No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
The Occurrence of Hop Latent Viroid in Cannabis sativa with symptoms of Cannabis Stunting Disease in California
... The hop latent viroid (HLVd) has recently been increasingly associated with severe cannabis symptoms [14,15,17] (Table 2) that impair seed and fiber production in industrial varieties and cannabinoid contents in medical varieties. Infected medical cannabis plants can suffer vigor loss and a 50% up to 70% reduction in THC content. ...
... HLVd infects dicots and was first described in hops, to which it causes altered cone development and the hyperaccumulation of alpha acids [37]. It was also isolated from Urtica dioica [38] and recently in C. sativa [14,15]. HLVd has no known vector: its horizontal transmission is mechanical (wounds or infected cutting tools) and it is unable to be transmitted through seeds or pollen [38]. ...
... HLVd has no known vector: its horizontal transmission is mechanical (wounds or infected cutting tools) and it is unable to be transmitted through seeds or pollen [38]. HLVd in cannabis causes symptomatology colloquially referred to as "dudding", which is characterized by brittle stems, reduced flower mass and trichomes, vigor loss and stunted growth, and a reduced rooting rate (Table 2) [14,15,39], which compromise the growth and productivity of infected plants. A comparison of the sequences of HLVd isolates from hops and cannabis revealed high conservation with only one mismatch between two isolates that still does not result in alterations in the RNA secondary structure [15]. ...
Cannabis sativa cultivation is experiencing a period of renewed interest due to the new opportunities for its use in different sectors including food, techno-industrial, construction, pharmaceutical and medical, cosmetics, and textiles. Moreover, its properties as a carbon sequestrator and soil improver make it suitable for sustainable agriculture and climate change mitigation strategies. The increase in cannabis cultivation is generating conditions for the spread of new pathogens. While cannabis fungal and bacterial diseases are better known and characterized, viral infections have historically been less investigated. Many viral infection reports on cannabis have recently been released, highlighting the increasing threat and spread of known and unknown viruses. However, the available information on these pathogens is still incomplete and fragmentary, and it is therefore useful to organize it into a single structured document to provide guidance to growers, breeders, and academic researchers. This review aims to present the historical excursus of cannabis virology, from the pioneering descriptions of virus-like symptoms in the 1940s/50s to the most recent high-throughput sequencing reports. Each of these viruses detected in cannabis will be categorized with an increasing degree of threat according to its potential risk to the crop. Lastly, the development of viral vectors for functional genetics studies will be described, revealing how cannabis virology is evolving not only for the characterization of its virome but also for the development of biotechnological tools for the genetic improvement of this crop.
... and Zucc.). The viroid was initially reported in cannabis in 2019 in California from two independent studies [9,10]. A 2021 survey from Dark Heart Nursery Research concluded that 90% of cannabis facilities in California were infected with HLVd. ...
... Hemp) (Cannabis sativa, Cannabis indica and Cannabis ruderalis). Once infected, the viroid spreads rapidly through cannabis plants, leading to stunted growth, weaker flower smell, diminished flower quality, lower yield, and up to 50% reduction in cannabinoid and terpene production [9][10][11]15]. ...
... The Can1 isolate has 100% sequence similarity with HLVd species [17], while the Can2 isolate has a point mutation, U225A [10]. Interestingly, both isolates are infectious and have been reported from HLVd-infected cannabis plants in the USA [9,18]. ...
Hop latent viroid (HLVd) is a severe disease of cannabis, causing substantial economic losses in plant yield and crop value for growers worldwide. The best way to control the disease is early detection to limit the spread of the viroid in grow facilities. This study describes MFDetectTM as a rapid, highly sensitive, and high-throughput tool for detecting HLVd in the early stages of plant development. Furthermore, in the largest research study conducted so far for HLVd detection in cannabis, we compared MFDetectTM with quantitative RT-PCR in a time course experiment using different plant tissues, leaves, petioles, and roots at different plant developmental stages to demonstrate both technologies are comparable. Our study found leaf tissue is a suitable plant material for HLVd detection, with the viroid titer increasing in the infected leaf tissue with the age of plants. The study showed that other tissue types, including petiole and roots, were equally sensitive to detection via MFDetectTM. The assay developed in this research allows the screening of thousands of plants in a week. The assay can be scaled easily to provide growers with a quick turnaround and a cost-effective diagnostic tool for screening many plants and tissue types at different stages of development.
... Heat-generated HLVd variants (i.e., thermomutants) can infect what otherwise are considered as non-susceptible species such as tomato (Solanum lycopersicum) and Nicotiana benthamiana [11]. In 2019, two independent groups reported the detection of HLVd in stunted cannabis plants in the USA [12,13]. With the globalization of agriculture, viroids have become widely distributed in both new environments and new geographical areas. ...
... [accessed on 13 February 2023]). The association of HLVd infection with symptomatic plants was confirmed in 2019 by two independent teams using high-throughput sequencing technology and subsequent bioassays [12,13]. In susceptible cultivars HLVd induces symptoms (Figure 2) such as shorter internodal spacing, smaller leaves, stunting, malformation (outwardly horizontal plant structure), chlorosis, brittle stems, reduced vigor, lower water intake, reduced flower mass and trichomes [12,13]. ...
... The association of HLVd infection with symptomatic plants was confirmed in 2019 by two independent teams using high-throughput sequencing technology and subsequent bioassays [12,13]. In susceptible cultivars HLVd induces symptoms (Figure 2) such as shorter internodal spacing, smaller leaves, stunting, malformation (outwardly horizontal plant structure), chlorosis, brittle stems, reduced vigor, lower water intake, reduced flower mass and trichomes [12,13]. At the flowering stage, susceptible plants typically show smaller and looser buds, weaker flower smell and less trichome production. ...
Hop latent viroid (HLVd) is the biggest concern for cannabis and hop growers worldwide. Although most HLVd-infected plants remain asymptomatic, research on hops has demonstrated a decrease in both the α-bitter acid and terpene content of hop cones, which affects their economic value. The HLVd-associated "dudding" or "duds" disease of cannabis was first reported in 2019 in California. Since then, the disease has become widespread in cannabis-growing facilities across North America. Although severe yield loss associated with duds disease has been recorded, little scientific information is available to growers in order to contain HLVd. Consequently, this review aims to summarise all of the scientific information available on HLVd so as to be able to understand the effect of HLVd on yield loss, canna-binoid content, terpene profile, disease management and inform crop protection strategies.
... Hop latent viroid can also cause 'dudding' of the buds, which are essentially destroyed as a result of infection. 22,23 The bud-infecting fungal pathogens are the most challenging to manage due to a lack of registered fungicides, a lack of information on the sources of inoculum and when infection occurs, and a small suite of biorationale products for use. The extensive development of fungi such as Fusarium and Penicillium within the inflorescences can also lead to mycotoxin accumulation in the tissues, [29][30][31][32][33] potentially posing additional health concerns for consumers. ...
... Viral and viroid pathogens of cannabis and hemp have been identified by molecular analysis that involves RT-PCR of RNA templates. 22,23 In addition, next-generation sequencing (NGS) approaches are revealing the presence of previously unreported viruses in hemp. 27 The number of virus diseases occurring on hemp is steadily increasing as more research identifies new symptomology and spread of these pathogens from other host species. ...
... The spread of pathogens from hop plants to cannabis plants has also been reported for powdery mildew and Hop latent viroid. 22,23,66,67 Hemp and cannabis plants are susceptible to both the hop powdery mildew pathogen (Podosphaeria macularis) as well as the predominant cannabis powdery mildew pathogen (Golovinomyces spp.). 67 The spread of pathogens from adjacent unrelated crop plants, and from hop plants, through release of inoculum, as well as spread by insect vectors of viruses, is an unexpected consequence of the expanding cannabis and hemp industries in Canada and the USA. ...
Cultivation of cannabis plants (Cannabis sativa L., marijuana) has taken place worldwide for centuries. In Canada, legalization of cannabis in October 2018 for the medicinal and recreational markets has spurned interest in large‐scale growing. This increased production has seen a rise in the incidence and severity of plant pathogens, causing a range of previously unreported diseases. The objective of this review is to highlight the important diseases currently affecting the cannabis and hemp industries in North America and to discuss various mitigation strategies. Progress in molecular diagnostics for pathogen identification and determining inoculum sources and methods of pathogen spread have provided useful insights. Sustainable disease management approaches include establishing clean planting stock, modifying environmental conditions to reduce pathogen development, implementing sanitation measures, and applying fungal and bacterial biological control agents. Fungicides are not currently registered for use and hence there are no published data on their efficacy. The greatest challenge remains in reducing microbial loads (colony‐forming units) on harvested inflorescences (buds). Contaminating microbes may be introduced during the cultivation and post‐harvest phases, or constitute resident endophytes. Failure to achieve a minimum threshold of microbes deemed to be safe for utilization of cannabis products can arise from organic cultivation methods or application of beneficial biocontrol agents. The current regulatory process for approval of cannabis products presents a challenge to producers utilizing biological control agents for disease management.
This article is protected by copyright. All rights reserved.
... However, viral infections are emerging as a significant threat to hemp cultivation [4]. Indeed, new viruses and a viroid have recently been reported as capable of infecting C. sativa and significantly reducing the yield [5][6][7][8][9]. Among other approaches for virus identification, Illumina transcriptome sequencing (Illumina, Inc., San Diego, CA, USA), followed by the de novo assembly of sequencing reads, was exploited to study C. sativa virome, revealing mixed infections of known and previously unreported viruses [10]. ...
... Nine leaf samples of Cannabis sativa collected in June 2022 (Table 1) were subjected to RT-PCR analysis to verify the presence of beet curly top virus (BCTV), lettuce chlorosis virus (LCV) and Cannabis cryptic virus (CanCV) and hop latent viroid (HLVd), previously reported as capable of infecting hemp plants [5][6][7][8][9][10]17,18]. The results were negative for all the tested samples, except ALYU-304 being positive for both RNA-dependent RNA polymerase (RdRP)-and coat protein (CP)-encoding genomic segments of CanCV. ...
Viral infections pose an emerging threat to hemp (Cannabis sativa) cultivation. We used Illumina small (s)RNA sequencing for virome reconstruction and characterization of antiviral RNA interference (RNAi) in monoecious and dioecious hemp varieties, which exhibited different virus-like symptoms. Through de novo and reference-based sRNA assembly, we identified and reconstructed Cannabis cryptic virus (family Partitiviridae), Cannabis sativa mitovirus 1 (Mitoviridae) and Grapevine line pattern virus (Bromoviridae) as well as a novel virus tentatively classified into Partiti-viridae. Members of both Partitiviridae and Bromoviridae were targeted by antiviral RNAi, generating 21 nt and, less abundant, 22 nt sRNAs from both strands of the entire virus genome, suggesting the involvement of Dicer-like (DCL) 4 and DCL2 in viral sRNA biogenesis, respectively. Mitovirus sRNAs represented predominantly the positive-sense strand and had a wider size range, with the 21 nt class being most abundant on both strands. For all viruses, 21 and 22 nt sRNAs had predominantly 5′-terminal uridine or cytosine, suggesting their binding to antiviral Argonaute (AGO) 1 and AGO5, respectively. As no clear association of any virus with symptoms was observed, further studies should clarify if these viruses individually or in combination can cause hemp diseases.
... More recently, cannabis cryptic virus (CanCV) was isolated from hemp plants (Ziegler et al., 2012;Righetti et al., 2018). In addition, hemp was found to be infected with hop latent viroid (HLVd) in California (Bektaş et al., 2019;Warren et al., 2019). A survey of cannabis farms in Israel detected the presence of lettuce chlorosis virus (LCV) in plants showing leaf yellowing, interveinal chlorosis, that are typically associated with general nutrient deficiency (Hadad et al., 2019). ...
... Hop latent viroid has been previously identified in hemp from symptomatic and asymptomatic plants (Bektaş et al., 2019) and from symptomatic plants (Warren et al., 2019). Viroids are small non-encapsulated infectious pathogens, comprised of closed single stranded RNA molecules and biological resources to drive host specificity (Flores et al., 2005). ...
Hemp ( Cannabis sativa L.) production has increased significantly in recent years; however, the crop has been understudied in the U.S. since its production declined in the late 1950s. Disease identification and management is an increasing challenge for hemp growers across the country. In 2019, beet curly top virus (BCTV) was first reported in hemp in Colorado. Hence, we were motivated to understand the diversity and prevalence of BCTV strains infecting hemp in Colorado. We detected BCTV at high incidence rate (81%) in leaf samples from 12 counties. Two different strains of BCTV, Worland (Wor) and Colorado (CO) were present as a single or mixed infection in hemp leaf samples. Phylogenetic analysis revealed BCTV sequences from hemp formed a distinct group along with BCTV strains CO and Wor. To determine other potential viral and viroid pathogens in hemp, we performed next generation sequencing (NGS). Virome analysis revealed the presence of both virus and viroid sequences that had high nucleotide sequence identity with GenBank accessions for cannabis cryptic virus, cannabis sativa mitovirus, citrus yellow vein associated virus, opuntia-like virus and hop latent viroid. In contrast, tobacco streak virus sequences were highly variable compared to sequences in GenBank suggesting a possible new genotype of this virus. The data presented here has important implications for the epidemiology and management of the various diseases of hemp and will lead to the development of integrated pest management strategies designed to interrupt transmission cycles and facilitate efficient crop production.
... McPartland et al. (2000) discussed a small number of viral pathogens of hemp including alfalfa mosaic virus, cucumber mosaic virus, and Arabis mosaic virus and suggested that a mycoplasma-like organism was detected in Cannabis. Recently, there were multiple reports of hop latent viroid (HLVd) causing brittle stems, chlorosis, yield reduction, and poor reproduction via propagation in greenhouse production in California (Bektaş et al. 2019;Warren et al. 2019). Additionally, beet curly top virus (BCTV) was identified as the causal agent of hemp leaf chlorosis and mosaic, leaf curling, and general stunting of hemp plants in Arizona and Colorado (Giladi et al. 2020;Hu et al. 2021). ...
... There is no evidence for insect transmission of HLVd (Pethybridge et al. 2008) while its presence in the PNW agroecosystem, especially in hop production, has been documented (Eastwell and Nelson 2007). Viroid pathogens can be challenging to manage in greenhouse production and are readily transmitted mechanically and through clonal propagation of plants (Bektaş et al. 2019;Pethybridge et al. 2008;Warren et al. 2019). Thus, this pathogen could become established in a field crop if vegetative propagation was used to create planting stock. ...
Hemp (Cannabis sativa) acreage in Oregon has increased by approximately 240 times in the last five 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 polymerase chain reaction (PCR), or reverse transcription (RT)-PCR. Diseases with fungal or oomycete, and virus causes accounted for 26.5%, and 42.9% of submissions, respectively; co-infection 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.
... been detected in a significant percentage of indoor growth facilities (Adkar-Purushothama et al. 2023). HLVd causes the "duds" disease that significantly decreases inflorescence size, trichome density, and cannabinoid synthesis (Bektaş et al. 2019;Warren et al. 2019). Recent research has demonstrated the presence of a wide variety of virus and viroid sequences in C. sativa leaf samples (Chiginsky et al. 2021). ...
i>Cannabis sativa is one of the oldest cultivated crops, used for its fiber and medicinal properties. The cannabis plant synthesizes a myriad of secondary metabolites, but the most valuable products from a medical and commercial standpoint are cannabinoids. Despite significant advances in elucidating the biochemistry and genetics that govern cannabinoid accumulation, we still do not have conclusive evidence for the role of these secondary metabolites in the physiology of C. sativa . In line with known functions of other secondary metabolites, the protective functions of cannabinoids against temperature stress, poor micronutrient soil content, drought, UV-B radiation, and as anti-microbial agents have been suggested, but are yet to be conclusively demonstrated. Recent research suggests that the environment has a major effect on cannabis growth and productivity, but the relationship between stress, cannabinoid accumulation, and plant health is complex. Here, we summarize the current insights on how abiotic and biotic stress affect C. sativa biology. We also examine the available evidence to support the hypothesis for the protective function of cannabinoids against environmental stressors. Maintaining optimal growth and high cannabinoid synthesis is a balancing act, one that can only be achieved by better understanding of the effects on the environment on the cannabis plant.
... The Can1 isolate has 100% sequence similarity with HLVd species, while the Can2 isolate has a point mutation, U225A (Warren et al., 2019). Interestingly, both isolates are infectious and have been reported from HLVd-infected cannabis plants in the USA (Bektaş et al., 2019, Chiginsky et al., 2021. ...
Hop latent viroid (HLVd) is a severe disease of cannabis, causing substantial economic losses in plant yield and crop value for growers worldwide. The best way to control the disease is early detection to limit the spread of the viroid in grow facilities. This study describes MFDetectTM as a rapid, highly sensitive, and high-throughput tool for detecting HLVd in the early stages of plant development. Furthermore, in the largest research study conducted so far for HLVd detection in cannabis, we compared MFDetectTM with quantitative RT-PCR in a time course experiment using different plant tissue, leaf, petiole, and roots at different plant development stages to demonstrate both technologies are comparable. Our study found leaf tissue is a suitable plant material for HLVd detection, with the viroid titer increasing in the infected leaf tissue with the age of plants. The study showed that other tissue types, including petiole and roots, were equally sensitive to detection via MFDetectTM. The assay developed in this research allows the screening of thousands of plants in a week. The assay can be scaled easily to provide growers with a quick turnaround and cost-effective diagnostic tool for screening many plants and tissue types at different stages of development.
... HLVd has been detected in all hop production areas worldwide and no serious HLVdrelated pathogenesis is known for crops produced in the hop production areas. However, RNA sequencing of cannabis plants (Cannabis sativa L.) with and without stunting symptoms suggested that the HLVd is the agent causing a severe stunting disease in cannabis (Bektaş et al., 2019;Warren et al., 2019). Thus, this research might have direct implications for a HLVd inactivationmethods as part of cannabis harvest decontamination strategy. ...
The citrus bark cracking viroid (CBCVd) was identified as causal agent for a severe stunting disease in hops. Viroids are highly stable parasitic RNAs, which can be easily transmitted by agricultural practices. Since CBCVd has recently been detected in two European countries a growing concern is that this pathogen will further spread and thereby threaten the European hop production. Biogas fermentation is used to sanitize hop harvest residues infected with pathogenic fungi. Consequently , the aim of this study was to test if biogas fermentation can contribute to viroid degradation at mesophilic (40°C) and thermophilic (50°C) conditions. Therefore, a duplex reverse transcription real-time PCR analysis was developed for CBCVd and HLVd detection in biogas fermentation residues. The non-pathogenic hop latent viroid (HLVd) was used as viroid model for the pathogenic CBCVd. The fermentation trials showed that HLVd was significantly degraded after 30 days at mesophilic or after 5 days at thermo-philic conditions, respectively. However, sequencing revealed that HLVd was not fully degraded even after 90 days. The incubation of hop harvest residues at different temperatures between 20 and 70°C showed that 70°C led to a significant HLVd degradation after 1 day. In conclusion, we suggest combining 70°C pretreatment and thermophilic fermentation for efficient viroid decontamination.
... Fr., a widespread and destructive pathogen of cannabis and hemp (Punja et al. 2019;Garfinkel 2020), as well as several species of Fusarium and Penicillium that can cause pre-and postharvest bud rots (Punja 2021a(Punja , 2021b(Punja , 2021c. Infection by Hop latent viroid can also reduce the quality of cannabis inflorescences (Bektas et al. 2019;Warren et al. 2019). ...
Bud rot pathogens cause diseases on Cannabis sativa L. (cannabis, hemp) worldwide through pre-and post-harvest infection of the inflorescence. Seven indoor or outdoor cannabis production sites and three hemp fields were sampled for bud rot and stem canker presence during 2019-2020. Among 178 isolates recovered from diseased tissues, sequences of the ITS1-5.8S-ITS2 region of rDNA, the glyceraldehde-3-phosphate dehydrogenase (G3PDH) gene and the heat shock 60 (HSP) gene identified the following: Botrytis cinerea (162 isolates), B. pseudocinerea (2), B. porri (1), Sclerotinia sclerotiorum (5), Diaporthe eres (3) and Fusarium graminearum (5). Pathogenicity studies conducted on fresh detached cannabis buds inoculated with spore suspensions or mycelial plugs showed that B. cinerea, S. sclerotiorum and F. graminearum were the most virulent, while B. pseudocinerea, B. porri and D. eres caused significantly less bud rot. Optimal growth of Botrytis species occurred at 15-25o C. In vitro antagonism tests showed that Bacillus spp., Trichoderma asperellum and Gliocladium catenulatum inhibited B. cinerea and S. sclerotiorum colony growth. When applied as a spray 48 h prior to B. cinerea inoculation, all biocontrol agents significantly (P<0.01) reduced disease development on detached inflorescences. Prolific growth and sporulation of T. asperellum and G. catenulatum were observed on bud tissues. The pathogens B. porri, S. sclerotiorum, D. eres and F. graminearum are described for the first time as cannabis bud rot pathogens. Inoculum from neighboring fields of diseased garlic, cabbage, blueberry and hay pasture, respectively, likely initiated infection of inflorescences. Several biological control agents show potential for disease reduction through competitive exclusion.
... Using the corn stunt pathosystem to study the mechanisms of vector-borne disease can contribute to our understanding not only of Spiroplasma-related plant diseases but also of phytoplasma and viral plant diseases, as D. maidis can be described as a super-vector due to its efficiency in transmitting MBSP (a phytoplasma pathogen) and MRFV (a viral pathogen) to corn plants. Scientific insights provided by the study of the corn stunt pathosystem may be applicable to other pathosystems (e.g., Bermudagrass stunt disease and Ratoon stunt disease of sugarcane, which cause major challenges in several other plants [149][150][151]). Finally, studying the molecular interactions taking place during corn stunt disease infection may provide candidate genes and molecules that can be targeted as part of genetic pest control strategies that can be used for the successful disruption of pathogen transmission by insect vectors to host plants. ...
Over 700 plant diseases identified as vector-borne negatively impact plant health and food security globally. The pest control of vector-borne diseases in agricultural settings is in urgent need of more effective tools. Ongoing research in genetics, molecular biology, physiology, and vector behavior has begun to unravel new insights into the transmission of phytopathogens by their insect vectors. However, the intricate mechanisms involved in phytopathogen transmission for certain pathosystems warrant further investigation. In this review, we propose the corn stunt pathosystem (Zea mays–Spiroplasma kunkelii–Dalbulus maidis) as an ideal model for dissecting the molecular determinants and mechanisms underpinning the persistent transmission of a mollicute by its specialist insect vector to an economically important monocotyledonous crop. Corn stunt is the most important disease of corn in the Americas and the Caribbean, where it causes the severe stunting of corn plants and can result in up to 100% yield loss. A comprehensive study of the corn stunt disease system will pave the way for the discovery of novel molecular targets for genetic pest control targeting either the insect vector or the phytopathogen.
... However, these studies lack disease cause diagnoses, which are based on serology and molecular biology [12]. Recent reports on cannabis diseases have shown the occurrence of cucumber mosaic virus (CMV), alfalfa mosaic virus (AMV), arabis mosaic virus (ArMV) [12] and the viroid hop latent viroid (HLVd) [13,14] in cannabis plants. In addition, a cryptic virus, cannabis cryptic virus (CCV) had been isolated from cannabis [15]. ...
In a survey conducted in Cannabis sativa L. (cannabis) authorized farms in Israel, plants showed disease symptoms characteristic of nutrition deprivation. Interveinal chlorosis, brittleness, and occasional necrosis were observed in older leaves. Next generation sequencing analysis of RNA extracted from symptomatic leaves revealed the presence of lettuce chlorosis virus (LCV), a crinivirus that belongs to the Closteroviridae family. The complete viral genome sequence was obtained using RT-PCR and Rapid Amplification of cDNA Ends (RACE) PCR followed by Sanger sequencing. The two LCV RNA genome segments shared 85–99% nucleotide sequence identity with LCV isolates from GenBank database. The whitefly Bemisia tabaci Middle Eastern Asia Minor1 (MEAM1) biotype transmitted the disease from symptomatic cannabis plants to un-infected ‘healthy’ cannabis, Lactuca sativa, and Catharanthus roseus plants. Shoots from symptomatic cannabis plants, used for plant propagation, constituted a primary inoculum of the disease. To the best of our knowledge, this is the first report of cannabis plant disease caused by LCV.
High cannabidiol‐containing plants of Cannabis sativa (high‐CBD) growing in farms in Israel displayed foliar symptoms of interveinal chlorosis and yellowing, brittleness and occasionally necrosis. These symptoms, which were more apparent in older leaves, resembled those caused by the crinivirus lettuce chlorosis virus (LCV). However, this virus was not detected by reverse transcription (RT)‐PCR using specific primer sets. High‐throughput sequencing of viral RNA extracted from symptomatic leaves revealed the presence of cucurbit chlorotic yellows virus (CCYV), a crinivirus in the Closteroviridae family. The complete viral genome sequence was obtained using RT‐PCR followed by Sanger sequencing. The two CCYV RNA genomic segments shared 99.5%–99.85% nucleotide sequence identity with CCYV isolates from the GenBank. The virus was transmitted from symptomatic cannabis leaves to healthy plants of cannabis and Cucumis sativus ‘King Star’ (cucumber) by the whitefly Bemisia tabaci Middle Eastern Asia Minor 1 (MEAM1) species, causing disease symptoms identical to those of the donor plants. Cannabis‐CCYV was also transmitted between infected cucumber plants and cannabis seedlings of unknown genotype. Severe disease symptoms of yellowing and leaf‐edge necrosis were observed on high‐CBD and high Δ ⁹ ‐tetrahydrocannabinol‐containing (high‐THC) flowering cannabis plants and were associated with mixed infections of LCV and CCYV. To the best of our knowledge, this is the first report of CCYV infecting C . sativa plants.
This review paper highlights the fungal diseases of both indoor and outdoor Cannabis cultivation environments and discusses the Artificial intelligence (AI) based crop disease detection and management. Pathogens are a pain in the neck of every Cannabis breeder. They affect the quality and quantity of yield, thus defeating the aim of cultivation. Some of the fungal pathogen that can attack Cannabis crops are Botrytis, Alternaria, Fusarium, Penicillium, Cladosporium, and Aspergillus. Fungal diseases are Powdery Mildew, Damping off, and Mildew. Of these fungal pathogens, the most common inflorescence disease is gray mold, caused by Botrytis cinerea. Botrytis cinerea and Erysiphe species complex are currently the most widespread pathogens of Cannabis worldwide. The greatest challenge facing Cannabis and hemp producers is the management of insect pests and pathogens that attack the roots, leaves and inflorescences. The common disease management strategies are-remove and destroy infected plants. Irradiate dried buds with gamma or electro-beam radiation. Another method is to apply biological control agents at rooting and vegetative stages of growth. Pesticides have been found in all Cannabis products, from flowers to edibles, vapes, and smokes. The pesticide pandemic in the Cannabis industry needs urgent attention. Cannabis can contain fungal pathogens and residues of pesticides, fungicides that cause serious and often fatal infections in persons with immunocompromised conditions, such as cancer, transplant, or infection with HIV. Contamination of Cannabis plants and products (i.e., recreational-and pharmaceutical-grades) with mycotoxigenic organisms, including species of Aspergillus, Penicillium, and Fusarium, pose serious health challenges. The manual Cannabis disease identification process is time-consuming and tedious work. Instead, automated methods save both time and effort. The technology of Artificial Intelligence (AI) in the detection and management of disease has already been employed in many crops. The machine learning (ML)-based models were proposed for the identification and classification of plant diseases. The PlantVillage dataset is the largest and most studied plant disease dataset, which is used as a reference for the disease detection and management of plant diseases.
After decades of prohibition of the cultivation and breeding of hemp ( Cannabis sativa < 0.3% ∆9‐tetrahydrocannabinol [THC]), there is untapped potential for genetic improvement of this crop to provide food, feed, fiber, and medicinal compounds. Successful breeding efforts will require the development and characterization of germplasm resources, optimization of crossing methods, better understanding of sex determination, high‐throughput phenotyping platforms, and deployment of genomic tools for rapid selection. This review provides a brief overview of these topics and some key opportunities for genetic improvement of hemp to support an emerging industry utilizing this newly legalized crop.
Il mercato della canapa attraversa un periodo di crescita economica ed innovazione
molto importante sia in Italia che a livello internazionale. Numerose varietà sono sotto
osservazione in questi ultimi anni e tra quelle di maggior interesse, risultano esserci
quelle ad alto contenuto di Cannabidiolo (CBD) e minima presenza di
tetraidrocannabinolo (THC). Il CBD è un principio attivo molto efficace per la cura di
severe patologie e, di conseguenza, numerose aziende sementiere e farmaceutiche
stanno investendo nella coltivazione e nello sviluppo di tali cultivar.
Plants of the cannabis (Cannabis sativa, marijuana) strain ‘Chronic Ryder’ grown outdoors in the Fraser Valley of British Columbia (BC) displayed symptoms of powdery mildew in late July 2019. The disease progressed rapidly under cool, wet conditions to infect leaves, stems, shoot tips and inflorescences by early September. To identify the pathogen, DNA was extracted from healthy and diseased leaves and subjected to PCR using eukaryotic universal primers that amplified the ITS1-5.8S-ITS2 region of rDNA. A 650 bp band present only in diseased plants showed 99.45% sequence homology to Podosphaeria macularis, the powdery mildew pathogen that infects hop plants. In greenhouse-grown cannabis infected with the powdery mildew pathogen Golovinomyces ambrosiae, a 700 bp size band was present. Conidial morphology also distinguished the two pathogens - P. macularis produced ovoid-oval conidia with fibrosin bodies, while G. ambrosiae produced cylindrical-oblong conidia with no fibrosin bodies. A survey of powdery mildew-infected hop fields and indoor cannabis growing facilities in different geographical locations in BC showed that plants were infected exclusively by either P. macularis or G. ambrosiae, respectively. Inoculations using P. macularis-infected leaf segments placed on cannabis ‘Pink Kush’ leaves under high humidity at 22-26o C gave rise to small mildew colonies after 24-35 days, confirmed to be P. macularis by PCR. Development of P. macularis on cannabis plants was slower compared with G. ambrosiae. To date, only one outdoor location of cannabis is confirmed to have P. macularis; the potential for spread to other sites or to indoor cultivation facilities is unknown.
The goal of many genome sequencing projects is to provide a complete representation of a target genome (or genomes) as underpinning data for further analyses. However, it can be problematic to identify which sequences in an assembly truly derive from the target genome(s) and which are derived from associated microbiome or contaminant organisms.
We present BlobTools, a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Using guanine+cytosine content of sequences, read coverage in sequencing libraries and taxonomy of sequence similarity matches, BlobTools can assist in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants.
Through simulated paired-end read dataset,s containing a mixture of metazoan and bacterial taxa, we illustrate the main BlobTools workflow and suggest useful parameters for taxonomic partitioning of low-complexity metagenome assemblies.
Monitoring the occurrence of virus diseases in plants is important for the implementation of early control measures and prevention of further disease spread. In Poland, in 2004 a health programme for hop was started to eliminate viruses and viroids. In 2012/13, in vitro plants, samples from the IUNG-PIB experimental station and commercial hop gardens in Poland were tested for Hop latent virus (HpLV), and Hop latent and Hop stunt viroids (HpLVd and HpSVd). For virus testing, RT-PCR and ELISA methods were used. In order to detect hop viroids, RT-PCR was employed. The overall incidence of HpLV and hop viroids was lower than reported before the start of the programme. Cloning and sequencing revealed that the HpLV and the HpLVd from Polish sources are very similar to the type sequences and the Czech sources.
DOI: 10.5073/JfK.2014.07.04, https://doi.org/10.5073/JfK.2014.07.04
Motivation:
Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
Results:
To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.
Availability and implementation:
STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
A new viroid which does not seem to produce any symptoms of disease, and is therefore tentatively named hop latent viroid
(HLV) was found to occur worldwide in hops. HLV proved to be infectious when mechanically inoculated onto viroid- and virus-free
hops. The viroid nature of HLV was also substantiated by sequence analysis which revealed that HLV is a circular RNA consisting
of 256 nucleotides, that can be arranged into the viroid-specific, rod-like secondary structure. HLV also contains the central
conserved region typical for most of the presently known viroids. However HLV does not contain the viroid-specific oligo(A)
stretch in the upper left part of its rod-like molecule. Because of this feature and a sequence similarity with the prototypes
of the other viroid groups below 55%, HLV can be regarded as the first member of a new viroid group.
Viroid status was investigated in commercial hop (Humulus lupulus) plantings in three regions of intensive hop production in Washington State. Hop stunt viroid (HSVd), the causal agent of hop stunt disease, was detected for the first time in hop plants in North America. HSVd was detected in samples from 10 of the 33 hop gardens sampled and in 19 of 126 plant samples. Infection with HSVd was associated with chlorosis and reduced plant vigor. Reverse transcription-polymerase chain reaction amplification, sequence identity, and pathogenicity of hop extracts on cucumber seedlings confirmed the presence of HSVd. Apple fruit crinkle viroid (AFCVd), recently reported in hops in Japan, was not detected by RT-PCR in any samples. Hop latent viroid (HLVd), which is frequently associated with hop germplasm world-wide, was detected with high frequency (98 of 126 hop plants surveyed).
Accepted for publication 23 September 2007. Published 27 November 2007.
Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.
