Search

Symptoms of ringspots and vein-clearing were observed on wasabi (Wasabia japonica (Miq) Matsum) plants in three greenhouses in British Columbia during 2017. Ten indicator plant species, including four Nicotiana species, were inoculated with sap extracts from symptomatic leaves; after 4–11 days, necrotic lesions developed on all plants. Transmission electron microscopy revealed rod-shaped virions, 250–300 nm in length, in leaves of N. occidentalis and N. clevelandii. Total RNA from symptomatic wasabi tissues was used in RT-PCR with universal primers corresponding to five virus genera and specific primers for turnip ringspot virus and alfalfa mosaic virus. Amplicons ~400 bp in size were obtained with tobamovirus primer set TobN up3/TobN do4 and amplicons of ~300 and ~600 bp were obtained with ilarvirus primer set Ilar1F5/Ilar1R7. Sequencing and MegaBLAST (NCBI) query of the Ilar amplicons showed 99% identity to wasabi mottle virus (WMoV), a member of the genus Tobamovirus. Next-generation Sequencing confirmed WMoV as the only virus present in diseased plants. BC isolates (GenBank accession no. MK431779) showed 99.43% sequence identity to isolate ‘Alishan’ (GenBank accession no. KJ207375.1) and 98.62% identity to ‘Tochigi’ strain (GenBank accession no. AB017504.1). Mechanical inoculation of wasabi cultivars ‘Green Thumb’ and ‘Daruma’ produced ringspots and vein-clearing symptoms after 22–23 days on the former while the latter was asymptomatic, but WMoV was detected in all plants by RT-PCR. WMoV may have been introduced into Canada on imported infected ‘Green Thumb’ plants and subsequently spread through commercial vegetative propagation. The effects on yield or rhizome quality are yet unknown.

Strawberry mild yellow edge virus (SMYEV) is a member of the genus Potexvirus, family Alphaflexiviridae. It is one of the most common pathogenic viruses infecting cultivated strawberries worldwide. In this study, we investigated the genetic diversity of SMYEV in strawberry fields that were severely affected by strawberry decline disease in the eastern Canadian provinces of New Brunswick, Nova Scotia, Prince Edward Island and Quebec. A total of 134 SMYEV coat protein (CP) gene sequences, representing 85 nucleic acid haplotypes, were identified in 56 field samples. A highly divergent SMYEV population was found in all four provinces, but there was little genetic differentiation among the populations, and moreover, the Canadian SMYEV isolates formed a unique dissimilar, genetically divergent population group when compared to those reported in other countries. Phylogenetic analysis revealed three new SMYEV subclades that consisted mainly of Canadian variants and were composed of 76 sequence haplotypes (76/85, 88%). Mixed infections by different SMYEV variants were observed in 38 samples (38/56, 68%). Evolutionary analysis suggested that the SMYEV strains in eastern Canada possibly originated outside of Canada but adapted to conditions in the region through genetic mutations.

Cherry mottle leaf virus (CMLV) is a pathogen of sweet cherry and several other plant species in the genus Prunus, but only two isolates of the virus were reported previously. Here we determined the complete genome sequences of three CMLV isolates that were collected during 1980s. The coat protein of the CMLV was estimated to be about 22 kDa by protein western blot assay, and agree with the size expected based on their genome sequences. The three isolates share 78.4 to 82.7 % identities at the nucleotide sequence level between each other and 78.7 to 84.3 % identities to the two previously published CMLV isolates SA1162-21 and 95CI215. The high genome sequence divergences among the CMLV isolates were supported by phylogeny analysis. Possible inter-species gene transfer between CMLV and the other species in the genus Trichovirus was revealed by the RDP recombination analysis algorithms.

The complete genome sequences of four new isolates of strawberry mild yellow edge virus (SMYEV) were determined and analysed. The isolates, designated as AB41-01, AB41-02, NB1165 and NS26, were found from strawberry fields showing strawberry decline symptoms in eastern Canada. AB41-01 and AB41-02 were from a single-plant sample originating from Prince Edward Island, while NB1165 came from New Brunswick and NS26 from Nova Scotia. Nucleotide sequence identities are 95.8% between AB41-01 and NB1165, 99.6% between AB41-02 and NS26, and 84% between AB41-01/NB1165 and AB41-02/NS26. The four isolates share nucleotide sequence identities of 83.5–89.9% to two previously identified SMYEV isolates, namely MY18 and D7. Phylogenetic analysis indicates that the four Canadian isolates represented two new SMYEV strain types and the strain divergences were not likely from recombination events among all presently known SMYEV isolates.

Strawberry decline disease, probably caused by synergistic reactions of mixed virus infections, threatens the North American strawberry industry. Deep sequencing of strawberry plant samples from eastern Canada resulted in the identification of a new virus genome resembling poleroviruses in sequence and genome structure. Phylogenetic analysis suggests that it is a new member of the genus Polerovirus, family Luteoviridae. The virus is tentatively named "strawberry polerovirus 1" (SPV1).

Artificial microRNA (amiRNA) technology utilizes microRNA (miRNA) biogenesis pathway to produce artificially selected small RNAs using miRNA gene backbone. It provides a feasible strategy for inducing loss of gene function, and has been applied in functional genomics study, improvement of crop quality and plant virus disease resistance. A big challenge in amiRNA applications is the unpredictability of silencing efficacy of the designed amiRNAs and not all constructed amiRNA candidates would be expressed effectively in plant cells. We and others found that high efficiency and specificity in RNA silencing can be achieved by designing amiRNAs with perfect or almost perfect sequence complementarity to their targets. In addition, we recently demonstrated that Agrobacterium-mediated transient expression system can be used to validate amiRNA constructs, which provides a simple, rapid and effective method to select highly expressible amiRNA candidates for stable genetic transformation. Here, we describe the methods for design of amiRNA candidates with perfect or almost perfect base-pairing to the target gene or gene groups, incorporation of amiRNA candidates in miR168a gene backbone by one step inverse PCR amplification, construction of plant amiRNA expression vectors, and assay of transient expression of amiRNAs in Nicotiana benthamiana through agro-infiltration, small RNA extraction, and amiRNA Northern blot.

It is of great importance and interest to develop crop varieties with low polyphenol oxidase (PPO) activity for the food industry because PPO-mediated oxidative browning is a main cause of post-harvest deterioration and quality loss of fresh produce and processed foods. We recently demonstrated that potato tubers with reduced browning phenotypes can be produced by inhibition of the expression of several PPO gene isoforms using artificial microRNA (amiRNA) technology. The approach introduces a single type of 21-nucleotide RNA population to guide silencing of the PPO gene transcripts in potato tissues. Some advantages of the technology are: small RNA molecules are genetically transformed, off-target gene silencing can be avoided or minimized at the stage of amiRNA designs, and accuracy and efficiency of the processes can be detected at every step using molecular biological techniques. Here we describe the methods for transformation and regeneration of potatoes with amiRNA vectors, detection of the expression of amiRNAs, identification of the cleaved product of the target gene transcripts, and assay of the expression level of PPO gene isoforms in potatoes.

It is of great importance and interest to develop crop varieties with low polyphenol oxidase (PPO) activity for the food industry because PPO-mediated oxidative browning is a main cause of post-harvest deterioration and quality loss of fresh produce and processed foods. We recently demonstrated that potato tubers with reduced browning phenotypes can be produced by inhibition of the expression of several PPO gene isoforms using artificial microRNA (amiRNA) technology. The approach introduces a single type of 21-nucleotide RNA population to guide silencing of the PPO gene transcripts in potato tissues. Some advantages of the technology are: small RNA molecules are genetically transformed, off-target gene silencing can be avoided or minimized at the stage of amiRNA designs, and accuracy and efficiency of the processes can be detected at every step using molecular biological techniques. Here we describe the methods for transformation and regeneration of potatoes with amiRNA vectors, detection of the expression of amiRNAs, identification of the cleaved product of the target gene transcripts, and assay of the expression level of PPO gene isoforms in potatoes.

Artificial microRNA (amiRNA) technology utilizes microRNA (miRNA) biogenesis pathway to produce artificially selected small RNAs using miRNA gene backbone. It provides a feasible strategy for inducing loss of gene function, and has been applied in functional genomics study, improvement of crop quality and plant virus disease resistance. A big challenge in amiRNA applications is the unpredictability of silencing efficacy of the designed amiRNAs and not all constructed amiRNA candidates would be expressed effectively in plant cells. We and others found that high efficiency and specificity in RNA silencing can be achieved by designing amiRNAs with perfect or almost perfect sequence complementarity to their targets. In addition, we recently demonstrated that Agrobacterium-mediated transient expression system can be used to validate amiRNA constructs, which provides a simple, rapid and effective method to select highly expressible amiRNA candidates for stable genetic transformation. Here, we describe the methods for design of amiRNA candidates with perfect or almost perfect base-pairing to the target gene or gene groups, incorporation of amiRNA candidates in miR168a gene backbone by one step inverse PCR amplification, construction of plant amiRNA expression vectors, and assay of transient expression of amiRNAs in Nicotiana benthamiana through agro-infiltration, small RNA extraction, and amiRNA Northern blot.

A complete method to regenerate adventitious shoots and to produce field-ready trees from three commercial cultivars of sweet cherry (Prunus avium L.) is described. The effects of explant types, pre-treatments, basal media, and phloroglucinol on cultivars Bing, Sweetheart, and Lapins were investigated. Callus developed on four explant types: apical shoot tips isolated from orchard trees; and punctured shoot tips, stem sections, and shoot bases of in vitro shoot cultures. Callus formed on Bing (5%), Sweetheart (8%), and Lapins (20%) shoot tips from orchard trees after 4 months on Murashige and Skoog medium (MS) at half-strength with 3 μM benzylaminopurine (BA). In vitro-derived explants formed callus after 3 months on Woody Plant Medium with 3 μM BA (W3B): punctured shoot tips (Sweetheart and Lapins 67%), stem sections (Sweetheart 31%, Lapins 27%), and shoot bases (Sweetheart 10%, Lapins 17%). Pre-treatment of shoot cultures on MS with 3 μM BA and 1 mM phloroglucinol increased callus formation three-fold on shoot base explants. Callus was separated from parental explants and maintained on MS with 3 μM BA. Shooting was induced by transferring callus to W3B. At 2 weeks, shoot development approached 100%. By 4 weeks, 7–17 shoots had formed on each explant. Callus was maintained for 1.5 years with no decrease in shoot production. Shoots were grafted onto Mazzard (P. avium) rootstocks with 54% (Sweetheart), 57% (Lapins), and 21% (Bing) success after 5 weeks.

In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

Shoot regeneration was achieved from leaves of in vitro cultures of Prunus avium L. cv. 'Lapins' and 'Sweetheart' using woody plant medium (WPM) supplemented with 1-naphthalene-acetic acid (NAA) and thidiazuron (TDZ) or benzyladenine (BA). Percent regeneration was influenced by plant growth regulators and by explant type, orientation and wounding. Optimal regeneration was observed with whole-leaf explants wounded by transverse cuts along the midrib and incubated abaxial surfaces uppermost, on media supplemented with 2.27 or 4.54 µM TDZ plus 0.27 µM NAA. The percent regeneration of the two cultivars was not significantly different. Optimum conditions for regeneration resulted in 71.4% of 'Lapins' and 54% of 'Sweetheart' explants producing one or more shoots per explant.

The insecticides acephate, dichlorvos, and imidacloprid were assayed, using in vitro shoot cultures of apple (Malus×domestica Borkh.), to determine their phytotoxicity at several concentrations and their effectiveness for eradication of the Western Flower Thrip (Frankliniella occidentalis, Pergande) from infested apple shoot cultures. Commercial formulations of acephate (Orthene), dichlorvos (VaportapeII), and imidacloprid (Admire) and a technical grade of imidacloprid were used in the experiments. For acephate and imidacloprid, concentrations of 1 to 80 mg·L-1 a.i. in shoot culture medium were used, while for dichlorvos, a fumigant, particles of the formulated product containing concentrations of 0.7 to 6.4 mg a.i. were suspended in the head space of the 500-mL glass culture jar. Acephate, dichlorvos, and the technical grade of imidacloprid did not cause phytotoxicity and growth of shoot cultures was unaffected at all treatment concentrations tested after a 6-week treatment period. Imidacloprid (20 to 80 mg·L-1 of the commercial formulation) caused chlorosis at the end of the 6-week treatment period. None of the treatments tested resulted in the death of shoots. Thrips were eradicated by acephate or imidacloprid treatments of 5 mg·L-1 and by dichlorvos treatment of 0.7 mg per 500-mL culture jar. Shoot cultures grew normally after the treatment period. Chemical names used: O,S-dimethyl acetylphosphoramidothioate (acephate), 2,2- dichlorovinyl dimethyl phosphate(dichlorvos),1-(6-chloro-3-pyridylmethyl)-N-nitroimidazolidin-2-ylideneamine (imidacloprid).

A protocol for micrografting shoot tips harvested from in vitro shoot cultures directly to transplanted rootstock plants in the greenhouse was developed. Shoot tips of the apple (Malus domestica) cultivars Golden Delicious, Granny Smith and Fuji clone, Nagafu12, were harvested, stored in a water bath then prepared for grafting by cutting the stem immediately below the tip into a wedge shape leaving the tip approximately 3 mm (0.12 inch) long. The rootstock cultivar, Malling 9 (M.9) (M. domestica), was prepared by cutting into a young fast growing side branch to expose the cambium, creating a pocket into which the shoot tip was inserted. The cut section of the tip was oriented so as to contact the exposed rootstock cambium and was held in place by wrapping with a strip of pliable plastic film. Two weeks later the wrapping was loosened and the grafted branch cut back. Side branches of the rootstock were not removed until later in order to support rootstock growth. The scion shoots developed into nursery whips suitable for transplanting to a screen house or field after 2 months. The protocol proved to be a simple efficient way to rapidly grow nursery trees from tissue culture clones developed in genetic modification experiments and was used to propagate several hundred plants. Grafting success was often 100% but was reduced if quality of shoot tips was poor due to injury indicated by brown tip color. The protocol eliminates the steps of rooting, acclimatizing and growing shoots into plants to serve as a scion wood source.

Multiple shoots were produced from nodal explants of cassava (Manihot esculenta Crantz) by a two-step procedure: a 6- to 8-day exposure to 0.11–0.22 µM thidiazuron (TDZ) in liquid Murashige and Skoog (MS) medium followed by culture on agar-solidified MS medium supplemented with 2.2 µM 6-benzyladenine (BA) and 1.6 μM gibberellic acid (GA3). TDZ caused the nodal explants to expand and this expansion (growth) continued during culture with BA and GA3. From this expanded explant, clusters of buds and fasciated stems developed continuously and these gave rise to shoots. The shoot proliferation process was open-ended, yielding an average of 31.5 shoots per nodal explant after 10 weeks of culture with genotype CG 1–56. A positive response was also obtained from seven other genotypes evaluated with this protocol.

The utility of artificial microRNAs (amiRNAs) to induce loss of gene function has been reported for many plant species, but expression efficiency of the different amiRNA constructs in different transgenic plants was less predictable. In this study, expressions of amiRNAs through the gene backbone of Arabidopsis miR168a were examined by both Agrobacterium-mediated transient expression and stable plant genetic transformation. A corresponding trend in expression of amiRNAs by the same amiRNA constructs between the transient and the stable expression systems was observed in the experiments. Plant genetic transformation of the constructs that were highly expressible in amiRNAs in the transient agro-infiltration assays resulted in generation of transgenic lines with high level of amiRNAs. This provides a simple method for rapid and effective selection of amiRNA constructs used for a time-consuming genetic transformation in plants.

The p20 protein encoded by the tombusvirus, Cucumber necrosis virus has previously been shown to be involved in host pathogenicity and shares sequence similarity with the Tomato bushy stunt virus p19 suppressor of silencing. Using a virus-induced gene silencing (VIGS) assay, we show that p20 is a viral suppressor of RNA silencing (VSR) in infected plants. In addition, a CNV p20-knockout mutant showed a decline in viral RNA accumulation in infected plants, consistent with the role of p20 in suppression of RNA silencing. However, unexpectedly, all GFP transgenic plants co-infiltrated with p20 and GFP displayed RNA silencing using an Agrobacterium-mediated silencing assay. Detailed RNA analysis of GFP mRNA levels in p20 agro-infiltrated plants revealed that p20 did initially display suppressor activity but this was rapidly overcome by RNA silencing. p20 expression levels in agro-infiltrated plants were shown to be approximately 50-fold lower than that of the TBSV p19 silencing suppressor, consistent with the notion that p20 dosage levels are not sufficient to suppress RNA silencing in the Agrobacterium-mediated system. Our results suggest that a viral-based VIGS assay may be required for identifying VSRs encoded by some plant viruses. Based on bioinformatics studies the mechanism of suppression of silencing by p20 is predicted to be similar to that of the TBSV p19 suppressor.

Background Polyphenol oxidase (PPO), often encoded by a multi-gene family, causes oxidative browning, a significant problem in many food products. Low-browning potatoes were produced previously through suppression of PPO gene expression, but the contribution of individual PPO gene isoform to the oxidative browning process was unknown. Here we investigated the contributions of different PPO genes to total PPO protein activity, and the correlations between PPO protein level, PPO activity and tuber tissue browning potential by suppression of all previously characterized potato PPO genes, both individually and in combination using artificial microRNAs (amiRNAs) technology. Results Survey of the potato genome database revealed 9 PPO-like gene models, named StuPPO1 to StuPPO9 in this report. StuPPO1, StuPPO2, StuPPO3 and StuPPO4 are allelic to the characterized POTP1/P2, POT32, POT33 and POT72, respectively. Fewer ESTs were found to support the transcriptions of StuPPO5 to StuPPO8. StuPPO9 related ESTs were expressed at significant higher levels in pathogen-infected potato tissues. A series of browning phenotypes were obtained by suppressing StuPPO1 to StuPPO4 genes alone and in combination. Down-regulation of one or several of the PPO genes did not usually cause up-regulation of the other PPO genes in the transgenic potato tubers, but resulted in reduced PPO protein levels. The different PPO genes did not contribute equally to the total PPO protein content in the tuber tissues, with StuPPO2 accounting for ~ 55% as the major contributor, followed by StuPPO1, ~ 25-30% and StuPPO3 and StuPPO4 together with less than 15%. Strongly positive correlations between PPO protein level, PPO activity and browning potential were demonstrated in our analysis. Low PPO activity and low-browning potatoes were produced by simultaneous down-regulation of StuPPO2 to StuPPO4, but the greatest reduction occurred when StuPPO1 to StuPPO4 were all suppressed. Conclusion StuPPO1 to StuPPO4 genes contributed to browning reactions in tuber tissues but their effect was not equal. Different PPO genes may be regulated independently reflecting their diversified functions. Our results show that amiRNAs can be used to suppress closely related members of highly conserved multi-gene family. This approach also suggests a new strategy for breeding low-browning crops using small DNA inserts.