Survey on Incidences and Severity of Rice Yellow Mottle Virus Disease in Eastern Uganda

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.

Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.

Assessment of Korean rice lines for their reaction to rice yellow mottle virus in Ghana

Rice yellow mottle virus (RYMV) is the most damaging viral disease of rice in Africa and can cause yield losses of up to 100%. The objective of this study was to characterize newly introduced rice lines from Korea into Ghana for their reaction to RYMV infection. One hundred and seventy-two rice lines from Korea were screened for their level of resistance RYMV in a screen house at Fumesua, Ghana. Four checks consisting of two highly resistant lines (Tog7291 and Gigante with rymv1-2 (resistant gene1-allele2) and rymv2 (resistant gene2) respectively), a moderately resistant line (CRI-Amankwatia) and a susceptible cultivar Jasmine 85 were used. The experiment was carried out in a 4 x 44 lattice design with four replicates. Screening for RYMV resistance was conducted by visual symptom scoring and virus-assessment through serology using enzyme linked immunosorbent assay (ELISA) test. Disease incidence and severity were assessed from 2 to 42 dpi. Data for disease severity and incidence were transformed (Log x+1) for ANOVA.

Five lines (8261112, 8261119, 8261133, 8261588, and 8261634) were identified to be highly resistant to the disease just like Tog7291 and Gigante. The study also revealed 24 lines that were resistant but not grouping with Tog7291 and Gigante, whereas 100 moderately resistant lines clustered with the moderately resistance check CRI-Amankwatia in a distinct group. Forty-three (43) susceptible lines were identified with the susceptible check Jasmine 85 falling in this group. No highly susceptible line was identified. The newly idenfied resistant genotypes can be used by breeders to develop RYMV resistant varieties.

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.

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.

Emergence of rice yellow mottle virus in eastern Uganda: Recent and singular interplay between strains in East Africa and in Madagascar

Epidemics of rice yellow mottle virus (RYMV) have developed recently in eastern Uganda, close to Lake Victoria in East Africa. Unexpectedly, all isolates from the affected area belonged to a single strain (named S4ug), a strain that is different from the S4lv strain that has been prevalent in the Lake Victoria basin for the past five decades. Interestingly, the S4ug strain is most closely related at the genomic level (except ORF1) to the strain present in Madagascar (S4mg), 2000km away. The minor parent of the S4mg recombinant strain could not be detected. Molecular clock dating analysis indicated that the singular sequence of events - that associated the emergence of a new strain (S4ug), a modular recombination between closely related strains (S4mg and S4ug) and a long distance transmission (S4mg) - occurred recently, within the past few decades. This finding is at variance with the process of gradual strain dispersal and diversification over two centuries throughout Africa that was previously established.