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

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.

Enhancing Crop Resilience: Insights from Labdane-Related Diterpenoid Phytoalexin Research in Rice (Oryza sativa L.)

Rice (Oryza sativa L.), as one of the most significant food crops worldwide, holds paramount importance for global food security. Throughout its extensive evolutionary journey, rice has evolved a diverse array of defense mechanisms to fend off pest and disease infestations. Notably, labdane-related diterpenoid phytoalexins play a crucial role in aiding rice in its response to both biotic and abiotic stresses. This article provides a comprehensive review of the research advancements pertaining to the chemical structures, biological activities, and biosynthetic pathways, as well as the molecular regulatory mechanisms, underlying labdane-related diterpenoid phytoalexins discovered in rice. This insight into the molecular regulation of labdane-related diterpenoid phytoalexin biosynthesis offers valuable perspectives for future research aimed at improving crop resilience and productivity.

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 in RYMV susceptibility. 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.

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.

Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.

Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies

Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.

A Review of Vector-Borne Rice Viruses

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.