Yellow Mottle Research Articles

Rice Yellow Mottle Virus (RYMV): A Review

Rice (Oryza spp.) is mostly grown directly from seed and sown on wet or dry seed beds or usually used as transplants on nursery beds. Among all the economically important viral diseases in the world, rice yellow mottle virus (RYMV) is only prevalent in rice-growing countries in Africa. RYMV has become the main rice production constraint in Africa over the last 20–25 years, causing yield losses of 10 to 100% depending on the age of the plant at the time of infection, degree of varietal susceptibility and the existing climatic conditions. Good agricultural practices and biotechnological tools in the development of improved resistant cultivars have been extensively utilized in controlling the disease. This review focuses on RYMV, its epidemiology, serological and molecular typing, disease management and the way forward for sustainable rice production.

First Report of Paprika mild mottle virus Infecting pepper (Capsicum annuum L.) in China.

Paprika mild mottle virus (PaMMV), a tobamovirus from the Virgaviridae family, has been reported to infect pepper (Capsicum annuum L.) in the Netherlands (García-Luque et al., 1993), Japan (Hamada et al., 2003), Bulgaria (Ruíz del Pino et al., 2003), and Israel (Luria et al., 2018). Pepper has become the most widely planted vegetable and the most heavily consumed spicy condiment, with a large planting area (>21,000 km2) in China (Zou et al., 2021). However, the crop's productivity is limited by viral diseases. In August 2021, a survey of viral diseases was conducted across five pepper-growing regions in Linyi, Shandong Province, China, revealed that 5% to 10% of plants in most fields exhibited symptoms such as stunting, leaf narrowing, chlorosis, and crinkling of leaf tissue (Fig. S1-a). Subsequently, seven symptomatic samples (Fig. S1-b) were collected from a plot (118° 29' E, 34° 65' N) where thin-skinned peppers were grown. All samples tested positive in a Western blot assay using a polyclonal antibody for tobacco mosaic virus (TMV), indicating the presence of a tobamovirus (Fig. S1-c). To identify the virus, total RNAs were extracted from 10 different symptomatic pepper plant samples, using the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) and combined into a single sample in equal amounts (100 ng/μL each). RNA-Seq was performed on this mixture using the Illumina NovaSeq 6000 (Illumina, San Diego, USA). Raw reads (6.92G) in fastq format were processed with in-house perl scripts to yield clean reads (6.68G), which were assembled into 780 contigs (mean length: 2036 bp) using Trinity software (v2.6.6). These contigs were then analysed using the NCBI BLASTX program (http://www.ncbi.nlm.nih.gov/blast) against the viral RefSeq database. The results demonstrated that the contigs exhibited an average genome coverage of 40.16%. Notably, one unique contig (6453 bp) was mapped to the PaMMV genome (reference sequence KX187305.1) with 98.34% identity. To verify the RNA-Seq result, a PaMMV-specific primer pair (forward: 5'-GAGTTCATAGAGGCAGTACC-3'; reverse: 5'-CTTCGATTTAAGTGGAGGGAT-3') was designed for amplifying an 800-nt fragment of the PaMMV coat protein (CP) gene by RT-PCR. The 800-nt fragment was successfully amplified from all the symptomatic samples (Fig. S1-d). Sequenced RT-PCR products (GenBank No. OR365081.1) showed 99.75% nucleotide identity with PaMMV isolates (OQ198318.1, China, goat) according to BLAST analysis. Mechanical transmission of PaMMV from three infected pepper plants collected in Linyi to healthy pepper plants confirmed pathogenicity. Three pepper cultivars (trade name: Qiemen, Tianyu, Haonong11) were tested and showed varying symptoms post-inoculation (Fig. S1-e). All cultivars were confirmed in the lab to be PMMoV-sensitive and exhibited significant viral disease symptoms after PMMoV inoculation (data not shown). Each variety was inoculated with at least 3 seedlings from different field-collected virulence sources. Qiemen (cultivar: sweet pepper) exhibited severe symptoms with necrotic spots, Tianyu (cultivar: Chaotian pepper) had mild leaf wrinkling, and Haonong11 (cultivar: Pickled pepper) showed yellow mottle and leaf shrinking. All tested seedlings were positive for PaMMV by RT-PCR (Fig. S1-f). To our knowledge, this is the first report of PaMMV infecting pepper in China, highlighting the need for vigilant monitoring to protect the chili industry and prevent the virus's spread to other crops.

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.

First Report of a Phytoplasma Strain in the Elm Yellows Group (16SrV) associated with Virginia Creeper in Maryland, USA.

Virginia creeper (Parthenocissus quinquefolia [L.] Planch.) is a deciduous flowering vine in the Vitaceae family. Native to eastern North America, it is often used ornamentally as a climbing vine or as ground cover due to its rapid growth and foliage color in the fall. In July of 2022, along exterior walls of a private property in Lanham, MD, two Virginia creeper (VC) vines were observed displaying symptoms of yellow mottling and premature reddening of leaves. To investigate the cause of these symptoms, two symptomatic leaf samples and one asymptomatic leaf samples from a third vine in the same vicinity were collected for further analysis. A Qiagen DNeasy Plant Mini Kit was used to extract total DNA from leaf tissues according to the manufacturer's instructions. A phytoplasma-specific real-time PCR (Hodgetts et al. 2009) was used to test the DNA extracts, which detected the presence of phytoplasmas in the two DNA samples derived from symptomatic vines. The near full-length of the 16S ribosomal RNA gene was then amplified by seminested PCR from these samples with primers P1/16S-SR followed by P1A/16S-SR (Deng, and Hiruki 1991; Lee et al. 2004) and Sanger sequenced using primers P1A and 16S-SR. Analysis of the obtained 16S rDNA sequences revealed no variation between the two plant samples, and one sequence was deposited in GenBank representing the phytoplasma strain named VC-MD1 (GenBank PP746981). A BLASTn search of the 16S rRNA gene sequence in the NCBI nucleotide database, showed 99.93% sequence identity with the phytoplasma strain AldY-WA1 (GenBank MZ557341) from red alder in Washington, a phytoplasma associated with VC plants in southern Florida (GenBank AF305198) (Harrison et al. 2001), and other strains detected in grapevines in Europe described as "flavescence dorée" phytoplasma (GenBank AF176319) (Davis, and Dally 2001). The virtual restriction fragment length polymorphism pattern derived from iPhyClassifier (Zhao et al. 2009), indicated that VC-MD1 is indeed a member of the 16SrV-C phytoplasma subgroup. To confirm the identification, the partial spc operon and the partial tuf gene were amplified as previously described (Lee et al. 2010; Makarova et al. 2012). Specifically, the spc operon region was amplified using a nested PCR approach with primer set L15F1A-a/MapR1 followed by L15F1A-b/MapR1A-b. Sequence data obtained from the two loci were deposited to GenBank with accession numbers PP746982 (spc) and PP746983 (tuf). BLAST searches querying the nucleotide sequences of the spc operon and tuf gene showed 95.39% and 99.05% identity, respectively, to the corresponding loci of 'Candidatus Phytoplasma rubi' strain RS (GenBank CP114006) and hemp dogbane yellows phytoplasma strain HD1 (GenBank FR686506). Phylogenetic analysis based on secY and tuf gene sequences suggest that the VC-MD1 strain is evolutionary closest to 16SrV-C phytoplasma strains detected in various hosts in the United States, including HD1 and AldY-WA1. These North American strains cluster together on a distinct branch within the elm yellows group phytoplasmas. For the State of Maryland, this detection represents the first report of a phytoplasma strain member of the16SrV-C subgroup infecting VC plants. A phytoplasma of the same subgroup was previously detected in Florida in asymptomatic VC vines (Harrison et al. 2001). The 16S rRNA gene sequences of the two VC phytoplasma strains are nearly identical, differing by just a single nucleotide. The disease transmission vectors of the VC-MD1 strain and the prevalence of the disease in the region remains undetermined.

First Report of Watermelon Crinkle Leaf-Associated Virus-2 (WCLaV-2) in Watermelon (Citrullus lanatus) in Georgia, USA.

Watermelon (Citrullus lanatus) is a key horticultural crop in Georgia with farmgate value of 142 million USD (2022 Farm Gate Value Report), yet faces challenges from whitefly-transmitted viruses, especially during periods of elevated whitefly populations in the fall. Foliar symptoms on watermelon plants including yellow mottling and chlorosis, wrinkling, bunching, and upward curling, were observed in experimental fields at UGA Tifton and commercial fields in Colquitt County in the fall of 2023. These were similar to those described for watermelon crinkle leaf-associated viruses (WCLaV-1 and WCLaV-2) from Florida (Hendrick et al, 2021) and Texas (Hernandez et al., 2021). The disease incidence reached 100% in both locations. WCLaV-1 was previously identified in Georgia (Adeleke et al., 2022a); however, WCLaV-2 remained undetected in further surveys (Adeleke et al., 2022b). Total nucleic acid was extracted from symptomatic leaf tissues with the MagMAXTM 96 Viral RNA isolation kit (ThermoFisher Scientific, USA), following the manufacturer's guidelines, with the omission of DNAse treatment. The presence of WCLaV-1 was identified through reverse transcription-polymerase chain reaction (RT-PCR) (Hernandez et al., 2021) in 17 out of 24 samples in Tift County, and 12 out of 15 samples from Colquitt County. Within the same set of samples, WCLaV-2 was identified in three samples from Tift County and four samples from Colquitt County by RT-PCR directed at the RdRp gene (Hernandez et al., 2021). WCLaV-1 was not detected in the three samples from Tift County that had WCLaV-2, while mixed infections of WCLaV-2 and WCLaV-1 were observed in the samples form Colquitt County. Two whitefly transmitted viruses, previously reported in Georgia were also identified as mixed infection in these samples (Table S1). The presence of WCLaV-2 was further confirmed by amplifying the movement protein (MP) gene of WCLaV-2 by RT-PCR assays (Hernandez et al., 2021). The amplicons, with expected sizes of 968bp for the RdRp gene and 562bp for the MP gene of WCLaV-2, located on RNA 1 and RNA 2 segments respectively, were directly sequenced from both directions (Genewiz, USA) from a sample collected in Tift County. The resulting data were analyzed via BLASTn search. The MP gene fragment (PP178543) shared 100% identity with isolates from Brazil (LC636074.1), Texas (MW559086.1), and Florida (MZ325858.1). RdRp gene (PP178542) shared >99.7% identity with isolates from Brazil (LC636073.1), Texas (MW559083.1) and Florida (MZ325855.1). WCLaV-1 and WCLaV-2, initially discovered in Asia (Xin et al., 2017), have been assigned to the genus Coguvirus, in the family Phenuiviridae (Walker et al., 2022). Subsequent reports from the USA (Hendrick et al., 2021; Hernandez et al., 2021), Australia (Mulholland et al., 2023), and Brazil (Maeda et al., 2022) indicate the global spread of these viruses. Watermelon is the primary host of WCLaV-2. Despite these findings, biological information, including vector relations, for both viruses and other members of the genus Coguvirus remains elusive. The impact of these viruses on watermelon production and yield in the identified regions remains largely unknown, underscoring the need for further investigations.

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.

First Report of Root Rot Caused by Fusarium incarnatum on Mongolian Snake gourd in China.

First Report of Root Rot Caused by Fusarium incarnatum on Mongolian Snake gourd in China.

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.

The complete genome sequence of a putative novel cytorhabdovirus identified in Chelidonium majus in China.

A new cytorhabdovirus, tentatively named "chelidonium yellow mottle associated virus" (CheYMaV), was identified in Chelidonium majus with yellow mottle symptoms by high-throughput sequencing and RT-PCR. Its genome is 12,121 nucleotides in length and contains eight open reading frames (ORFs) in the order 3'-N-P'-P-P3-M-G-P6-L-5'. Amino acid sequence comparisons between the putative proteins of CheYMaV and the corresponding proteins of other cytorhabdoviruses showed that it shares the highest sequence similarity with Trifolium pratense virus A (TpVA, MH982250) and Glehnia littoralis virus 1 (GllV1, BK014304), but with sequence identity values below the species demarcation threshold for cytorhabdoviruses (<80%). Phylogenetic analysis showed that CheYMaV is most closely related to TpVA and GllV1. CheYMaV should therefore be considered a new member of the genus Cytorhabdovirus. This is the first report of a cytorhabdovirus identified in Chelidonium majus.

Attenuation of Zucchini mosaic virus disease in cucumber plants by mycorrhizal symbiosis

Key messageArbuscular mycorrhizal fungi generated systemic acquired resistance in cucumber to Zucchini yellow mosaic virus, indicating their prospective application in the soil as a sustainable, environmentally friendly approach to inhibit the spread of pathogens.The wide spread of plant pathogens affects the whole world, causing several plant diseases and threatening national food security as it disrupts the quantity and quality of economically important crops. Recently, environmentally acceptable mitigating practices have been required for sustainable agriculture, restricting the use of chemical fertilizers in agricultural areas. Herein, the biological control of Zucchini yellow mosaic virus (ZYMV) in cucumber (Cucumis sativus L.) plants using arbuscular mycorrhizal (AM) fungi was investigated. Compared to control plants, ZYMV-infected plants displayed high disease incidence (DI) and severity (DS) with various symptoms, including severe yellow mosaic, mottling and green blisters of leaves. However, AM fungal inoculation exhibited 50% inhibition for these symptoms and limited DS to 26% as compared to non-colonized ones. The detection of ZYMV by the Enzyme-Linked Immunosorbent Assay technique exhibited a significant reduction in AM-inoculated plants (5.23-fold) compared with non-colonized ones. Besides, mycorrhizal root colonization (F%) was slightly reduced by ZYMV infection. ZYMV infection decreased all growth parameters and pigment fractions and increased the malondialdehyde (MDA) content, however, these parameters were significantly enhanced and the MDA content was decreased by AM fungal colonization. Also, the protein, proline and antioxidant enzymes (POX and CAT) were increased with ZYMV infection with more enhancements due to AM root colonization. Remarkably, defence pathogenesis-related (PR) genes such as PR-a, PR-b, and PR-10 were quickly expressed in response to AM treatment. Our findings demonstrated the beneficial function of AM fungi in triggering the plant defence against ZYMV as they caused systemic acquired resistance in cucumber plants and supported their potential use in the soil as an environment-friendly method of hindering the spread of pathogenic microorganisms sustainably.

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

&lt;p&gt;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%.&lt;/p&gt;

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.

Detection and characterization of a putative emaravirus infecting Clematis brevicaudata DC. in China.

A novel emaravirus, tentatively named "clematis yellow mottle associated virus" (CYMaV), was identified through transcriptome sequencing and RT-PCR analysis of yellow-mottled leaf samples from Clematis brevicaudata DC. The genome of CYMaV consists of five viral RNAs: RNA1 (6591 nucleotides, nt), RNA2 (1982 nt), RNA3a (1301 nt), RNA3b (1397 nt), and RNA4 (1192 nt). The 13-nt sequences at the 5'- and 3'-termini of the CYMaV RNAs are conserved and have reverse complementary, as typically seen in emaraviruses. The proteins encoded by CYMaV shared the highest amino acid sequence similarity with those of the unclassified Karaka Okahu purepure emaravirus (KOPV), with 60.2% identity in the RNA-dependent RNA polymerase (RdRp), 44.4% in the glycoprotein precursor, and 46.9% in the nucleocapsid protein. A phylogenetic tree based on amino acid sequences of the RdRp revealed that CYMaV is most closely related to KOPV and clusters with ChMaV (chrysanthemum mosaic-associated virus, LC576445) and PCLSaV (pear chlorotic leaf spot-associated virus, MK602177) in one distinct clade. Transmission electron microscopy observation of negatively stained samples from C. brevicaudata revealed spherical virus-like particles (VLPs) approximately 100 nm in diameter. Five primers, specific for each viral RNA, were used to detect CYMaV in 11 symptomatic and two asymptomatic C. brevicaudata samples, but the results failed to show a consistent association of viral infection with symptoms. CYMaV can be considered a putative new member in the genus Emaravirus, and this marks the first report of an emaravirus found infecting C. brevicaudata plants.

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.

Complete genome sequence of seed-transmitted soybean yellow mottle mosaic virus from soybeans in Korea

ABSTRACT Soybean yellow mottle mosaic virus (SYMMV), a member of the genus Gammacarmovirus , remains poorly understood in terms of its transmission pathway. This study reveals the complete genome sequence of a seed-transmitted isolate, ST-HB56, contributing to the understanding of SYMMV’s ecological dynamics.

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.