Rice Yellow Mottle Virus Isolates Research Articles

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.

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.

Resistance of selected Oryza glaberrima landraces and their intra-specific breeding lines to Beninese Rice yellow mottle virus isolates

Rice yellow mottle virus (RYMV) is a widespread and damaging pathogen, endemic to Africa and affecting rice in lowland, irrigated and upland ecologies. Yield losses of 10–100% have been recorded, depending on rice genotypes, time of infection, cropping system, vector abundance and isolate pathogenicity. Control measures for this disease are based mainly on cultural practices and the use of varietal resistance. Specifically, Oryza glaberrima, the cultivated African rice species, has provided several of the known resistance alleles/genes. In this study, 160 O. glaberrima landraces, 55 of their intra-specific progenies and two controls - Tog5681 (resistant) and IR64 (susceptible) - were screened against five RYMV isolates collected from Northern Benin. Disease severity was measured on plants at 21 and 42 days after inoculation. Two cultivars - IRGC104019 and IRGC96787 (Tog5644) - from Tanzania and Nigeria respectively - and 16 intra-specific lines were identified as highly resistant to all five isolates. The genotyping of IRGC104019 and IRGC96787 revealed that they share allele rymv1-3, identified in Tog5681 (the resistant control) and that confers resistance, bringing the number of O. glaberrima accessions known to date to harbor this allele to 11. The importance of this finding and the level of resistance displayed by these two accessions strengthen the hypothesis that the African rice collection is a potential RYMV resistance donor. It is, therefore, necessary to further screen it for valorizing its usefulness in breeding programs.

English

Virus is the most constraint of rice production in West Africa. Genetic diversity of rice yellow mottle virus (RYMV) was assessed in two rice growing areas of Mali. Forty-three (43) infected rice leaf samples were collected from five locations within the Niger Office and Selingue Development Rural Office rice’s growing areas. The infected samples were confirmed by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using primers pair Prymv1 and Prymv2. A total of twenty-six RYMV isolates were obtained and classified into two genotypes A and B with Prymv1 and one genotype with Prymv2. Sequencing of the cDNA fragments with Prymv2 shared isolates into three distinct groups I, II and III. Most of the isolates were under Group I whereas isolates from the Selingue Development Rural Office area and Moussa-Were (Niger Office) area constituted respectively Groups II and III. This study provided baseline data for monitoring the genetic diversity of rice yellow mottle virus in the two rice-growing areas of Mali which could contribute to strategies development for the disease control.   Key words: Genetic diversity, reverse transcriptase polymerase chain reaction (RT-PCR), rice yellow mottle virus (RYMV), sequencing, Mali.

Evaluation of rice cultivars for resistance to rice yellow mottle virus

Rice yellow mottle virus (RYMV), which is only found in Africa, threatens rice farming on the continent. A local Oryza sativa cultivar collected from Burkina Faso (named BM24), was evaluated with that of well known highly resistant and tolerant cultivars. Firstly, three RYMV isolates were used to characterise the differential interaction within the cultivars. Secondly, disease kinetics of symptom expression and virus titer on leaves at 21 days after inoculation were assessed using the BF1 isolate. Thirdly, the allelic profile of O. sativa varieties using SSR marker RM101 located on chromosome 12 was also assessed. IR64 showed susceptibility to all isolates; while Tog5681 was resistant to all isolates. Ng122 overcame the resistance of Gigante, with mild leaf symptoms at 42 dpi. Azucena and BM24 had, therefore, different resistance level regarding the three isolates (Ng117b, Ng122 and Ng144). When infected with the isolate, BF1, BM24 and Azucena exhibited same resistance patterns in early growth stages with delayed of symptoms appearance, but BM24 outperformed Azucena at later stages. The virus content in the two accessions, at 14 days post inoculation, was statistically different with BM24, showing less virus compared to Azucena. However, the two accessions depicted an identical allelic profile at RM101 locus. Key words: Azucena, Burkina Faso, local variety, Oryza sativa

Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima.

A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV. The specificity of Tog5307 resistance was analyzed using 18 RYMV isolates. While three of them were able to infect Tog5307 very rapidly, resistance against the others was effective despite infection events attributed to resistance-breakdown or incomplete penetrance of the resistance. Segregation of resistance in an interspecific backcross population derived from a cross between Tog5307 and the susceptible Oryza sativa variety IR64 showed that resistance is dominant and is controlled by a single gene, named RYMV3. RYMV3 was mapped in an approximately 15-kb interval in which two candidate genes, coding for a putative transmembrane protein and a CC-NBS-LRR domain-containing protein, were annotated. Sequencing revealed non-synonymous polymorphisms between Tog5307 and the O. glaberrima susceptible accession CG14 in both candidate genes. An additional resistant O. glaberrima accession, Tog5672, was found to have the Tog5307 genotype for the CC-NBS-LRR gene but not for the putative transmembrane protein gene. Analysis of the cosegregation of Tog5672 resistance with the RYMV3 locus suggests that RYMV3 is also involved in Tog5672 resistance, thereby supporting the CC-NBS-LRR gene as the best candidate for RYMV3.

Mutations in Rice yellow mottle virus Polyprotein P2a Involved in RYMV2 Gene Resistance Breakdown.

Rice yellow mottle virus (RYMV) is one of the major diseases of rice in Africa. The high resistance of the Oryza glaberrima Tog7291 accession involves a null allele of the RYMV2 gene, whose ortholog in Arabidopsis, CPR5, is a transmembrane nucleoporin involved in effector-triggered immunity. To optimize field deployment of the RYMV2 gene and improve its durability, which is often a weak point in varietal resistance, we analyzed its efficiency toward RYMV isolates representing the genetic diversity of the virus and the molecular basis of resistance breakdown. Tog7291 resistance efficiency was highly variable depending on the isolate used, with infection rates ranging from 0 to 98% of plants. Back-inoculation experiments indicated that infection cases were not due to an incomplete resistance phenotype but to the emergence of resistance-breaking (RB) variants. Interestingly, the capacity of the virus to overcome Tog7291 resistance is associated with a polymorphism at amino-acid 49 of the VPg protein which also affects capacity to overcome the previously studied RYMV1 resistance gene. This polymorphism appeared to be a main determinant of the emergence of RB variants. It acts independently of the resistance gene and rather reflects inter-species adaptation with potential consequences for the durability of resistance. RB mutations were identified by full-length or partial sequencing of the RYMV genome in infected Tog7291 plants and were validated by directed mutagenesis of an infectious viral clone. We found that Tog7291 resistance breakdown involved mutations in the putative membrane anchor domain of the polyprotein P2a. Although the precise effect of these mutations on rice/RYMV interaction is still unknown, our results offer a new perspective for the understanding of RYMV2 mediated resistance mechanisms. Interestingly, in the susceptible IR64 variety, RB variants showed low infectivity and frequent reversion to the wild-type genotype, suggesting that Tog7291 resistance breakdown is associated with a major loss of viral fitness in normally susceptible O. sativa varieties. Despite the high frequency of resistance breakdown in controlled conditions, this loss of fitness is an encouraging element with regards to RYMV2 resistance durability.

Impact of eight isolates of Rice Yellow Mottle Virus (RYMV) from Gagnoa (Côte d’Ivoire) on rice (<i>Oryza</i> sp) cultivars production

Rice yellow mottle virus, of the genus Sobemovirus, causes a major disease in Africa especially in the lowland and irrigated rice ecologies. Yield losses due to the virus were estimated between 5-100% and depend on genotype. This study, conducted in a screen house, aimed at assessing the impact of eight RYMV isolates from a restrictive environment Gagnoa (Côte d’Ivoire) on 10 differential rice varieties. The plants were inoculated manually by rubbing the leaves from the leaf base to the tip with fingers moistened with inoculum. Virus content and percentage yield reduction of different rice cultivars have been assessed. Result showed that an important variability was observed in the reaction of different rice genotypes infected by different isolates of RYMV. In susceptible cultivars Bouaké 189, PNA647F4-56 and H232-44-1-1 virus content and yield reduction varied respectively from 0.08 to 0.264 and 20 to 95%. In resistant cultivars, Gigante, Lac 23, Morobérékan and Faro 11, virus content and yield reduction varied respectively from 0.03 to 0.188 and 5 to 17%. The lowest virus content and yield reduction was observed with the isolate 7 from upland rice. The significant difference in the interaction observed between the different genotypes of rice and isolates of RYMV suggested the existence of different strains of RYMV within a restrictive environment.© 2015 International Formulae Group. All rights reserved.Keywords: AfricaRice, Sobemovirus, aggressive, virus content, yield reduction, virulence

Analysis of Serological Variability and Hierarchical Distribution of Rice Yellow Mottle Sobemovirus Isolates in Northern Nigeria

A panel of four monoclonal antibodies (MAbs) was used to study the immunological profile of Rice yellow mottle virus (RYMV) genus Sobemovirus. Serological profiles of 35 representative isolates of RYMV from Borno, Gombe, Kaduna, Kano, Niger, Sokoto and Zamfara states in Northern Nigeria. All the RYMV isolates were classified into three major serogroups (SG1, SG2 and SG3) and further separated into six subgroups (Sg1a, Sg1b, Sg2a, Sg2b, Sg3a and Sg3b). The results demonstrate a significant serological variability among RYMV isolates in Northern Nigeria. The hierarchical analysis of the serological profiles data revealed high viral load in Kano, Kaduna and Gombe states, these show they are suitable locations for strategic RYMV diagnostic and field epidemiological studies

Analysis of Serological Variability and Hierarchical Distribution of Rice Yellow Mottle Sobemovirus Isolates in Northern Nigeria

A panel of four monoclonal antibodies (MAbs) was used to study the immunological profile of Rice yellow mottle virus (RYMV) genus Sobemovirus. Serological profiles of 35 representative isolates of RYMV from Borno, Gombe, Kaduna, Kano, Niger, Sokoto and Zamfara states in Northern Nigeria. All the RYMV isolates were classified into three major serogroups (SG1, SG2 and SG3) and further separated into six subgroups (Sg1a, Sg1b, Sg2a, Sg2b, Sg3a and Sg3b). The results demonstrate a significant serological variability among RYMV isolates in Northern Nigeria. The hierarchical analysis of the serological profiles data revealed high viral load in Kano, Kaduna and Gombe states, these show they are suitable locations for strategic RYMV diagnostic and field epidemiological studies

The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing

In plants RNA silencing is a host defense mechanism against viral infection, in which double-strand RNA is processed into 21-24-nt short interfering RNA (siRNA). Silencing spreads from cell to cell and systemically through a sequence-specific signal to limit the propagation of the virus. To counteract this defense mechanism, viruses encode suppressors of silencing. The P1 protein encoded by the rice yellow mottle virus (RYMV) displays suppression activity with variable efficiency, according to the isolates that they originated from. Here, we show that P1 proteins from two RYMV isolates displaying contrasting suppression strength reduced local silencing induced by single-strand and double-strand RNA in Nicotiana benthamiana leaves. This suppression was associated with a slight and a severe reduction in 21- and 24-nt siRNA accumulation, respectively. Unexpectedly, cell-to-cell movement and systemic propagation of silencing were enhanced in P1-expressing Nicotiana plants. When transgenically expressed in rice, P1 proteins induced specific deregulation of DCL4-dependent endogenous siRNA pathways, whereas the other endogenous pathways were not affected. As DCL4-dependent pathways play a key role in rice development, the expression of P1 viral proteins was associated with the same severe developmental defects in spikelets as in dcl4 mutants. Overall, our results demonstrate that a single viral protein displays multiple effects on both endogenous and exogenous silencing, not only in a suppressive but also in an enhancive manner. This suggests that P1 proteins play a key role in maintaining a subtle equilibrium between defense and counter-defense mechanisms, to insure efficient virus multiplication and the preservation of host integrity.

Evidence of non-transmission of Rice yellow mottle virus through seeds of wild host species.

Rice yellow mottle virus (RYMV) is a widespread and damaging rice pathogen in Africa. The presence, infectivity and transmissibility of RYMV in seeds of six wild host species were investigated. In serological analyses by enzyme-linked immunosorbent assay (ELISA), each of four RYMV isolates used was detected in individual seeds of wild rice species (Oryza barthii and O. longistaminata) and the standard susceptible rice BG 90-2 (O. sativa). Virus detection in seeds of other host species (Dactyloctenium aegyptium, Eragrostis ciliaris, E. tenella and E. tremula) was unsuccessful in single seeds but positive reactions were obtained for extracts made from several seeds. RYMV was infectious in freshly-harvested seed extracts whatever the plant species or the virus isolate. However, most infectivity was lost in dried seeds, possibly due to virus inactivation following dehydration of the seeds. Despite the presence of RYMV in dry seeds, no evidence was obtained for transmission of the virus through seeds of rice or wild host species, whatever the plant species-virus isolate combination. RYMV is unlikely to be transmitted through seeds of its host species and, therefore, virus dissemination or epidemics of rice yellow mottle do not originate from infected seeds.

Evaluation and potential of Double Immunodifusion Gel Assay for serological characterization of rice yellow mottle virus isolates in West Africa

Rice yellow mottle virus is not only highly infectious to rice plants but also a highly variable pathogen. Forty-two isolates were obtained from five countries in West Africa. Utilizing 26 polyclonal antisera, the serological diversity of these isolates was determined using Double Immunodifusion Gel Assay. All the antisera were classified into three serogroups, PSg-1a, PSg-1b and PSg-2. Antisera belonging to PSg- 1a, PSg-1b andPSg-2 serogroups had diagnostic potential of 86-90%, 69-76% and 52-64%, respectively, for the 42 RYMV isolates analyzed using a dilution of up 1:200. Moreover, all isolates were separated into three serogroups, Sg-1a, Sg-1b and Sg-2. The first two groups are widely distributed across West Africa. The high diagnostic potential exhibited by the 26 RYMV polyclonal antisera indicates that Double Immunodifusion Gel Assay is useful and reliable for diagnosing RYMV. As the use of ELISA (Enzyme- Linked Immunosorbent Assay) is expensive and unavailable in most of the national agricultural research institute in West Africa, they can adopt Double Immunodifusion Gel Assay for the identification and characterization of Rice yellow mottle virus isolates. This is the first phylogenetic analysis report on the use of Double Immunodifusion Gel Assay to characterize Rice yellow mottle virus isolates in West Africa. Key words: Rice yellow mottle virus, rice, double immunodifusion gel assay, phylogenetic tree, polyclonal antisera, serological diversity, West Africa

Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies.

Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle sobemovirus. The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.

Molecular epidemiology of the RNA satellite of Rice yellow mottle virus in Africa.

Satellite RNA was sought in 51 isolates of Rice yellow mottle virus (RYMV) representative of the geographical, molecular and pathogenic variability of the virus in Africa. Three-quarters of the isolates from cultivated rice and wild gramineaceous hosts supported a satellite RNA. The prevalence of RYMV isolates that were associated with a satellite differed among regions, being c. 100% in West and Central Africa and c. 36% in East Africa. The RYMV satellite showed a low diversity as only seven of the 220 sequenced positions were variable. One insertion also occurred after serial host passages of the satellite. Two forms of the satellite differed by six substitutions forming three base pairs in one branch of the predicted RNA secondary structure. There was no evidence of intermediates between these two forms, but double-infection occurred. Each form had a specific geographical distribution: one occurred in Central Africa, the other elsewhere in Africa. There was no relation between the occurrence or the forms of the satellite and the phylogeny of the helper virus. The satellite was not involved in symptom modulation or ability to break host-plant resistances to the disease.

First Report and Characterization of Rice yellow mottle virus in Central Africa.

Rice yellow mottle virus (RYMV) of the genus Sobemovirus is the main virus infecting rice (Oryza sativa) in Africa. First reported in Kenya (East Africa), RYMV was later found in most countries of East and West Africa where rice is grown, and in Madagascar in the Indian Ocean. In Central Africa however, the disease had never been reported in rice fields. Ninety-eight field samples with typical yellow mottle symptoms from cultivated rice and two wild rice species (Oryza longistaminata and O. barthii) were collected in the Soudano-Sahelian zones, in the north of Cameroon and the south of Chad (Central Africa) in September 2000. RYMV was detected by ELISA with polyclonal antisera (1) in all samples. All virus isolates were also mechanically transmitted to rice cv. BG 90-2, which is highly susceptible to RYMV. Tests with monoclonal antibodies showed that most isolates from Central Africa were of the SI serotype, which is widespread in the Soudano-Sahelian zones of West Africa (1). The coat protein gene of 7 isolates was amplified by RT-PCR and the expected 720 bp fragment was obtained. Resulting sequences (AJ306735, AJ317949, AJ317950, AJ317951, AJ317952, AJ317953, AJ317954) shared over 95% sequence identity. They were compared to a set of sequences of RYMV isolates from cultivated rice of different geographical origins (2). Phylogenetic analyses by maximum parsimony (PAUP 4) showed that isolates from Central Africa belonged to a monophyletic group, a sister group of West African isolates from the Soudano-Sahelian zones, further supporting the geographic basis of RYMV diversity (2). RYMV incidence was generally less than 10% but reached 20% in some irrigated plots in the two countries.

Molecular variability of geographically distinct isolates of Rice yellow mottle virus in Africa.

The coat protein gene (ORF4) and the 3' untranslated region of a sample of 40 isolates of Rice yellow mottle virus (RYMV), 32 from West Africa and 8 from East Africa, have been sequenced. Five major strains were differentiated, three from West Africa (S1, S2, S3) and two from East Africa (S4, S5), with a spatial overlap of the strains within each of these two regions. Nucleotide and amino-acid divergence between strains was up to 11%. Although more isolates from West African were sequenced, variability was twofold lower than among East African isolates. Variability in ORF4 and in ORF2 coincided. Within strain and within isolate variations in nucleotide sequences were low. Bipartite nuclear targeting motif, Ca2+ binding sites and at least two stretches of amino-acids were conserved among the 40 RYMV isolates and the other sobemoviruses. Variants associating sequence motifs characteristic of different strains have been found, possibly resulting from recombination events. Differences in pathogenicity among isolates were associated with changes of amino-acids in the bipartite nuclear targeting motif of the R domain of the capsid protein, and around conserved positions 151-154 of the S domain. We hypothesise that the observed pattern of variation of RYMV reflects the effect of spatial isolation between East and West Africa coupled with adaptive changes associated to the original virus reservoirs of the different strains.

Characterization of rice yellow mottle virus isolates in Sudano-Sahelian areas.

The use of a panel of polyclonal antisera and monoclonal antibodies (MAbs) raised against West African isolates of rice yellow mottle virus (RYMV) in ELISA resulted in separation of 73 RYMV isolates into three distinct serogroups. Using a set of differential rice varieties, the serogroups could be correlated to two RYMV pathotypes. A relationship was found between serological properties of the RYMV isolates and their probable ecological origin. It was concluded that RYMV isolates originating in closely related agroecological zones displayed variability in coat protein and pathogenicity. This should be taken into account in developing tolerant or resistant rice varieties.

Serological relationships among rice yellow mottle virus isolates

SummarySerological studies on five isolates of RYMV collected from the Ivory Coast (IC), Sierra‐Leone (SL), Niger (Nr), Kenya (K) and Nigeria (N) indicated that these isolates are serologically related. Gel double diffusion and direct ELISA tests showed that the five isolates could be arranged into three serological groups here designated RYMV‐N, SL‐IC and K‐NR. However, the ISEM studies did not reveal any clear grouping of the heterologous isolates tested.

Occurrence of rice yellow mottle virus resistance breaking isolates in lowland catchment zones of Uganda

Rice (Oryza spp; 2n=24.) production in Uganda and Africa in general, is seriously threatened by the Rice yellow mottle virus disease (RYMVD), a disease caused by Rice yellow mottle virus (RYMV) within the genus Sobemovirus; family Sobemoviridae. This study investigated the existence and distribution of resistance-breaking RYMV pathotype in the three major lowland rice catchment areas in Uganda. Four known rice accessions resistant to Rice yellow mottle virus (RYMV) namely; Gigante, Tog5672, Tog5674 and Tog5681, carrying resistant allele’s rymv1-2, rymv1-4 & RYMV3, rymv1-5 and rymv1-3, respectively, were tested for their response to different RYMV isolates. The isolates were collected from three major lowland rice catchment areas of Doho, Kibimba, and Olweny in Uganda. Out of 100 leaf samples collected from the field and assayed for RYMV and confirmed to be positive using RT-PCR, 83 isolates induced symptoms on IR64- the RYMV susceptible line. Seventy-seven (92.8%) isolates were able to overcome resistance in at least one of the four differential rice accessions, as confirmed by the presence of RYMV symptoms; while 6 (7.2%) isolates were asymptomatic. Variation in time (days) for symptom development post-inoculation (dpi) and AUDPC were observed. Symptoms appeared within 5-7 days on IR64; while it took on average 11, 18, 36, and 18 days to appear on Gigante, Tog5672, Tog5674 and Tog5681, respectively. The highest AUDPC was observed on IR64 (254.7); while the lowest was observed on Tog5681 (74.1). Two major patho-groups were observed; those that broke down resistance in Gigante only (25.3%) and Gigante & Tog5672 (33.7%). Five isolates from Doho (Budaka & Bugiri districts) and Kibimba (Butaleja district) catchment areas broke down RYMV resistance in three accessions i.e. (Tog5681, Gigante & Tog5672) and (Tog5674, Gigante & Tog5672), respectively. Resistance breaking isolates were confirmed in all the three sampled catchment zones, however, Doho and Kibimba had some unique isolates that broke down resistance in accessions carrying resistance allele rymv 1-3 and rymv1-5 in addition to rymv1-2. Results from this study showed that RYMV isolates in Uganda can break down resistance conferred by the rymv1-2 resistance gene allele. However, accessions Tog5681 and Tog5674 seem to hold stable RYMV resistance and, thus are recommended for RYMV breeding.