Rice Tungro Bacilliform Virus Research Articles

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>

P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing.

Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.

Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.

Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.

The relationship between vector insect populations, natural enemies, and disease incidence of tungro virus during wet and dry seasons

Abstract. Hutasoit RT, Jihad M, Listihani L, Selangga DGW. 2023. The relationship between vector insect populations, natural enemies, and disease incidence of tungro virus during wet and dry seasons. Biodiversitas 24: 4001-4007. Tungro virus is one of the most prevalent viruses affecting rice plants. The tungro virus is frequently found in rice plantations because its green planthopper vector is always present. This study aimed to determine the relationship between the population density of green planthoppers and its natural enemies with the incidence of tungro disease during the rainy and dry seasons in Lanrang, Sidenreng Rappang, South Sulawesi. The research method employed was field monitoring of the population density of green planthoppers, natural enemies, and the incidence of tungro disease. The presence of the tungro virus was confirmed by the molecular method using RTSV and RTBV-specific primers. The results showed three types of tungro vector insects: Nephotettix virescens, Nephotettix nigropictus, and Recilia dorsalis. Nephotettix virescens was the dominant vector insect, with the highest population in March and August of 101 and 51 individuals, respectively. During the dry season, the high population of the three vector insects in August was followed by a high incidence of tungro disease in September, reaching 29.38%. Symptoms of yellow leaves have been confirmed by molecular methods, which indicated that the infection was caused by RTSV and RTBV, as evidenced by the amplification of DNA bands measuring 787 bp and 1400 bp. Data on the population of vector insects and the incidence of tungro disease indicated the importance of determining the ideal time to plant to avoid the plant's susceptible phase during the peak vector population between March and August. The dominant natural enemies found during the observations included Araneus inustus, Tetragnatha maxillosa, Agriocnemis pygmaea, and Menochilus sexmaculatus. Increasing the population of natural enemies could suppress the population of vector insects.

First report of Tomato spotted wilt orthotospovirus infecting agapanthus (Agapanthus praecox) in South Africa.

Agapanthus praecox Willd. is an ornamental flowering plant that is indigenous to southern Africa and was reported to be a host of tomato spotted wilt orthotospovirus (TSWV) in Australia in 2000 (Wilson et al. 2000). Tomato spotted wilt orthotospovirus (TSWV) belonging to the genus Orthotospovirus of the family Tospoviridae is a single-stranded negative sense RNA virus known to cause disease symptoms in many crops and ornamental plant species. This virus is in the top 10 of most economically important plant viruses worldwide (Rybicki 2015; Scholthof et al. 2011). In May 2021, leaf material from three agapanthus (Agapanthus praecox) plants displaying chlorotic mottling, and yellow lesions (Supplementary material 1A) was collected in Mbombela, South Africa. One gram of symptomatic leaf material was used for total RNA extraction from each of the three samples using a CTAB extraction protocol (Ruiz-García et al. 2019). The three RNA extracts were pooled, and a sequencing library was constructed using the Ion Total RNA-Seq Kit v2.0 and RiboMinus™ Plant Kit for RNA-Seq (ThermoFisher Scientific) (Central Analytical Facility (CAF), Stellenbosch University). The RNA library was sequenced on an Ion Torrent Proton Instrument (CAF). A total of 34,392,939 single-end reads were obtained. Data was trimmed for quality with Trimmomatic (CROP:250, MINLEN:50). De novo assembly was performed on the remaining 32,281,645 trimmed reads (average readlength: 100 nt, range: 50-250 nt) using SPAdes 3.13.0 and resulted in 4,788 contigs. BLASTn analysis identified viral contigs longer than 1,000 nucleotides (nts) with high nucleotide (nt) identity to TSWV (6 contigs), as well as to the newly discovered viruses, agapanthus tungro virus (AgTV) (1 contig), and agapanthus velarivirus (AgVV) (4 contigs) (Read et al 2021). Read mapping was performed against the relevant reference sequence with the highest nt identity to the contigs. For TSWV, 4995, 21221 and 14574 reads mapped to segment L (KY250488), M (KY250489) and S (KY250490) of isolate LK-1, respectively resulting in 99.97%, 100.00% and 99.97% genome coverage of the reference accessions. The nt identity between the reference accessions and the consensus sequences generated (OP921761-OP921763) were 97.26%, 97.64% and 97.82% for segment L, M and S. The presence of TSWV was confirmed in the HTS sample using an RT-PCR assay (primers L1 and L2) targeting the L segment of TSWV (Mumford et al. 1994). In July 2022, additional leaf samples displaying symptoms of chlorotic mottling, streaking, and ringspots were collected from 31 symptomatic and 3 asymptomatic agapanthus plants in public gardens in Stellenbosch, South Africa. Using the above-mentioned RT-PCR assay, 13 of the symptomatic samples tested positive for TSWV. All six plants displaying ring spot symptoms (Supplementary material 1B) were infected with TSWV. However, plants that displayed yellow streaking (five samples) and chlorotic mottling (two samples) (Supplementary material 1C-D) were also positive for TSWV which could be due to the presence of other viruses, plant growth stage, infection time or just variable symptom expression in a single host species as reported previously (Sherwood et al. 2003). The 275 bp RT-PCR amplicons of the HTS sample and three additional positive samples were validated with bidirectional Sanger sequencing (CAF) and had 96% identity to accession KY250488. The pairwise nt identity between amplicons was 98.55-100%. This is the first report of TSWV infecting agapanthus in South Africa. This study contributes information towards the distribution and incidence of TSWV and highlights the need for nurseries to screen plant material before propagation.

Bioecology and Management of Major Insect Pests of Rice in West Bengal

West Bengal is considered a large producer state of rice in India with an output of nearly 55.48% of total crop production of Bengal. In West Bengal, rice has grown in three different cropping seasons such as Aus (autumn rice), Aman (winter rice) and Boro (summer rice), contributing about 20.69% to the total net State Domestic Product (SDP). Rice production in West Bengal hampered by many biotic stresses mostly by stem borers [Scirphophaga incertulas (Walker, 1863), Sesamia inference (Walker, 1856), Chilo polychrysus (Meyrick, 1932), Chilo suppressalis(Meyrick, 1863)] leaf folder [Cnaphalocrocis medinalis (Guenee, 1854)], plant hoppers [Nilaparvata lugens(Stal, 1854), Sogatella furcifera (Horvath, 1899)], leaf hoppers [Nephotettix virescens (Distant, 1908), Nephotettix nigropictus (Stal, 1870)], rice hispa [Dicladispa armigera (Olivier, 1808)], rice bugs [Leptocorisa acuta (Thunberg, 1783), Leptocorisa oratorius (Fabricius, 1794), Brevennia rehi (Lindinger, 1943)], gall midge [Orseolia oryzae (Wood-Mason, 1889)], etc. Demographic parameter has shown that rice pests are greatly affecting rice host either caused directly by creating dead heart (DH), hopperburn, onion leaf, silver shoot during different stages of harvesting or by indirectly transmitting grassy stunt virus (RGSV), rice ragged stunt virus (RRSV), rice tungro viruses (RTV), rice tungro bacilliform virus (RTBV) etc. resulting 9.5% production loss. For minimize the infestation farmers use different rice varieties which provide resistance effect in pest population. For controlling rice pest population farmers mostly use chemical insecticide [e.g. fipronil, acephate, fipronil, monocrotophos] which exhibit good results against rice pests. Beside those other techniques including using biological and biochemical pesticides [neem oil, karanj oil, mahua oil, conidial suspension of M. anisopliae], pheromones [(Z)-11-hexadecinal, (Z)-9-hexadecenal], allomones [5: 1 mixture of 2-(E)-octenyl acetate and octanol 3-octenal], cultutal methods [synchronized planting, using of trap crop etc.] are effective for controlling rice pests. The population ecology based sustainable management of such pest species will support E 3 strategy [Ecosystem service-based ecological engineering for ecological pest management (ESS-EE-EPM)] of pest management for successful cultivation of rice in the near future.

Endogenous like sequence Rice Tungro Bacilliform Virus (RTBV) fragments in the local rice genome and its role in controlling tungro disease

Tungro disease is one of the important diseases in rice plants because it can cause a large decrease in production. Therefore, tungro disease needs to be controlled in wise ways that ensure environmental sustainability. This can be done by using resistant varieties, while also preventing rice from resistance to the green leafhopper vector Nepothettix virescens, the death of natural enemies, resurgence and emergence of secondary pests which become the main pests. The territory of Indonesia has many very diverse rice germ plasm which its resistance properties can be used to control tungro disease. Resistance genes are an effective control machine especially when combined with other control strategies. One of the triggers for the resistance of rice varieties is eRTBV, which is a group of RTBV nucleotides in rice DNA. The purpose of this study was to detect the presence of the eRTBV piece in the rice genome and its role in controlling tungro disease. The method used wasthe insilico method by comparing the eRTBV found in local rice varieties with that found in Genbank. The results indicated that endogenous RTBV was joined into the rice genome at 1200 bp using the primer eRTBV-7. Nucleotide blast results showed that the similarity of endogenous Indonesian local rice RTBV to endogenous RTBV in the genbank ranged between 95% and 99%, then protein blast results showed that the eRTBV fragment of local rice varieties contained ORF 3 RTBV protein with a range of similarity to the genbank of 66.9% and 93.35%. The role of eRTBV is to produce the Isoleucine protein motif which produces a physical, chemical and biochemical resistance system capable of inhibiting the green leafhopper virus vector (Nepothettix virescens) and the growth and development of tungro disease, RTBV.

Salibu Rice Cultivation in Tungro Endemis Region

Salibu is modified ratoon rice which has advantages in economic and time-saving. Tungro disease is one of probable handicap for salibu to be controlled in their endemic area. Rice virus tungro disease is caused by Rice Tungro Bacilliform Virus (RTBV) and Rice Tungro Spherical Virus (RTSV) which are transmitted by leafhopper. The research goals are to know the growth of leafhopper population and the spread of the tungro disease in salibu and conventional rice farming system as well as their effect on yield. The research was conducted in split plot experiment and designed in a randomized block design. The main plot were 1) salibu system and 2) conventional system (non-salibu). The subplots were varieties 1) TN1 (sensitive variety), 2) Ciherang (commonly used by the farmer), and 3) Inpari 36 (tungro new resistant variety). The results revealed that the tungro attack rate, dry milled grain yield, and 1000 dry grain weight were significantly higher in conventional cultivation than salibu (P < 0.05). The number of leafhopper populations tended to be higher in salibu system than in conventional system. The number of natural enemies did not show a particular pattern related to green leafhopper's presence. The Shannon Wiener diversity index for natural enemies ranged from low to medium. Regarding to the results, salibu system is not recommended yet in the tungro endemic areas. Keywords: Salibu, rice tungro virus disease, green leafhopper, natural enemies

Molecular detection of rice tungro bacilliform virus (RTBV) on weed host in South Sulawesi

Rice tungro bacilliform Virus (RTBV) is one of the viruses that cause tungro disease in rice plants causing leaf yellow and plant stunting. Some weed species have also been described as potential hosts for RTBV in addition to rice. However, RTBV cannot be diagnosed in weeds only by looking at their morphological symptoms because weeds infected with RTBV do not show typical symptoms. Hence this research was conducted to detect the presence of RTBV molecularly on several weed hosts in rice fields in South Sulawesi. The polymerase Chain Reaction technique with coat protein gene-specific primers was used to detect RTBV. A total of 29 leaf samples consisting of 12 weed species collected from Sidrap, Pinrang, Maros, and Gowa were then extracted genomic DNA from the leaf samples for PCR analysis. The results of PCR analysis showed that weed samples that tested positive for RTBV were Panicum repens (Lawawoi/Sidrap), Echinochloa crusgalli (Lawawoi/Sidrap), Cyperus difformis (Lanrang/Sidrap), Echinochloa crusgalli (Palangga/Gowa), Fimbristilys miliacea (Lanrang/Sidrap), and Eleusine indica (Lawawoi/Sidrap) which were indicated by the presence of RTBV virus DNA fragments with 430 bp in length in all these weeds. Weeds infected by RTBV formed 2 clusters. The first cluster consisted of RTBV in P.repens and E.crusgalli from Lawawoi/Sidrap, RTBV in C.difformis and F.miliacea from Lanrang/Sidrap, and RTBV in E.indica from Palangga/Gowa. At the same time, the second cluster consisted of RTBV in E.indica from Lawawoi/Sidrap.

Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses

Rice tungro disease (RTD), caused by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causing a series of outbreaks over the years after being first reported in International Rice Research Institute (IRRI), Philippines, in 1963. One of the effective ways to combat viruses is through RNA silencing. microRNA is an important player in the RNA silencing mechanism. Genome sequences analysis shows RTBV-SP isolate (8 Kb) is composed of four open reading frames (ORF 1, ORF 2, ORF 3, and ORF 4), meanwhile, RTSV-SP (12 Kb) consists of one open reading frame encoded by seven different polyproteins (P1, CP1, CP2, CP3, NTP, Pro, and Rep). Therefore, this study investigated possible rice-encoded miRNAs targeted on RTBV and RTSV using in silico analysis. Five bioinformatics tools were employed using five different prediction algorithms: miRanda, RNA22, RNAhybrid, Tapirhybrid, and psRNATarget. The results revealed each RTBV and RTSV can be silenced by three potentially best candidate rice-encoded miRNA. For RTBV, osa-miR5510 (accession no. MIMAT0022143), osa-miR3980a-3p (accession no. MIMAT0019676), and osa-miR3980b-3p (accession no. MIMAT0019678) are being predicted by all five algorithms. Meanwhile, for RTSV, three miRNAs predicted are osa-miR414 (accession no. MIMAT0001330), osa-miR5505 (accession no. MIMAT00221138) and osa-miR167a-3p (accession no. MIMAT0006780). The predicted data provide useful material for developing RTBV and RTSV-resistant rice varieties.

Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3

BackgroundRice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing. ResultsUsing an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus. ConclusionThe finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.

Analysis and Optimal Control of the Tungro Virus Disease Spread Model in Rice Plants by Considering the Characteristics of the Virus, Roguing, and Pesticides

Farmers have an essential role in maintaining food security. One of the food crops that occupies a high position in Indonesia is rice. However, farmers often experience problems when cultivating rice plants, one of which is affected by the tungro virus disease in rice plants. The spread of the disease can be controlled by the roguing process and applying pesticides. In this study, an analysis of the model of the spread of tungro virus disease in rice plants took into account the characteristics of the rice tungro spherical virus (RTSV) and rice tungro bacilliform virus (RTBV), as well as control in the form of roguing processes and application of pesticides. The analysis carried out was in the form of dynamic analysis, sensitivity analysis, and optimal control. In addition, numerical simulations were also carried out to describe the results of the analysis. The results showed that the roguing process and the application of pesticides could control the spread of the tungro virus disease. The application is sufficient, at as much as 75%.

Performance of tungro disease resistant rice lines in Lanrang, South Sulawesi, Indonesia

Efforts to increase rice production and productivity nationally are still being disturbed by plant pest organisms. One of the diseases that have received serious attention is the tungro disease, which has the ability to attack rice plants in endemic areas. The purpose of this study was to investigate the resistance of several rice lines towards the Lanrang South Sulawesi tungro virus inoculum including morphological characteristics. This study was conducted at the Tungro Disease Research station from June to September 2020. A total of 14 lines were tested for resistance compared to the Tukad Petanu, Tukad Balian, Inpari 8 and Tukad Unda lines against the tungro disease. The rice lines were planted in the form of an augmented design consisting of five blocks. Each block contained three test lines and four comparison varieties, the lines were planted in plots (1 × 5) m, with 25 × 25 cm spacings. The results showed that the population of green leafhoppers at the age of 20 DAP and 30 DAP was found to range from 1 to 95 individuals per line/variety, while the incidence of tungro disease was 1.3 to 11.3% in the three test lines, namely STLRG17 15 LR 1, STLRG17 15 LR 2, and STLRG17 108 LR 1. The highest 1000 seed weight was found in the STLRG17 176 LR 2 line (25.1 g) and the lowest was STLRG17 51 LR 1 (17.6 g). The STLRG17 175 LR 1, STLRG17 176 LR, STLRG17 -175-LR-1, STLRG17-28-LR-1, and STLRG17-26-LR-2 5 lines had a fairly good and consistent appearance at 1000 seed weight, higher yield, productive tillers, plant height, and resistance to tungro disease compared to the comparison varieties.

Mathematical Model for Analyzing the Dynamics of Tungro Virus Disease in Rice: A Systematic Literature Review

One of the main obstacles in rice cultivation is the tungro virus disease caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). These viruses are transmitted by green leafhopper (Nephotettix virescens) vector, semi-persistently after sucking infected plants. Subsequently, the vectors migrate and suck susceptible plants, but they can be controlled chemically and biologically. Mathematical modeling is one of the tools that can be used to analyze the spread of disease in plants. A literature review was conducted regarding the mathematical model of the spread of tungro virus disease in rice plants with the data sourced from scholarly references available in the dimension database, Google Scholar, and Scopus in 2012–2021. The steps followed include conducting a literature analysis and examining the mathematical model of the transmission of tungro virus disease in rice plants to identify gaps for future research. The results show that since 2016, few studies have analyzed mathematical models of the spread of tungro virus disease in rice plants. This is evident from the data search results, which show that only four articles were acquired through the option of duplication and visualization using VOSviewer software.

Klasifikasi Penyakit Daun Padi Menggunakan Convolutional Neural Network

Rice (Oryza sativa) is a grain that comes in third place among all grains after corn and wheat. 80 percent of Indonesians eat rice as a staple diet, especially in Southeast Asian countries, but the International Rice Research Institute (IRRI) reports that farmers lose 37 percent of their rice crops each year owing to pests and illnesses. Based on this study, it is critical to investigate the detection of rice pests and illnesses. Using the Convolution Neural Network (CNN) technique, an automatic classification system to identify and predict plant illnesses has been developed. A study titled Classification of Rice Leaf Diseases was undertaken by the author. The CNN Algorithm is being used to help farmers learn how to combat rice leaf diseases. Bacterial leaf blight, Rice blast, and Rice tungro virus were among the rice leaf types classified in this study. There are 6000 datasets in all, with 80% of them being training data, 10% being validation data, and 10% being testing data. The accuracy of the results obtained for epochs 25, 50, 75, and 100 varies. The best training accuracy results come from epoch 100, which has a 98% accuracy rate, and testing using a confusion matrix has a 98% accuracy rate. In diagnosing rice leaf diseases, the Convolutional Neural Network (CNN) algorithm delivers great accuracy.

Coordinated Action of RTBV and RTSV Proteins Suppress Host RNA Silencing Machinery.

RNA silencing is as an adaptive immune response in plants that limits the accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing machinery for efficient replication and systemic spread in the host. The viruses encode proteins with the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro is a viral disease caused by a complex of two viruses and it provides an excellent system to understand the host and virus interactions during infection. It is known that Rice tungro bacilliform virus (RTBV) is the major determinant of the disease while Rice tungro spherical virus (RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway. The ORF-IV is a weak suppressor of the S-PTGS or stable silencing, but its suppression activity is augmented in the presence of specific RTSV proteins. Among these, RTBV ORF-IV and RTSV CP3 proteins interact with each other. This interaction may lead to the suppression of localized silencing as well as the spread of silencing in the host plants. The findings present a probable mechanistic glimpse of the requirement of the two viruses in enhancing tungro disease.

RTBV-Based VIGS Vector for Functional Genomics in Rice: Methodology, Advances, Challenges, and Future Implications.

The availability of protocols for virus-induced gene silencing (VIGS) in rice has opened up an important channel for the elucidation of gene functions in this important crop plant. Here, we present an updated protocol of a VIGS system based on Rice tungro bacilliform virus (RTBV) for gene silencing in rice. We present complete updated protocols for VIGS in rice, compare the system with other existing ones for monocots, identify some of the challenges faced by this system and discuss ways in which the vector could be improved for better silencing efficiency.

Molecular detection of tungro virus on mekongga and inpari 4 rice varieties in West Papua

Tungro disease is one of the important diseases in rice plants. One of the efforts to reduce the spread of tungro virus is to ensure the presence of the virus in the field. This is the first step to prevent the spread and control of tungro disease, especially in West Papua. One detection technique that can be done is molecular detection through PCR techniques. Rice samples detected were Mekongga and Inpari varieties taken from rice plants in West Papua. Total DNA of RTBV, one of the viruses that cause tungro disease, was extracted and amplified using DAF primers (5-GGAATTCCGGCCCTCAaA AACCTAGAAG-3) and DAR (5-GGGGGTACCCCCCTC CGATTTCCCATGTATG-3). The PCR RTBV results showed that the positive samples were infected with Rice tungro bacilliform virus (RTBV). This is indicated by amplification of DNA measuring ± 1400 bp which is the target size of the DAF and DAR primers. The results of this study are preliminary information that can be used as a basis for tungro control and recommendations for future cropping.

Telangana Vari 4 [IET 27869 (JGL 25958)] – Mid early duration, long slender, high yielding rice variety

Telangana Vari 4 was derived through pedigree method of breeding from a cross MTU 1010 and NLR 34449 with an aim to develop a high yielding short duration variety. It has long slender grains with mid early duration and suitable for both kharif and rabi seasons. It was evaluated during 2018 to 2020 in AICRIP trials and recorded +10.51, +63.73 and +21.18 percent increase in yield over national, zonal and local checks, respectively in overall mean. Telangana Vari 4 was found to have moderate resistance to neck blast and rice tungro virus. Telangana Vari 4 was recommended by Varietal Identification Committee (VIC) during 2021 and approved by Central Sub-Committee on Crop Standards, Notification and Release of Varieties for irrigated conditions in the states of Odisha, Bihar and Jharkhand (Zone III) and notified vide Gazette Publication No. S.O. 8 (E) Dated 24.12.2021.st

PENYAKIT TUNGRO PADA TANAMAN PADI (Oryza sativa) DI KECAMATAN TABA PENANJUNG : INSIDENSI PENYAKIT DAN DETEKSI VIRUS SECARA MOLEKULER

[TUNGRO DISEASE ON RICE PLANT (Oryza sativa) IN TABA PENANJUNG DISTRICT: DISEASE INCIDENCE AND MOLECULAR DETECTION OF VIRUSES]. Tungro is one of the important diseases of rice plants. Tungro disease caused by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). This research aims to obtain information on the spread of the disease, vector population, and molecular detection by polymerase chain reaction method. This research was conducted from December 2019 to April 2020 in rice fields in Taba Penanjung sub-district, Bengkulu Tengah district at ± 540 meters above sea level and virus detection in the Laboratory of Biotechnology and Genetics Department of Biology Faculty of Mathematics and Natural Sciences (MIPA) and Laboratory of Plant Protection, Agriculture Faculty, Bengkulu University. Data analysis used descriptive analysis. The results showed that the highest disease incidence on the seven weeks after planting (wap) is 1.7% and the highest population of the vector on the 7 wap with an average of 7.7 vector/100m2 in the village of Taba Penanjung. Detection of viruses with the PCR method with the specific primer DAF/DAR succeeded in amplification of DNA band measuring 1,400 bp. RTSV was not detected by RT- PCR using a specific primer or RTSV. The result of this detection shows that the symptoms of tungro on rice plants in the cultivation of Taba Penanjung district associated with RTBV infection. RTSV unable to detect can be caused by many factors in the detection process, including total RNA extraction, cDNA synthesis, DNA amplification, and DNA visualization of PCR products.