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

Abstract

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.

Pathogenic Variation and Occurrence of Multiple Resistance-Breaking <i>Rice yellow mottle virus</i> Strains in Tanzania

“…Several highly resistant varieties with known genes of resistant to RYMV have been identified that include rice cultivars Gigante (rymv1-2) [3], Tog12387 (rymv1-3) [6], Tog5681 (rymv1-3) [4], Tog5438 (rymv1.4), Tog5672 (rymv1-4+rymv2) and Tog5674 (rymv1-5) [7]. Resistance conferred by RYMV2 and RYMV3 genes have currently been identified on Oryza glaberrima Tog7291 and Tog5307, respectively [2] [8]. Partial genetic resistance quantitative trait locus (QTLs) which is polygenic has been reported to be widespread in Oryza sativa subsp.…”

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

“…In West-Central Africa, we identified that the hypervirulent pathotype T9 is able to overcome all of the resistance alleles of RYMV1, even the most efficient ones, rymv1-3 and rymv1-5. Isolates of this pathotype are able to infect sources of resistance carrying the RYMV2 and RYMV3 resistance alleles (Pidon et al 2017;Pinel-Galzi et al 2016). Preliminary results also suggested resistance breakdown of the Tog5672 accession (carrying both rymv1-4 and RYMV2).…”

“…In our study, we assessed the first step of the viral adaptation to resistant accessions (i.e., the qualitative ability to overcome resistance). Different isolates that are able to overcome Tog7291 (RYMV2) show high or very low frequencies of RB events (Pinel-Galzi et al 2016). In future studies, measures of variability and frequency should be performed to quantify and predict the RB risks in real conditions.…”

“…In addition to these well-characterized isolates, four new isolates from the S1ca lineage were included in this study as candidates for the new pathotype. They belong to the collection from Niger that was described previously or were recently collected in Togo (Oludare et al 2016) and have previously been inoculated to the RYMV2-and RYMV3-resistant Tog7291 and Tog5307 accessions (Pidon et al 2017;Pinel-Galzi et al 2016).…”

Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice

“…In Arabidopsis, the CPR5 nucleoporin gene is involved in the regulation of defense mechanisms and senescence [15,16]. Considering the sequence homology and in line with previous studies [13,17], the candidate gene for RYMV2 is hereafter referred to as CPR5-1, although its nucleoporin role and involvement in defense mechanisms has yet to be documented in rice. More recently, a gene of the nucleotide binding domain and leucine-rich repeat gene (NLR) superfamily was pinpointed as the best candidate for the RYMV3 dominant resistance gene [18].…”