Specificity of TAS-ELISA for Beet Necrotic Yellow Vein Virus and Its Application for Determining Rhizomania Resistance in Field-Grown Sugar Beets

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

Salivary gland morphology, tissue tropism and the progression of tospovirus infection in Frankliniella occidentalis

Tomato spotted wilt virus (TSWV) is transmitted by thrips in a propagative manner; however, progression of virus infection in the insect is not fully understood. The goal of this work was to study the morphology and infection of thrips salivary glands. The primary salivary glands (PSG) are complex, with three distinct regions that may have unique functions. Analysis of TSWV progression in thrips revealed the presence of viral proteins in the foregut, midgut, ligaments, tubular salivary glands (TSG), and efferent duct and filament structures connecting the TSG and PSG of first and second instar larvae. The primary site of virus infection shifted from the midgut and TSG in the larvae to the PSG in adults, suggesting that tissue tropism changes with insect development. TSG infection was detected in advance of PSG infection. These findings support the hypothesis that the TSG are involved in trafficking of TSWV to the PSG.

Proteomic Profiling of Sugar Beet (Beta vulgaris) Leaves during Rhizomania Compatible Interactions

Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), severely impacts sugar beet (Beta vulgaris) production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors that elicit resistant interactions with BNYVV, but as resistance breaking strains become more prevalent, effective disease control strategies will require the application of novel methods based on better understanding of disease susceptibility and symptom development. Herein, proteomic profiling was conducted on susceptible sugar beet, infected with two strains of BNYVV, to clarify the types of proteins prevalent during compatible virus-host plant interactions. Total protein was extracted from sugar beet leaf tissue infected with BNYVV, quantified, and analyzed by mass spectrometry. A total of 203 proteins were confidently identified, with a predominance of proteins associated with photosynthesis and energy, metabolism, and response to stimulus. Many proteins identified in this study are typically associated with systemic acquired resistance and general plant defense responses. These results expand on relatively limited proteomic data available for sugar beet and provide the ground work for additional studies focused on understanding the interaction of BNYVV with sugar beet.

Sugar Beet Cultivar Evaluation for Storability and Rhizomania Resistance

To reduce storage losses and improve resistance to rhizomania caused by Beet necrotic yellow vein virus (BNYVV), studies were initiated to establish a storage cultivar selection program. In 2006 and 2007, 30 or more commercial sugar beet (Beta vulgaris) cultivars were grown in soil naturally infested with BNYVV. At harvest, two root samples from each plot were collected and used to establish percent sugar. Additional samples were placed on top of an indoor pile (set point 1.7°C) and inside an outdoor pile in a randomized complete block design with four replications. After 142 and 159 days in indoor storage, sucrose reduction ranged from 13 to 90% in 2007 and 57 to 100% in 2008. Outdoor storage sucrose reduction ranged from 13 to 32% in 2007 and 28 to 60% in 2008. An average of 31 and 45% of the root surface was covered with fungal growth in 2007 and 2008, respectively. Cultivars that retained the most sucrose had resistance to BNYVV and the least fungal growth and weight loss. Indoor storage with BNYVV-infested roots allowed for the most consistent cultivar separation and will potentially lead to selection of cultivars for improved storability and rhizomania resistance.

Suppression of Resistance-Breaking Beet necrotic yellow vein virus Isolates by Beet oak-leaf virus in Sugar Beet

Rhizomania, a serious disease of sugar beet (Beta vulgaris), is caused by Beet necrotic yellow vein virus (BNYVV). Resistance allele Rz1 has been widely incorporated into commercial cultivars. Recently, resistance-breaking isolates of BNYVV (RB-BNYVV) were identified and characterized. When the occurrence of RB-BNYVV was surveyed throughout the sugar-beet-growing areas in the United States, most soil samples contained Beet oak-leaf virus (BOLV) as well. BNYVV and BOLV often occurred in the same field and sometimes in the same sugar beet plant. The possibility of interactions between these two Polymyxa betae-transmitted sugar beet viruses was tested. Plants grown in soils infested with aviruliferous P. betae or carrying RB-BNYVV and BOLV, alone and in combination, were compared with plants grown in noninfested soil for differences in plant fresh weight and virus content as measured by enzyme-linked immunosorbent assay (ELISA). Rz1 and Rz2 resistance genes that condition resistance to BNYVV did not confer resistance to BOLV. BNYVV ELISA values were significantly higher in single infections than in mixed infections with BOLV in both the rhizomania-resistant and -susceptible cultivars. In contrast, ELISA values of BOLV were not significantly different between single and mixed infections in both the rhizomania-resistant and -susceptible cultivars. Results indicate that BOLV may suppress BNYVV in mixed infections. Soils infested with P. betae significantly reduced fresh weight of sugar beet seedlings regardless of whether they were with or without one or both viruses or resistance genes.

Screening of sugar beet tissue culture clones for resistance to rhizomania disease

In this study, sugar beet tissue culture clones were used to screen rhizomania resistant genotypes. At first, explants derived from shoot tips of sugar beet seedlings were transferred to shoot tip elongation media after surface sterilization. Then, the grown shoots were transferred to media containing various hormonal combinations NAA, BA, IBA and GA3 for multiplication, growth and rooting. Later, the clones were transferred to soil-peatmoss mixture were adapted to greenhouse conditions. For screening clones against rhizomania, the genotypes of adapted clones were selected and inoculated to rhizomania-infested soil. This experiment was in a randomized complete block design with three replicates (three inoculation times) in greenhouse. Adapted plants were transferred to the soil containing rhizomania virus. All infested soils were diluted 3 to 7 with sand. After two months, infested plants were examined by DAS-ELISA test also optical densities of the samples were analyzed by SAS program. Significant differences among genotypes and blocks were observed. Genotypes were classified to few groups (ranked from completely susceptible to completely resistant). The difference between blocks was because of difference of inoculation time temperature. Use of clones of each genotype caused an increase in selection accuracy of resistant genotypes. By use of this method, chance of escaping from inoculation factor decrease and researchers can determine to be resistance of plants with high level of confidence and apply in breeding programs.

Changes in the intraisolate genetic structure of Beet necrotic yellow vein virus populations associated with plant resistance breakdown

The causal agent of rhizomania disease, Beet necrotic yellow vein virus (BNYVV), typically produces asymptomatic root-limited infections in sugar beets (Beta vulgaris) carrying the Rz1-allele. Unfortunately, this dominant resistance has been recently overcome. Multiple cDNA clones of the viral pathogenic determinant p25, derived from populations infecting susceptible or resistant plants, were sequenced to identify host effects on the viral population structure. Populations isolated from compatible plant-virus interactions (susceptible plant-wild type virus and resistant plant-resistant breaking variants) were large and relatively homogeneous, whereas those from the incompatible interaction (resistant plant-avirulent type virus) were small and highly heterogeneous. All populations from susceptible plants had the same dominant haplotype, whereas those from resistant cultivars had a different haplotype surrounded by a spectrum of mutants. Selection and diversification analyses suggest an evolutionary trajectory of BNYVV with positive selection for changes required to overcome resistance, followed by elimination of hitchhiking mutations through purifying selection.

Influence of Beet necrotic yellow vein virus on Sugar Beet Storability

Rhizomania caused by Beet necrotic yellow vein virus (BNYVV) and storage losses are serious sugar beet production problems. To investigate the influence of BNYVV on storability, six sugar beet cultivars varying for resistance to BNYVV were grown in 2005 and 2006 in southern Idaho fields with and without BNYVV-infested soil. At harvest, samples from each cultivar were placed in an outdoor ventilated pile in Twin Falls, ID and were removed at 40-day intervals starting at the end of October. After 144 and 142 days in storage, sugar reduction across cultivars averaged 20 and 13% without and 68 and 21% with BNYVV for the 2005 and 2006 roots, respectively. In the December samplings, frozen root area was 1 and 2% without and 25 and 41% with BNYVV for the 2005 and 2006 roots, respectively. Root rot was always worse with stored roots from BYNVV-infested soil in December, January, and February samplings. Root weight loss was variable in 2005; however, in 2006, an increase in weight reduction always was associated with BNYVV-infested roots. In order to prevent losses in rhizomania-infested areas, cultivars should be selected for storability as well as rhizomania resistance.

Resistance gene analogues are clustered on chromosome 3 of sugar beet and cosegregate with QTL for rhizomania resistance

Worldwide, rhizomania is the most important disease of sugar beet. The only way to control this disease is to use resistant varieties. Four full-length resistance gene analogues (RGAs) from sugar beet (cZR-1, cZR-3, cZR-7, and cZR-9) were used in this study. Their predicted polypeptides carry typical nucleotide-binding sites (NBSs) and leucin-rich repeat (LRR) regions, and share high homology to various plant virus resistance genes. Their corresponding alleles were cloned and sequenced from a rhizomania resistant genotype. The 4 RGAs were mapped as molecular markers, using sequence-specific primers to determine their linkage to the rhizomania resistance locus Rz1 in a population segregating for rhizomania resistance. One cZR-3 allele, named Rz-C, together with 5 other molecular markers, mapped to the Rz1 locus on chromosome 3 and cosegregated with quantitative trait loci for rhizomania resistance. After screening a bacterial artificial chromosome (BAC) library, 25 cZR-3-positive BACs were identified. Of these, 15 mapped within an interval of approximately 14 cM on chromosome 3, in clusters close to the Rz1 locus. Rz-C differentiates between susceptible and resistant beet varieties, and its transcripts could be detected in all rhizomania resistant varieties investigated. The potential of this RGA marker for cloning of rhizomania resistance genes is discussed.

Distribution and Molecular Characterization of Resistance-Breaking Isolates of Beet necrotic yellow vein virus in the United States

Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania in sugar beet (Beta vulgaris). The virus is transmitted by the plasmodiophorid Polymyxa betae. The disease is controlled primarily by the use of partially resistant cultivars. During 2003 and 2004 in the Imperial Valley of California, partially resistant sugar beet cultivars with Rz1 allele seemed to be compromised. Field trials at Salinas, CA have confirmed that Rz1 has been defeated by resistance-breaking isolates. Distinct BNYVV isolates have been identified from these plants. Rhizomania-infested sugar beet fields throughout the United States were surveyed in 2004-05. Soil surveys indicated that the resistance-breaking isolates not only existed in the Imperial Valley and San Joaquin Valley of California but also in Colorado, Idaho, Minnesota, Nebraska, and Oregon. Of the soil samples tested by baited plant technique, 92.5% produced infection with BNYVV in 'Beta 6600' (rz1rz1rz1), 77.5% in 'Beta 4430R' (Rz1rz1), 45.0% in 'Beta G017R' (Rz2rz2), and 15.0% in 'KWS Angelina' (Rz1rz1+Rz2rz2). Analyses of the deduced amino acid sequence of coat protein and P-25 protein of resistance-breaking BNYVV isolates revealed the high percentage of identity with non-resistance-breaking BNYVV isolates (99.9 and >98.0%, respectively). The variable amino acids in P-25 proteins were located at the residues of 67 and 68. In the United States, the two amino acids found in the non-resistance-breaking isolates were conserved (AC). The resistance-breaking isolates were variable including, AF, AL, SY, VC, VL, and AC. The change of these two amino acids cannot be depended upon to differentiate resistance-breaking and non-resistance-breaking isolates of BNYVV.

Mutations Associated with Resistance-Breaking Isolates of Beet necrotic yellow vein virus and Their Allelic Discrimination Using TaqMan Technology

ABSTRACT Genetic resistance in sugar beet (Beta vulgaris) to Beet necrotic yellow vein virus (BNYVV), which causes the disease rhizomania, is conferred by the single dominant gene Rz1. However, since 2002, Rz1 cultivars grown in the Imperial Valley of California have been increasingly damaged by a new strain of BNYVV. Viral RNA 3 was extracted from asymptomatic and symptomatic sugar beets and, after amplification and sequencing of a region including the p25 cistron, two polymorphic sites, A67V and D135E, associated with the capability of the virus to overcome resistance were identified. Using the real-time reverse transcription-polymerase chain reaction allelic discrimination technique, TaqMan probes designed to detect the responsible nucleotide substitutions permitted the differentiation between wild type (WT) and resistance-breaking (RB) isolates. This method also allowed easy detection of mixed infections by giving a heterozygous call, which was verified by DNA sequencing of individual clones. The capability of this technology to typify numerous isolates facilitated the analysis of the spatial distribution of virus haplotypes in the field. Thus, RB variants were mostly baited from yellow strips with high incidence of rhizomania, whereas WT variants predominated in the surrounding green areas. Mixed infections were found mainly in green areas and transitional zones. The predominance of the RB isolates in yellow strips suggests that they have gained fitness in Rz1 cultivars and will eventually become the dominant haplotype.

Occurrence of Resistance-Breaking Beet necrotic yellow vein virus of Sugar Beet

Rhizomania is an important virus disease of sugar beet and is caused by Beet necrotic yellow vein virus (BNYVV). During 2002-03, several sugar beet fields with cultivars partially resistant to BNYVV grown in the Imperial Valley of California were observed with severe rhizomania symptoms, suggesting that resistance conditioned by Rz1 had been compromised. Soil testing with sugar beet baiting plants followed by enzyme-linked immunosorbent assay (ELISA) was used to diagnose virus infection. Resistant varieties grown in BNYVV-infested soil from Salinas, CA, were ELISA-negative. In contrast, when grown in BNYVV-infested soil collected from the Imperial Valley, CA, all resistant varieties became infected and tested positive by ELISA. Based on host reaction, eight distinct BNYVV isolates have been identified from Imperial Valley soil (IV-BNYVV) by single local lesion isolation. Reverse transcription-polymerase chain reaction (RT-PCR) assays showed that the eight IV-BNYVV isolates did not contain RNA-5. Singlestrand conformation polymorphism banding patterns for the IV-BNYVV isolates were identical to A-type and different from P-type. Sequence alignments of PCR products from BNYVV RNA-1 near the 3' end of IV-BNYVV isolates revealed that both IV-BNYVV and Salinas BNYVV isolates were similar to A-type and different from B-type. Our results suggest that the resistancebreaking BNYVV isolates from Imperial Valley likely evolved from existing A-type isolates.

Interactions Between Beet necrotic yellow vein virus and Beet soilborne mosaic virus in Sugar Beet

Soils naturally infested with cultures of aviruliferous Polymyxa betae and viruliferous P. betae carrying two sugar beet benyviruses, Beet necrotic yellow vein virus (BNYVV) and Beet soilborne mosaic virus (BSBMV), alone and in combination, were compared with noninfested soil for their effects on seedling emergence, plant fresh weight, and virus content as measured by enzyme-linked immunosorbent assay (ELISA). Studies examined sugar beet with and without resistance to the disease rhizomania, caused by BNYVV. The Rz gene, conferring resistance to BNYVV, did not confer resistance to BSBMV. BSBMV ELISA values were significantly higher in single infections than in mixed infections with BNYVV, in both the rhizomania-resistant and -susceptible cultivars. In contrast, ELISA values of BNYVV were high (8 to 14 times the healthy mean) in single and mixed infections in the rhizomania-susceptible cultivar, but were low (approximately three times the healthy mean) in the rhizomania-resistant cultivar. Results indicate BNYVV may suppress BSBMV in mixed infections, even in rhizomania-resistant cultivars in which ELISA values for BNYVV are extremely low. Soils infested with P. betae, and with one or both viruses, showed significantly reduced fresh weight of seedlings, and aviruliferous P. betae significantly decreased sugar beet growth in assays.

A century of plant virus management in the Salinas valley of California, 'East of Eden'

The mild climate of the Salinas Valley, CA lends itself well to a diverse agricultural industry. However, the diversity of weeds, crops and insect and fungal vectors also provide favorable conditions for plant virus disease development. This paper considers the incidence and management of several plant viruses that have caused serious epidemics and been significant in the agricultural development of the Salinas Valley during the 20th century. Beet curly top virus (BCTV) almost destroyed the newly established sugarbeet industry soon after its establishment in the 1870s. A combination of resistant varieties, cultural management of beet crops to provide early plant emergence and development, and a highly coordinated beet leafhopper vector scouting and spray programme have achieved adequate control of BCTV. These programmes were first developed by the USDA and still operate. Lettuce mosaic virus was first recognized as causing a serious disease of lettuce crops in the 1930s. The virus is still a threat but it is controlled by a lettuce-free period in December and a seed certification programme that allows only seed lots with less than one infected seed in 30000 to be grown. 'Virus Yellows' is a term used to describe a complex of yellows inducing viruses which affect mainly sugarbeet and lettuce. These viruses include Beet yellows virus and Beet western yellows virus. During the 1950s, the complex caused significant yield losses to susceptible crops in the Salinas Valley. A beet-free period was introduced and is still used for control. The fungus-borne rhizomania disease of sugarbeet caused by Beet necrotic yellow vein virus was first detected in Salinas Valley in 1983. Assumed to have been introduced from Europe, this virus has now become widespread in California wherever beets are grown and crop losses can be as high as 100%. Movement of infested soil and beets accounts for its spread throughout the beet-growing regions of the United States. Control of rhizomania involves several cultural practices, but the use of resistant varieties is the most effective and is necessary where soils are infested. Rhizomania-resistant varieties are now available that perform almost as well as the non-resistant varieties under non-rhizomania conditions. Another soil-borne disease termed lettuce dieback, caused by a tomato bushy stunt-like tombusvirus, has become economically limiting to romaine and leaf lettuce varieties. The virus has no known vector and it seems to be moved through infested soil and water. Heavy rains in the past 4 years have caused flooding of the Salinas River and lettuce fields along the river have been affected severely by dieback. Studies are now in progress to characterize this new virus and identify sources of resistance. Agriculture in the Salinas Valley continues to grow and diversify, driven by demands for 'clean', high quality food by the American public and for export. The major aspects of plant virus control, including crop-free periods, breeding for resistance, elimination of inoculum sources, and vector control will continue to be vital to this expansion. Undoubtedly, the advances in crop production through genetic manipulation and advances in pest management through biological control will eventually become an important part of agricultural improvement.