DAG motif and Q to P near the carboxyl terminus, significantly reduced seed transmission. The Q-to-P substitution in SMV 413 also abolished virus-induced seed-coat mottling in plant introduction 68671. This is the first report associating P1, CP, and the DAG motif with seed transmission of a potyvirus and suggests that HC-Pro interactions with CP are important for multiple functions in the virus infection cycle.

Analysis of Soybean mosaic virus genetic diversity in Iran allows the characterization of a new mutation resulting in overcoming Rsv4-resistance

The genetic variation and population structure of Soybean mosaic virus (SMV) in Iran was analysed through the characterization of a set of isolates collected in the soybean-growing provinces of Iran. The partial nucleotide sequence of these isolates showed a single, undifferentiated population with low genetic diversity, highly differentiated from other SMV world populations. These traits are compatible with a population bottleneck associated with the recent introduction of SMV in Iran. Phylogenetic analyses suggest that SMV was introduced into Iran from East Asia, with at least three introduction events. The limited genetic diversification of SMV in Iran may be explained by strong negative selection in most viral genes eliminating the majority of mutations, together with recombination purging deleterious mutations. The pathogenicity of Iranian SMV isolates was typified on a set of soybean differential lines either susceptible or carrying different resistance genes or alleles to SMV. Two pathotypes were distinguished according to the ability to overcome Rsv4 resistance in line V94-5152. Amino acid sequence comparisons of virulent and avirulent isolates on V94-5152 (Rsv4), plus site-directed mutagenesis in a biologically active cDNA clone, identified mutation S1053N in the P3 protein as the determinant for virulence on V94-5152. Codon 1053 was shown to be under positive selection, and S1053N-determined Rsv4-virulence occurred in isolates with different genealogies. The V94-5152 (Rsv4)-virulence determinant in Iranian isolates maps into a different amino acid position in the P3 protein than those previously reported, indicating different evolutionary pathways towards resistance breaking that might be conditioned by sequence context.