First report of Rice stripe necrosis virus infecting rice in Sierra Leone

While Rice stripe necrosis virus (RSNV, Benyvirus, Benyviridae) has been reported on rice plants on two continents, little is known about the diversity of this multipartite virus which is transmitted by the plasmodiophorid protist Polymyxa graminis. First identified in 1983 in the Côte d´Ivoire (Fauquet & Thouvenel, 1983), the disease had previously been observed in Sierra Leone without formal identification of the causal agent (Buddenhagen, pers. comm.). Later, the virus was reported in South and Central America (Colombia, Ecuador, Panama and Brazil) causing up to 40% yield losses (Morales et al., 1999). Recently, RSNV was identified for the first time in several African countries including Burkina Faso (Sérémé et al., 2014), Benin (Oludare et al., 2015) and Mali (Decroës et al., 2017) suggesting a re-emergence of the virus in Africa.In 2019, symptoms of leaf-crinkling and stripe necrosis were observed on a rice plant from the Bo District in Sierra Leone (Fig. 1). Leaf samples were analysed by serological and molecular methods to confirm the presence of RSNV in Sierra Leone. RSNV was detected by plate-trapped antibody (PTA)- ELISA using a polyclonal antiserum against RSNV (Fauquet & Thouvenel, 1983).The presence of the virus was confirmed after total RNA extraction using 0.05 g of leaves and the RNeasy Plant Mini Kit (Qiagen) and RT-PCR amplification (10 U/μl M-MLV-reverse transcriptase, Promega; 10 U/μl Dynazyme, Finnzyme) as described previously (Sérémé et al., 2014, Oludare et al., 2015) with primers RSNV1-2901F 5′-TGAATTTGGTGCTCTCTTG-3′ / RSNV1-3827R 5′-TGTGGCGTTTCCAGACCTAAA-3´ and RSNV2-5´ 5´-TATCACTACTGACGAATTCCACCTAC-3´ / RSNV2-1223R 5´-AATCTGCGGCCTGTTTTGTA-3´. Specific amplicons, 926 and 1241 nt in length, were generated corresponding to sequences in the helicase domain and the coat protein (CP) genes on RSNV RNA 1 and RNA 2, respectively. The amplicons were sequenced directly and the sequences deposited in GenBank (Accession Nos. MN750254 and MN750255, respectively).The helicase sequence obtained from the Sierra Leone RSNV isolate showed 1.8-7.3% genetic distance with those from South America (EU099844.3, MG792544, MG792545, MG792546) and only 1.4-2.2% with those from Africa (KP099623, MF115599, MF115600, MF115601, MF115602, MF115603, MK170452, MK170453). The phylogenetic analysis based on the helicase domain included the sequence obtained from the Sierra Leone within a cluster represented by RSNV from South America and West Africa (Fig. 2a). In contrast, the CP sequence from the Sierra Leone RSNV isolate revealed an unexpected genetic differentiation as compared to all the other sequences from South America (5.6%; NC_038774) or Africa (5.2-6.5%; LK023710, MF115604, MF115605, MF115606, MF115607, MF115608, MK170454, MK170455). Interestingly, the CP sequence from Sierra Leone is located at a basal position in the phylogeny (Fig. 2b).To our knowledge, this is the first confirmed report of RSNV in Sierra Leone. Further studies are needed to assess the molecular and biological diversity of RSNV, the spatial distribution and the incidence of this re-emerging rice disease in Africa.Fil: Tucker, M. J.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Giovani Celli, Marcos Giovani. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Conteh, A. B.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Taylor, D. R.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Hebrard, Andrés. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; FranciaFil: Poulicard, N.. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; Franci

Historical Contingencies Modulate the Adaptability of Rice Yellow Mottle Virus

The rymv1-2 and rymv1-3 alleles of the RYMV1 resistance to Rice yellow mottle virus (RYMV), coded by an eIF(iso)4G1 gene, occur in a few cultivars of the Asiatic (Oryza sativa) and African (O. glaberrima) rice species, respectively. The most salient feature of the resistance breaking (RB) process is the converse genetic barrier to rymv1-2 and rymv1-3 resistance breakdown. This specificity is modulated by the amino acid (glutamic acid vs. threonine) at codon 49 of the Viral Protein genome-linked (VPg), a position which is adjacent to the virulence codons 48 and 52. Isolates with a glutamic acid (E) do not overcome rymv1-3 whereas those with a threonine (T) rarely overcome rymv1-2. We found that isolates with T49 had a strong selective advantage over isolates with E49 in O. glaberrima susceptible cultivars. This explains the fixation of the mutation T49 during RYMV evolution and accounts for the diversifying selection estimated at codon 49. Better adapted to O. glaberrima, isolates with T49 are also more prone than isolates with E49 to fix rymv1-3 RB mutations at codon 52 in resistant O. glaberrima cultivars. However, subsequent genetic constraints impaired the ability of isolates with T49 to fix rymv1-2 RB mutations at codons 48 and 52 in resistant O. sativa cultivars. The origin and role of the amino acid at codon 49 of the VPg exemplifies the importance of historical contingencies in the ability of RYMV to overcome RYMV1 resistance

Rice yellow mottle virus diversification impact on the genetic control of RYMV

Abstract Rice yellow mottle is the most important virus disease of rice in Africa. The disease is a major constraint due to its wide geographical distribution and the extent of yield losses it induces. The role of the causal agent Rice yellow mottle virus (RYMV) in virus-host interactions was studied in relation to the current knowledge of rice genetics. Most cultivated rice varieties are susceptible to the virus, but a monogenic and recessive high resistance has been found in two varieties of Oryza sativa and a few varieties of O. glaberrima. The high resistance RYMV1 encodes an eukaryotic translation initiation factor eIF(iso)4G and at least five alleles have been identified. However, studies on virus diversity indicated the occurrence of virus pathotypes capable of overcoming the high resistance gene at rates up to 40%. Such pathotypes could also be generated experimentally. At molecular level, RYMV pathogenicity was associated with mutations in the viral protein genome-linked (VPg), which interacts with the eIF(iso)4G factor. Patterns of the breakdown of alleles rymv1-2 in O. sativa and rymv1-3 in O. glaberrima cv. Tog5681 differed greatly and were modulated by virus adaptation features found in the VPg. The specificity of virus-host interactions between RYMV and rice suggests that the deployment of resistant varieties should take into account a good knowledge of virus populations

Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa

Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T′, that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T′, molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa

Molecular basis of virus resistance mediated by host factors required for the infectious cycle

National audienceln recent year, one of the most interesting results that has enabled plant virology to make a significant step forward is the identification of components of the translation initiation complex as essential host factors required for RNA virus multiplication. Although translation initiation factors were demonstrated to be highly conserved determinants of plant resistance to viruses, preliminary data indicate that the molecular basis underlying translation initiation factors-mediated resistance are highly variable. ln parallel, several recessive resistance genes against viruses were identified and demonstrated to be distinct from translation initiation factors. These genes are therefore very good candidates for the discovery of new susceptibility factors. ln this context, the MOVle project airns at (i) the characterization of mechanisms underlying molecular specificity of translation initiation factors mediated resistance, (ii) the study of the potential role of translation initiation factors in RNA virus resistance in economically important crops such as grapevine, and (iii) the identification of new host factors required for viral infection The project is likely to provide fundamental insights into the molecular basis of plant-virus interactions and to greatly facilitate the exploitation of host factors required for the viral cycle as targets to improve plant resistance to viruses