The Detection and Variation of Strawberry mottle virus

Viral diseases of fruit and berry crops in the South of the Russian Far East

Aim. To systematise data on pathogens of viral diseases of garden and berry crops in the south of the Russian Far East.

Discussion. The peculiar climatic features of the Far East limit the range of garden and berry crops. However, there are a significant number of species of wild fruits and berry plants in the region, which have increased (often – record breaking) frost resistance and are therefore actively used for breeding new cultural forms. At the same time, for the last century and a half new varieties of garden crops have been actively introduced to the Far East, which has lead to an increase in the risk of penetration of entire phytovirus complexes together with vegetatively propagated (cuttings, vaccinations) plants. The greatest damage to garden crops in the Far East is caused by a number of representatives of the genus Nepovirus (Picornavirales: Secoviridae): Tomato ringspot virus, Arabis mosaic virus, Raspberry ringspot virus, Grapevine fanleaf virus, Grapevine linear pattern virus as well as several still unidentified viruses. Among other taxonomic groups of phytoviruses dangerous for fruit and berry crops one could point out Potato virus Y (Patatavirales: Potyviridae, Potyvirus), Carnation ringspot virus (Tolivirales: Tombusviridae, Dianthovirus), Clover yellow mosaic virus (Tymovirales: Alphaflexiviridae, Potexvirus), Cucumber mosaic virus (Martellivirales: Bromoviridae, Cucumovirus), Alfalfa mosaic virus (Martellivirales: Bromoviridae, Alfamovirus). The paper considers the species composition of aphids‐carriers of phytoviruses affecting garden crops of the region.

Conclusions. In connection with the further prospects for the development of horticulture in the Russian Far East, it is necessary to intensify ecological and virological studies of this section of phytovirology as well as to increase access to agricultural producers with available test systems.

Rapid detection of strawberry mottle virus using reverse transcription recombinase polymerase amplification with lateral flow strip

Strawberry mottle virus (SMoV) is one of the main RNA viruses that profoundly affects the growth of strawberries worldwide. The rapid on-site detection of SMoV described here can be applied to produce virus-free strawberry seedlings. Reverse transcriptase recombinase polymerase amplification (RT-RPA) was combined with lateral flow (LF) strip to rapidly detect SMoV. The detection limit was 500 fg of RNA under optimized conditions. The SMoV-RT-RPA-LF assay was optimal with a combination of 2 μL reverse primer (5 μM) and 0.6 μL probe (10 μM) in a 50 μL RT-RPA reaction mixture for isothermal amplification at 40 ℃ for 15 min. In addition, 100 suspected samples were collected from different regions in the Shanghai suburbs. The SMoV-RT-RPA-LF assay showed that 3 of these 100 samples were positive for SMoV, which was in good concordance with the reverse transcription polymerase chain reaction (RT-PCR) results. The primers and probe had a unique specificity to SMoV because there was no cross-reaction with other strawberry viruses. This study provides an effective technique for the rapid on-site detection of SMoV to ensure a virus-free strawberry nursery.

Identification of Silencing Suppressor Protein Encoded by Strawberry Mottle Virus

Strawberry mottle virus (SMoV) is associated with strawberry decline disease, causing losses to fruit yield and quality. In this study, using a screening system that enables detection of both local and systemic plant host (RNA silencing) defense responses, we found that Pro2Glu and P28, encoded by SMoV RNA2 genome, functioned to suppress local and systemic RNA silencing triggered by single- but not double-stranded GFP RNA. Subcellular localization assay revealed that both Pro2Glu and P28 were localized to nucleus and cytoplasm. The deletion of 11 amino acid residues at the C-terminus destabilized Pro2Glu protein, and the disruption of two conserved GW motifs deprived Pro2Glu of ability to suppress RNA silencing. Additionally, SMoV Pro2Glu and P28 enhanced the accumulation of potato virus X (PVX) in Nicotiana benthamiana 22 days post-infiltration, and P28 exacerbated significantly the symptoms of PVX. Collectively, these data indicate that the genome of SMoV RNA2 encodes two suppressors of RNA silencing. This is the first identification of a stramovirus suppressor of RNA silencing.

Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays

Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.

Molecular and Biological Characterization of a New Strawberry Cytorhabdovirus

Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-inoculated to N. benthamiana, N. benthamiana DCL2/4i, N.occidentalis 37B, and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae, and A. ruborum were shown to transmit StrV-1 under experimental conditions.

Genetic Diversity of Seven Strawberry mottle virus Isolates in Poland

The studies on detection of the Strawberry mottle virus (SMoV) have been conducted in Poland for breeding programme purpose and for producers of strawberry plant material. Leaf samples collected from infected strawberry plants were grafted on Fragaria sp. Indicators which were maintained in greenhouse for further study. Seven Fragaria vesca var. semperflorens 'Alpine' indicators infected by SMoV were used for the study aimed on molecular characterization of virus isolates. Partial RNA2 was amplified from total nucleic acids using the RT-PCR method. The obtained amplicons separately digested with BfaI, FauI, HaeIII, HincI, and TaqI enzymes showed different restriction profiles. The nucleotide sequences analysis of RNA2 fragment confirmed the genetic diversity of the SMoV isolates as their similarity ranged from 94.7 to 100%. Polish isolates shared 75.7-99.2% identity with sequence of the virus strains from the Czech Republic, the Netherlands, and Canada. Phylogenetic analysis resulted in grouping of the isolates found in Poland together with one of the Czech strain whereas two other from the Czech and the strains from the Netherlands and Canada created the separate cluster.

Meristem culture and subsequent micropropagation of Chilean strawberry (Fragaria chiloensis (L.) Duch.)

BACKGROUND

Vegetative propagation of Fragaria sp. is traditionally carried out using stolons. This system of propagation, in addition to being slow, can spread plant diseases, particularly serious being viral. In vitro culture of meristems and the establishment of micropropagation protocols are important tools for solving these problems. In recent years, considerable effort has been made to develop in vitro propagation of the commercial strawberry in order to produce virus-free plants of high quality. These previous results can serve as the basis for developing in vitro-based propagation technologies in the less studied species Fragaria chiloensis.

RESULTS

In this context, we studied the cultivation of meristems and establishment of a micropropagation protocol for F. chiloensis. The addition of polyvinylpyrrolidone (PVP) improved the meristem regeneration efficiency of F. chiloensis accessions. Similarly, the use of 6-benzylaminopurine (BAP) in the culture media increased the average rate of multiplication to 3-6 shoots per plant. In addition, the use of 6-benzylaminopurine (BAP), had low levels (near zero) of explant losses due to oxidation. However, plant height as well as number of leaves and roots were higher in media without growth regulators, with average values of 0.5 cm, 9 leaves and 4 roots per plant.

CONCLUSIONS

For the first time in Chilean strawberry, meristem culture demonstrated to be an efficient tool for eliminating virus from infected plants, giving the possibility to produce disease free propagation material. Also, the addition of PVP into the basal MS medium improved the efficiency of plant recovery from isolated meristems. Farmers can now access to high quality plant material produced by biotech tools which will improve their technological practices.

Detection of Strawberry necrotic shock virus using conventional and TaqMan(®) quantitative RT-PCR

Graft-indexing of an advanced selection from the University of Florida strawberry breeding program produced virus-like symptoms on Fragaria vesca. However; RT-PCR testing of the material did not detect the presence of any of 16 strawberry virus species or members of virus groups for which strawberries are routinely indexed. Large scale sequencing of the material revealed the presence of an isolate of Strawberry necrotic shock virus. The nucleotide sequence of this isolate from Florida shows a significant number of base changes in the annealing sites of the primers compared to the primers currently in use for the detection of SNSV thereby explaining the most probable reason for the inability to detect the virus in the original screening. RT-PCR and Taqman(®) qPCR assays were developed based on conserved virus sequences identified in this isolate from Florida and other sequences for SNSV currently present in GenBank. The two assays were applied successfully on multiple samples collected from several areas across the United States as well as isolates from around the world. Comparison between the RT-PCR and the qPCR assays revealed that the qPCR assay is at least 100 times more sensitive than conventional PCR.

Virus testing by PCR and RT-PCR amplification in berry fruit

Berry fruit crops are prone to infection by a wide range of viruses, with the list expanding every year, primarily because of the expansion of the crops to new geographic regions. Although some methods allow for virus detection in a nonspecific manner, the advent of cheap and effective nucleic acid sequencing technologies has allowed for the development of species-specific tests. This chapter describes methods for extraction of nucleic acids for molecular testing from a range of different berry fruit crops and lists oligonucleotide primers that have been developed for amplification of a large number of berry fruit viruses.

Multiplex RT-PCR detection of four aphid-borne strawberry viruses in Fragaria spp. in combination with a plant mRNA specific internal control

The principal aphid-borne viruses infecting Strawberry (Fragaria spp.) Strawberry crinkle virus (SCV), Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV) and Strawberry vein banding virus (SVBV) can cause serious crop losses. In this paper, a multiplex reverse transcriptase polymerase chain reaction (RT-PCR) method is described for the simultaneous detection of all four viruses in combination with a plant mRNA specific internal control which can be used as an indicator of the effectiveness of the extraction and RT-PCR. In total, 18 strawberry isolates infected naturally were analysed by this method. Every combination of RNA virus was able to be detected and a full complement of all four viruses were found together in three isolates, all taken from wild strawberry (Fragaria chiloensis (L.) Duch.) in Chile. The upper detection limit for the four viruses was at an extract dilution of 1/200. The broad applicability of the RNA specific internal control primers-which produced a PCR fragment of the expected size in 25 of 27 plant species tested-combined with improvements, made in extraction methods described provides potentially a standard method for comparable RT-PCR analyses in a wide variety of plant species.