Yellow Mottle Virus Research Articles

Characterization of Two Novel Viruses Within a Complex Virome from Flowering Ginger in Hawaii.

Flowering ginger (Alpinia purpurata) is economically and culturally important in Hawaii. In the past decade, a slow decline syndrome has impacted the production of this crop in the state. RNA sequencing analyses and virus indexing surveys were done on samples collected from four of the Hawaiian Islands. Viral sequences corresponding to six viruses were recovered from transcriptomic data from samples with virus-like symptoms. Canna yellow mottle virus (CaYMV, genus Badnavirus) and two novel viruses, Alpinia vein clearing virus (ApVCV, genus Ampelovirus) and Alpinia vein streaking virus (ApVSV, genus Betanucleorhabdovirus), were found at a moderate incidence in diseased plants. Conversely, three other viruses, including the two potyviruses, banana bract mosaic virus and bean common mosaic virus, and a badnavirus, banana streak GF virus, were also found but at a low incidence. Virus detection in potential insect vectors and transmission assays identified the mealybug Planococcus citri as a vector of CaYMV and ApVCV, whereas the aphid Pentalonia caladii was identified as a vector of the novel ApVSV. Both P. citri and P. caladii are common pests of flowering ginger in Hawaii. Transmission of ApVSV was achieved using P. caladii colonies either established in the laboratory or naturally feeding on infected plants, although no transmission was obtained using viruliferous aphids originally reared on taro (Colocasia esculenta). Our study provides insights into the potential association between viral infections and the observed decline symptoms of flowering ginger in Hawaii. However, more definitive studies are needed to link single or mixed viral infections with decline symptoms.

Old Foe, New Host: Epidemiology, Genetic Diversity, and Pathogenic Characterization of Maize Streak Virus in Rice Fields from Burkina Faso

Rice is of critical significance regarding food security worldwide, including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus ( Solemoviridae) and the rice stripe necrosis virus ( Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on interacting communities associated with plants in rice landscapes and exploring the diversity and epidemiological status of viruses circulating in rice fields from Burkina Faso. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmers’ rice fields under two production systems: rainfed lowlands and irrigated areas. More than 2,700 rice samples were collected without regard to disease symptoms following a regular scheme. Wild and cultivated Poaceae (maize and sugarcane) growing in nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV) ( Geminiviridae) in analyzed rice samples. Further molecular analyses using rolling circle amplification-polymerase chain reaction showed that MSV was widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified thus far in wild grasses, was the most prevalent strain, whereas MSV-A, known to cause severe symptoms in maize, was sporadically identified. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains in rice. Thus, in addition to contributing to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Rice yellow mottle virus is a suitable amplicon vector for an efficient production of an anti-leishmianiasis vaccine in Nicotiana benthamiana leaves

BackgroundSince the 2000’s, plants have been used as bioreactors for the transient production of molecules of interest such as vaccines. To improve protein yield, “amplicon” vectors based on plant viruses are used. These viral constructs, engineered to carry the gene of interest replicate strongly once introduced into the plant cell, allowing significant accumulation of the protein. Here, we evaluated the suitability of the monocot-infecting RNA virus Rice yellow mottle virus (RYMV) as an amplicon vector. The promastigote surface antigen (PSA) of the protozoan Leishmania was considered as a protein of interest due to its vaccine properties against canine leishmaniasis.ResultsSince P1 (ORF1) and CP (ORF3) proteins are not strictly necessary for viral replication, ORF1 was deleted and the PSA gene was substituted to ORF3 in the RYMV-based vector. We evaluated its expression in the best described plant bioreactor system, Nicotiana benthamiana which, unlike rice, allows transient transformation by Agrobacterium. Despite not being its natural host, we demonstrated a low level of RYMV-based vector replication in N. benthamiana leaves. Under optimized ratio, we showed that the P19 silencing suppressor in combination with the missing viral CP ORF significantly enhanced RYMV amplicon replication in N. benthamiana. Under these optimized CP/P19 conditions, we showed that the RYMV amplicon replicated autonomously in the infiltrated N. benthamiana cells, but was unable to move out of the infiltrated zones. Finally, we showed that when the RYMV amplicon was expressed under the optimized conditions we set up, it allowed enhanced PSA protein accumulation in N. benthamiana compared to the PSA coding sequence driven by the 35S promoter without amplicon background.ConclusionThis work demonstrates that a non-dicot-infecting virus can be used as an amplicon vector for the efficient production of proteins of interest such as PSA in N. benthamiana leaves.

Occurrence of piper yellow mottle virus (PYMoV) on Piper betle and Piper cubeba in Indonesia

Occurrence of piper yellow mottle virus (PYMoV) on Piper betle and Piper cubeba in Indonesia

Inventory of insect pests of rice in agro-ecosystems of far north region of Cameroon

The entomofauna vector of rice yellow mottle virus was studied from June to September 2023 in the rainfed rice ecosystem of Maroua and in the main irrigated rice ecosystems of Yagoua and Maga in the Far North Region, Cameroon . Insect vector sampling was conducted in rainfed and irrigated rice fields every two weeks using a sweep net and a D-Vac (vacuum trap). From the samples obtained in the different rice-growing sites, the dominant structure of insect vectors of rice yellow mottle as well as their natural enemies was analyzed according to the phenology of rice. It appears from the inventory of insects in irrigated rice (Maga, Yagoua) and rainfed rice (Maroua) that this crop harbors many vectors of the rice yellow mottle virus. In the different rice-growing sites, we have numbers of vector insect individuals captured of 267, 286 and 385 respectively in Maroua (rainfed rice), Maga and Yagoua (irrigated rice). The vector insects captured are distributed as follows, eight species of vector insects in irrigated rice in Maga belonging to five families divided into three orders: Chnootriba similis (Coleoptera: Coccinellidae), Chaetocnema pulla (Coleoptera: Chrysomelidae), Locris rubra ( Hemiptera: Cicadellidae), Nephotettix nigropictus (Hemiptera: Cicadellidae), Sogatella furcifera (Hemiptera: Delphacidae), Cofana spectra (Hemiptera: Cicadellidae), Niparvata lugens (Hemiptera: Delphacidae) and Diopsis thoracica (Diptera: Diopsidae). In irrigated rice in Yagoua, eleven species of vector insects belonging to seven families divided into three orders were collected: Chnootriba similis (Coleoptera: Coccinellidae), Chaetocnema pulla (Coleoptera: Chrysomelidae), Locris rubra (Hemiptera: Cicadellidae), Nephotettix nigropictus (Hemiptera: Cicadellidae), Sogatella furcifera (Hemiptera: Delphacidae), Cofana spectra (Hemiptera: Cicadellidae), Recilia dorsalis (Hemiptera: Cicadellidae), Niparvata lugens (Hemiptera: Delphacidae), Leptocorisa oratorius (Hemiptera: Alydidae), Diploxys spp. (Hemiptera: Pentatomidae) and Diopsis thoracica (Diptera: Diopsidae). As for rainfed rice in Maroua, thirteen vector insect species belonging to seven families and three orders were collected: Chnootriba similis (Coleoptera: Coccinellidae), Chaetocnema pulla (Coleoptera: Chrysomelidae), Trichispa sericea (Coleoptera: Chrysomelidae), Locris rubra (Hemiptera: Cicadellidae), Nephotettix nigropictus (Hemiptera: Cicadellidae), Sogatella furcifera (Hemiptera: Delphacidae), Cofana spectra (Hemiptera: Cicadellidae), Recilia dorsalis (Hemiptera: Cicadellidae), Niparvata lugens (Hemiptera: Delphacidae) and Diopsis thoracica (Diptera: Diopsidae). These species proved to be particularly important by the size of their populations at the tillering stage of rice. The irrigated rice ecosystems of Yagoua and Maga are the most infested by insect vectors of rice yellow mottle virus and among these insect vectors Nephotettix nigropictus (Hemiptera: Cicadellidae) is the abundant species with 87 and 90 individuals collected respectively from Maga and Yagoua. Nephotettix nigropictus (Hemiptera: Cicadellidae) was collected in abundance at the tillering stage of rice. As for the predators and parasitoids present in the rice fields, there were spiders Araneus sp. (Araneae: Araneidae), Tetragnatha sp. (Araneae: Tetragnatidae), Pardosa injucunda (Araneae: Lyconidae) and lady beetles Xanthadalia effusa (Coleoptera: Coccinellidae) as predators and Hydrellia griseola (Diptera: Ephydridae), Bracon sp. (Hymenoptera: Braconidae), Xiphosomella sp. (Hymenoptera: Braconidae), Platygaster sp. (Hymenoptera: Platygasteridae) as parasitoids. The parasitoid species Hydrellia griseola (Diptera: Ephydridae) and the predatory species Araneus sp. (Araneae: Araneidae) are the most abundant natural enemies in the rice ecosystems of the Far North.

WITHDRAWN: Rice Pests and Diseases Around the World: Who, Where and What Damage Do They Cause?

Rice stands as one of the most important staple crops for nearly half of the world’s population. Its productivity is pivotal in ensuring global food security, yet pests and diseases are one of the most important constraints. Despite its paramount significance, a comprehensive overview of the primary pests and diseases affecting rice worldwide has not been previously undertaken. This systematic review, following PRISMA guidelines and drawing upon three online databases (PubMed, WOS, and CAB Abstract), enabled the identification of distribution patterns of these pests and diseases across the globe. From an initial pool of 13.983 articles, exclusion criteria were applied, resulting in 838 final articles. Given that rice cultivation primarily occurs in Asia and Africa, it's unsurprising that the majority of documented pests and diseases are found on these continents. In Africa, the genera Diopsis, Maliarpha and Chilo are the most important pests affecting rice productivity, while in Asia the most important are Nilaparvata, Scirpophaga, Sogatella, Chilo, Cnaphalocrocis, Sesamia, and Nephotettix genera, demonstrating different pests under a continent overview. Regarding diseases, in Africa, the fungi Pyricularia, the bacteria Xanthomonas and the virus Sobemovirus are the most significant. In Asia, the fungal genera Fusarium, Pyricularia, Rhizoctonia, Bipolaris, Curvularia, Ustilaginoidea, Alternaria, and Sarocladium, and bacteria Xanthomonas, Pantoea, Pseudomonas, and Burkholderia are the most frequently reported. These findings reveal distinct geographic patterns in the distribution of rice pests and diseases, implying the development of specific regional management guidelines. In terms of yield loss, the most severe fungi are Pyricularia and Bipolaris, responsible for blast and brown spot diseases, respectively. Both occur in Africa and Asia and affect different parts of the plant, with Bipolaris being more evident on the leaves. A big concern restricted to Africa is the Sobemovirus (causing rice yellow mottle virus), which can lead to yield losses of up to 100%, primarily affecting the leaves. This study significantly contributes to identifying global rice pests and diseases, assessing their current distribution patterns and evaluating their effects on future rice productivity. Furthermore, it highlights the overlooked reporting of studies in Africa, despite the region’s significance in rice cultivation and production.

Performance analysis of various deep learning models for detecting rice diseases

<p>A major portion of the world’s population relies on rice as a staple diet, hence rice is essential to maintaining food security worldwide. Unfortunately, rice crops are susceptible to a number of illnesses that, if detected and treated promptly, can result in significant output losses. Expert visual inspection is a time-consuming and arbitrary part of the conventional procedures for diagnosing diseases in rice. An effective method for automated illness diagnosis in agriculture has evolved in recent years: deep learning, a branch of artificial intelligence. The objective of this research is to compare AlexNet, DCNN, MobileNet, GoogleNet, VGG16, ResNet50 and Xception, these are various deep learning models in order to choose the one that would produce the highest levels of accuracy, precision recall, specificity, and F1-score for detecting rice diseases. In this study we train the model for nine different types of rice diseases named as Rice Blast (Pyricularia oryzae), Rice Sheath Blight (Rhizoctonia Solani), Bacterial Leaf Blight (Xanthomonas oryzae pv. oryzae), Tungro Disease, Rice Grassy Stunt Virus (RGSV), Rice Yellow Mottle Virus (RYMV), Bakanae Disease (Fusarium moniliforme), Brown Spot (Cochliobolus miyabeanus) and Rice Tungro Bacilliform Virus (RTBV) with 30,000 images. For this we used the secondary dataset for analyzing the performance of models. We trained the model for both normalized and non-normalized dataset. After comparing the various models we get the better result from ResNet50 model with accuracy of 97.50%.</p>

Virus-mealybug relationship in the transmission of piper yellow mottle virus

Virus-mealybug relationship in the transmission of piper yellow mottle virus

Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2.

Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role inRYMVsusceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.

Evaluation of Camellia Cultivars and Selections for Growth, Cold-hardiness, Flowering, and Disease Resistance in Tennessee, USA

Susceptibility to low-temperature injury and diseases is a major concern associated with ornamental camellia production. To comprehensively understand their growth, cold-hardiness, flowering, and disease resistance, 24 camellia (Camellia spp. and hybrids) cultivars and selections were evaluated in McMinnville, TN, USA (USDA plant hardiness zone 7a). During Mar 2011, camellias were planted in the field plots. Plant height and canopy width were measured annually from 2011 to 2019, and low-temperature damage was recorded in 2014 and 2023. The flowering duration was recorded each year from 2011 to 2020. The Camellia Yellow Mottle Virus, monochaetia leaf spot (Monochaetia sp.), edema, flower blight (Ciborinia camelliae), and flower spot (Botrytis cinerea) severity (% affected) were evaluated from Oct to Nov in 2016 and 2017. The season-long area under the disease progress curve (AUDPC) was calculated. Cultivars Arctic Snow and Pink Icicle exhibited the greatest height, and Autumn Spirit, Elaine Lee, Arctic Snow, and Survivor had the widest canopy width, whereas Shishigashira had the lowest height and canopy width. ‘April Remembered’, ‘April Rose’, ‘Arctic Snow’, ‘Ashton’s Ballet’, ‘Autumn Carnival’, ‘Autumn Spirit’, ‘Elaine Lee’, ‘Survivor’, and C. chekiangoleosa selection were least affected by winter low temperatures, whereas ‘Korean Snow’, ‘One Alone’, C. sasanqua selection, ‘Pink Icicle’, and ‘Shishigashira’ were severely damaged. ‘Arctic Snow’ flowered most reliably (6 of 8 years), whereas ‘April Remembered’, ‘April Rose’, ‘Ashton’s Ballet’, ‘Autumn Spirit’, and ‘Survivor’ flowered five times. ‘Korean Fire’, ‘Classic Pink’, ‘Maroon Mist’, and ‘Spring’s Promise’ displayed the highest virus severity and AUDPC. ‘Arctic Snow’, C. sasanqua selection, and the C. chekiangoleosa selection had no viral symptoms. C. sasanqua selection and ‘Red Aurora’ were significantly impacted by edema disorder, with severity ratings of ∼43% and 26%, respectively. Monochaetia leaf spot severity was highest in ‘Red Aurora’ and ‘Spring’s Promise’, whereas ‘Anacostia’, ‘Arctic Snow’, ‘Ashton’s Ballet’, ‘Autumn Spirit’, ‘Classic Pink’, ‘Kuro Delight’, ‘One Alone’, ‘Pink Icicle’, ‘Shishigashira’, and ‘Survivor’ exhibited the least monochaetia leaf spot severity and AUDPC. Flower blight and flower spot were observed only in ‘Arctic Snow’ and ‘Survivor’. These findings will aid landscapers and nursery growers with selecting and managing camellia cultivars effectively.

Molecular Diversity of Rice Yellow Mottle Virus in Uganda and Relationships with Other Strains from Africa.

Rice yellow mottle virus disease, caused by Rice yellow mottle virus (RYMV), is the most important disease of lowland rice in Uganda. However, little is known about its genetic diversity in Uganda and relationships with other strains elsewhere across Africa. A new degenerate primer pair that targets amplification of the entire RYMV coat protein gene (circa 738 bp) was designed to aid virus variability analysis using RT-PCR and Sanger sequencing. A total of 112 rice leaf samples from plants with RYMV mottling symptoms were collected during the year 2022 in 35 lowland rice fields within Uganda. The RYMV RT-PCR results were 100% positive, and all 112 PCR products were sequenced. BLASTn analysis revealed that all isolates were closely related (93 to 98%) to those previously studied originating from Kenya, Tanzania, and Madagascar. Despite high purifying selection pressure, diversity analysis on 81 out of 112 RYMV CP sequences revealed a very low diversity index of 3 and 1.0% at the nucleotide and amino acid levels, respectively. Except for glutamine, amino acid profile analysis revealed that all 81 Ugandan isolates shared the primary 19 amino acids based on the RYMV coat protein region examined. Except for one isolate (UG68) from eastern Uganda that clustered alone, phylogeny analysis revealed two major clades. The Ugandan RYMV isolates were phylogenetically related to those from the Democratic Republic of Congo, Madagascar, and Malawi but not to RYMV isolates in West Africa. Thus, the RYMV isolates in this study are related to serotype 4, a strain common in eastern and southern Africa. RYMV serotype 4 originated in Tanzania, where evolutionary forces of mutation have resulted in the emergence and spread of new variants. Furthermore, mutations are evident within the coat protein gene of the Ugandan isolates, which may be attributed to changing RYMV pathosystems as a result of rice production intensification in Uganda. Overall, the diversity of RYMV was limited and most noticeably in eastern Uganda.

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

AbstractRice yellow mottle virus (RYMV) is widespread in mainland Africa and adjoining islands but to date its occurrence in Zambia is unknown. In March 2022, field surveys were conducted in Luapula, Northern, Western and Eastern provinces of Zambia to determine the occurrence of RYMV and its genetic relationship with global isolates of the virus. Thirty‐three paddy rice fields were visited and 108 leaf tissue samples were collected for analysis. The incidence of yellow mottle symptoms ranged from 25% to 43% in 10 (30.3%) of 33 fields and RYMV was detected in 35 (32.4%) of 108 samples by RT‐PCR with virus‐specific primers. A subset of 27 RYMV‐positive samples was constituted from which full‐length (720 bp) coat protein (CP) regions were amplified followed by bidirectional Sanger sequencing. Phylogenetic analysis of the CP cistron revealed distinct clustering of the isolates from Zambia in a monophyletic clade as subtype of the RYMV strain S4. Three isolates were randomly selected and used to obtain complete RYMV genomes of 4448–4449 nucleotides (nt). Comparative analysis of both the CP and the complete RYMV genomes from Zambia with their corresponding sequences in GenBank revealed that they shared 92%–93.2% nt identities with strain S4 isolates. These results confirm for the first time occurrence of RYMV strain S4 in Zambia and further reinforce the need for phytosanitary vigilance to safeguard rice production in Zambia.

Dynamics ofthe rice yellow mottle disease inwestern Burkina Faso: Epidemic monitoring, spatio-temporal variation ofviral diversity, andpathogenicity ina disease hotspot.

The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.

Begomovirus diversity in tomato crops in Costa Rica

AbstractBegomoviruses (Geminiviridae family) are characterized by their high recombination rate and a wide range of hosts, making their control difficult. In Costa Rica, various species of bipartite begomoviruses have been reported, which are Pepper golden mosaic virus (PepGMV), Tomato yellow mottle virus (ToYMoV), Tomato leaf curl Sinaloa virus (ToLCSiV) and the monopartite begomovirus Tomato yellow leaf curl virus (TYLCV). Since the TYLCV first report in Costa Rica, neither additional knowledge has been produced on how this begomovirus has spread in the country's territory nor on the distribution of the other bipartite species. A total of 429 tomato samples collected during the years 2015–2016 were used to study these aspects. Each sample was georeferenced and analysed with various techniques such as nucleic acid hybridization, polymerase chain reaction (PCR) and sequencing for the begomoviruses previously reported in Costa Rica. It was found that the presence/absence of the different species can vary, depending on the province. TYLCV is present in the six provinces analysed in this work, with a proportion from 3.7 to 86.6 per cent. Alajuela, Cartago, and Heredia are the provinces most affected by tomato‐infecting begomoviruses. Fourteen different haplotypes of TYLCV were detected, but all were identified as TYLCV‐IL. The distribution of TYLCV was related to the presence of the whitefly Bemisia tabaci MED, especially in the country's main tomato production areas. This information allows the phytosanitary surveillance services to develop strategies for the integrated management of the disease and to contribute data to the genetic improvement programmes of the crop.

Mathematical modeling and optimal control of a vector-borne rice yellow mottle virus disease

Mathematical modeling and optimal control of a vector-borne rice yellow mottle virus disease

Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates.

Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.

Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana

Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.

Rapid onsite detection of piper yellow mottle virus infecting black pepper by recombinase polymerase amplification-lateral flow assay (RPA-LFA)

Piper yellow mottle virus (PYMoV) is a pararetrovirus associated with stunt disease in black pepper. As the primary spread of the virus occurs through vegetative propagation, effective diagnostics are required for the production of virus-free plants. Currently available assays are time-consuming, require expensive equipment, and are not suitable for on-site detection. In the present study, two rapid assays based on the recombinase polymerase amplification (RPA) coupled with lateral flow assay (LFA) using (i) 6-carboxyfluorescein (FAM) labeled nfo probe and biotin-labeled reverse primer and (ii) FAM labeled forward and biotin-labeled reverse primer was developed for the detection of PYMoV. The assays were performed using TwistAmp DNA amplification reagents and crude extract from the infected plant and mealybug as templates. Both assays were optimized for parameters like concentration of magnesium acetate, temperature, and time. The RPA product was then diluted and applied to the sample pad of a lateral flow device for visualizing the results. The formation of a colored line at the test line was considered positive for PYMoV. The entire process from sample preparation to visualization of results could be completed in about 30 min. The developed assays were specific and 10 times more sensitive than PCR. The assays were validated using field samples of black pepper and mealybug vectors.

Coat Protein Genealogy and Complete Genome Characterization of Field Isolates of Rice Yellow Mottle Virus from Zambia

Coat Protein Genealogy and Complete Genome Characterization of Field Isolates of Rice Yellow Mottle Virus from Zambia

Rapid evolution of an RNA virus to escape recognition by a rice nucleotide-binding and leucine-rich repeat domain immune receptor.

Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underlying the extremely fast adaptation of the virus to its host. We found that the RYMV3 gene that protects rice against the virus codes for a nucleotide-binding and leucine-rich repeat domain immune receptor (NLRs) from the Mla-like clade of NLRs. RYMV3 detects the virus by forming a recognition complex with the viral coat protein (CP). The virus escapes efficiently from detection by mutations in its CP, some of which interfere with the formation of the recognition complex. This study establishes that NLRs also conferin monocotyledonous plants immunity to viruses, and reveals an unexpected functional diversity for NLRs of the Mla clade that were previously only known as fungal disease resistance proteins. In addition, it provides precise insight into the mechanisms by which viruses adapt to plant immunity and gives important knowledge for the development of sustainable resistance against viral diseases of cereals.