Characterization of Beet curly top virus Strains Circulating in Beet Leafhoppers (Hemiptera: Cicadellidae) in Northeastern Oregon

Interactions of beet leafhopper (Hemiptera: Cicadellidae), vector of beet curly top virus, and hemp in New Mexico

The beet leafhopper, Circulifer tenellus (Baker 1896), is the sole vector of beet curly top virus (BCTV). Both the virus and the vector have very wide host ranges, including many crops and weeds. Industrial hemp (Cannabis sativa L.) has been reported as a host for both the virus and leafhopper in the past few years with the legal cultivation of the crop in the United States. This research assessed the interactions of the beet leafhopper and hemp in New Mexico by determining the natural infection of hemp with BCTV in 3 field plots in 2021 and 2022 and monitoring the numbers of leafhoppers using yellow sticky traps. The relative preference of beet leafhopper for hemp types and varieties of hemp was assessed using cafeteria-style choice tests. Higher numbers of beet leafhoppers were trapped in and around hemp fields in 2022 than in 2021 in all 3 locations. BCTV was found to infect all 3 types of hemp (cannabidiol or CBD, fiber, and grain) in 2022 in 1 location and only a single CBD variety of hemp in the other 2 locations. Two BCTV strains were identified in CBD hemp, while an additional BCTV strain was found infecting chile pepper grown at the same location.

Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection

Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the 'R' lines (vs. 'S') included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the 'R' lines (vs. 'S'). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development.

A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.)

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance.

Curly Top Disease of Hemp (Cannabis sativa) in California Is Caused by Mild-Type Strains of Beet curly top virus Often in Mixed Infection

Interest in industrial hemp (Cannabis sativa) as a potential crop led to the establishment of commercial fields in a number of counties in California in 2019 and 2020. Plants in these fields developed different types of virus-like symptoms. The most prevalent type was stunted and bushy plants with distorted, upcurled, and yellowed leaves, which were similar to those associated with curly top disease (CTD) caused by the beet curly top virus (BCTV). This beet leafhopper-vectored virus is endemic in California and can cause economic losses to processing tomato production. Using a multiplex PCR test, BCTV infection was detected in 89% of hemp samples with CTD-like symptoms from Fresno, San Bernardino, and Ventura counties. Other symptom types had low incidence of BCTV infection and were associated with other factors. Hemp plants in California were infected only with the mild-type strains, BCTV-CO and BCTV-Wor, and often in mixed infection (43% of samples). Finally, using an infectious clone of a BCTV-CO isolate from hemp, we demonstrated that agroinoculated hemp plants developed these CTD-like symptoms, thereby fulfilling Koch's postulates for the disease.

An Overview of Pathogens Associated with Biotic Stresses in Hemp Crops in Oregon, 2019 to 2020

Hemp (Cannabis sativa) acreage in Oregon has increased by approximately 240 times in the last 5 years, and a greater number of hemp diseases have been observed. This special report documents pathogens, particularly those causing virus and virus-like diseases, that have been detected from field and greenhouse-grown hemp crops in Oregon, based on plant samples submitted to the Hermiston Agricultural Research and Extension Center Plant Clinic of Oregon State University in 2019 and 2020. Symptoms and signs were used to evaluate disease types and determine diagnostic assays used on each submission. Plants with signs or symptoms of fungal or oomycete infection were cultured to isolate pathogenic organisms and plants with symptoms suspected to be caused by virus infection were assayed for the presence of Beet curly top virus (BCTV), viroids, and phytoplasmas using PCR, or reverse transcription (RT)-PCR. Diseases with fungal or oomycete, and virus causes accounted for 26.5 and 42.9% of submissions, respectively; coinfection of viral and fungal or oomycete pathogens were detected from 6.1% of submissions between 2019 and 2020. BCTV, a curtovirus, and hop latent viroid (HLVd) were the predominant pathogens detected from field and indoor grown hemp. Worland-like strains of BCTV represented 93% of all curtovirus detections. Eighty percent of HLVd detections occurred from plants that originated from indoor growing facilities. Based on BCTV vector, beet leafhopper, prevalence, field-grown hemp in western production regions may be affected by curly top and increasing hemp acreage in the landscape may have potential implications on other crops affected by curtoviruses. Virus and virus-like diseases could be a limiting factor for hemp production in some regions of the United States.

First Report of 'Candidatus Phytoplasma trifolii' Related Strain Associated with Yellowing and Witches'-Broom of Industrial Hemp (Cannabis sativa) in Arizona

In Arizona, industrial hemp (Cannabis sativa) is a newly cultivated crop for fiber, oil, cosmetic products, and health food. During July to September 2020, two fields of industrial hemp crops were identified in southern Arizona with 10 to 30% incidence of plants showing witches' broom. Disease incidence was assessed by counting symptomatic plants in 4 randomly selected rows of 25 plants in each field. Symptoms ranged from leaf mottling and yellowing on mildly affected plants to leaf curling and shortened internode length of stem on severely affected plants (Fig. 1). Shoots were randomly collected from eight symptomatic plants and three asymptomatic plants in the same area. Genomic DNA was extracted from 200 mg of each sample using DNeasy Plant Pro Kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. Phytoplasma was tested by a real-time PCR assay and TaqMan probe targeting the 23S ribosomal RNA gene that detects a wide range of known Phytoplasmas (Hodgetts et al., 2009). Beet curly top virus (BCTV) was targeted using BCTV-specific primers BCTV1 and BCTV2 following a method by Rondon (Rondon et al., 2016). BCTV was not detected in the plants, but Phytoplasmas were detected in all eight symptomatic plants, but not in the three control plants. The positive DNA samples were used to identify the phytoplasma by nested PCR using universal phytoplasma-specific primer pairs P1/P6 (Deng, S. et al. 1991) and R16F2n/R16R2 (Gundersen et al., 1996) targeting the 16S rRNA gene and the resulting 1.25 kb fragment in 4 positive samples was subjected to Sanger sequencing (Eton Bioscience, San Diego). All 4 sequences were identical and deposited in GenBank under accession MW981356. BLASTn results indicated 100% identity with that of several 'Candidatus Phytoplasma trifolii' strains on potato (KR072666, KF178706) in Washington and chile peppers (HQ436488) in New Mexico. It also shared 99.84% identity with the sequence of the reference strain of Candidatus Phytoplasma trifolii' (AY390261) that caused clover proliferation. The phytoplasma AZH1 was classified as a member of subgroup A within group16SrVI using iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment (Zhao et al., 2013). Phylogenetic analysis revealed that the phytoplasma AZH1 clustered with other isolates of 'Candidatus Phytoplasma trifolii' (Fig. 2), including the strain NV1 associated with witches' broom on C. sativa in Nevada (Feng et al. 2019). This is the first report of 'Candidatus Phytoplasma trifolii' related strain associated with yellowing and witches' broom on hemp in Arizona. This finding is significant as the observation of symptoms at 30% incidence in one field suggested that the identified pathogen may pose a significant threat to the production of industrial hemp production in Arizona.

First Report of Beet Curly Top Virus Infecting Industrial Hemp (Cannabis sativa) in Arizona

Industrial hemp (Cannabis sativa) is an emerging crop in Arizona, with many uses, including fiber, cosmetic products, and health food. In 2020, severe curly top disease outbreaks were observed in several hemp fields in Yuma and Graham Counties, Arizona, where disease incidence and severity were considerably high, up to 100% crop loss occurring in some fields. A wide range of symptoms have been observed at different infection stages and plant growth stages at the time of infection. Early stage symptoms manifest as light green-to-yellowing of new growth, similar to sulfur or micronutrient deficiency, usually combined with older leaves with dark green "blotchy" mosaic mottling overlaying light green chlorosis. Mosaic mottling of older leaves continues into mid-growth stage, and is coupled with more severe yellowing and witch's broom (stunted leaves and shortened internode length of stem) of apical meristematic tissue. Curling and twisting of new leaves has also been observed. Symptoms often appear to be isolated to individual branches, with other branches showing no visual symptoms, often outgrowing and covering affected branches until harvest. Late stage symptoms include severe leaf curling with or without twisting, continued stunting, and necrosis of yellow leaves, resulting in significant yield reduction. Severely affected plants dwarfed by the virus experienced high mortality rates later into the season, most likely attributed to reduced ability to overcome abiotic stress conditions. These symptoms indicated the likelihood of curly top caused by Beet curly top virus (BCTV), which has been recently reported in Colorado (Giladi et al., 2020). Shoots were collected from thirty-eight symptomatic and nine asymptomatic hemp plants from July to August, 2020. Leaves were also collected as positive control from four chili pepper plants with or without curly top symptoms in Cochise County. Genomic DNA was extracted using DNeasy Plant Pro Kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. BCTV-specific primers BCTV1 and BCTV2 were used to detect BCTV following a method by Rondon (Rondon et al., 2016). A 500 bp DNA fragment, indicative of BCTV, was amplified from all symptomatic hemp and chili pepper samples, but not from asymptomatic samples. Sequence analysis of this 500 bp DNA fragment revealed 98.99 % identity with GenBank accession MK803280, which is Beet curly top virus isolate from hemp identified in Western Colorado (Giladi et al., 2020). The full-length genomes of BCTV isolates from hemp and chili peppers were generated with additional primers 328F/945R (620bp), 455F/ 945R (490bp), OutR/ 2213F (1,190bp), 2609R/ 1278R (1,340bp), BCTV2/ 2609R (1,890bp) (Rondon et al., 2016, Strausbaugh et al., 2008). The complete nucleotide sequence (MW182244) from hemp was 2,929 bp and had 99.35% sequence identity with GenBank accession KX867055, which was a Worland strain of Beet curly top virus isolated from an Idaho sugar beet plant (Strausbaugh et al., 2017). Our hemp BCTV genome sequences shared 96.08% identity with the hemp strain of BCTV from Colorado (MK803280) and 99.50% identity with the BCTV isolate (MW188519) from chili pepper identified in this study. BCTV was reported on outdoor hemp in Western Colorado, in 2020 (Giladi et al., 2020). This is the first report of BCTV in Arizona causing curly top of industrial hemp in the field. In Arizona, BCTV is widespread on many agronomic crops including chili peppers and spread primarily by the phloem-feeding beet leafhoppers: Circulifer tenellus (Hemiptera: Cicadellidae) (Bennett, 1967). Due to the wide distribution of beet leafhoppers and abundant range of host plants for the virus, BCTV may become one of the most yield-limiting factors affecting the emerging industrial hemp production systems in Arizona.

Pest categorisation of Beet curly top virus (non-EU isolates)

The EFSA Panel on Plant Health performed a pest categorisation of non-EU isolates of Beet curly top virus (BCTV) for the European Union territory. The virus causes severe diseases in beet, tomatoes and pepper crops, occurs predominantly in warm and dry zones and is reported from many countries outside the EU in particular from western USA and Mexico. New data from complete virus genomes make BCTV a well characterised virus species of which currently 11 strains are known and for which diagnostic methods are available. BCTV has a very broad host range of more than 300 species some of which may remain symptomless. Aside from vegetative propagation of infected plants, the only mode of BCTV transmission and spread is by the leafhopper Circulifer tenellus which efficiently transmits the virus in a persistent mode and which is present in several southern EU Member States. No current reports of BCTV presence in the EU exist and because of doubts about the accuracy of older reports, BCTV likely is absent from the EU territory. BCTV can enter into the EU with viruliferous insects and with imports of plants not subject to specific EU regulation. Because both the virus and its vector have a wide host range, BCTV is expected to establish and spread in the Member States where its vector is present and to cause severe diseases in sugar beet and tomato as well as in other crops. Overall, BCTV non-EU isolates meet all the criteria evaluated by EFSA to qualify as a Union quarantine pest and do not meet the criterion of presence in the EU to qualify as a Union regulated non-quarantine pest (RNQP). The main uncertainties concern (1) the presence of BCTV in the EU, (2) the distribution of C. tenellus and (3) the main commodities for virus entry.

Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection

Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2006-to-2007 collection but changes in disease severity suggested a need for reevaluation. Therefore, 406 leaf samples symptomatic for curly top were collected from sugar beet plants in commercial sugar beet fields in Idaho and Oregon from 2012 to 2015. DNA was isolated and BCTV strain composition was investigated based on polymerase chain reaction assays with strain-specific primers for the Severe (Svr) and California/Logan (CA/Logan) strains and primers that amplified a group of Worland (Wor)-like strains. The BCTV strain distribution averaged 2% Svr, 30% CA/Logan, and 87% Wor-like (16% had mixed infections), which differed from the previously published 2006-to-2007 collection (87% Svr, 7% CA/Logan, and 60% Wor-like; 59% mixed infections) based on a contingency test (P < 0.0001). Whole-genome sequencing (GenBank accessions KT276895 to KT276920 and KX867015 to KX867057) with overlapping primers found that the Wor-like strains included Wor, Colorado and a previously undescribed strain designated Kimberly1. Results confirm a shift from Svr being one of the dominant BCTV strains in commercial sugar beet fields in 2006 to 2007 to becoming undetectable at times during recent years.