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Discovery of the first resistance gene to rice yellow mottle virus.

Rice yellow mottle virus (RYMV) was first identified in 1966 in Kenya. It has since been reported in most African countries where rice is grown. The disease is characterized by the appearance of mottling and then tissue death on the leaves. The fertility and development of seeds are affected, which causes considerable yield losses at harvest.

Transmission of RYMV occurs by way of insect vectors or by straightforward contact between plants. Prevention measures, like direct sowing or the burying of straw, have been implemented in order to limit the spread of the disease, but the real potential for reducing the impact of RYMV is to be found in the use of resistant varieties.

Variété de riz sensible au RYMV ou virus de la panachure jaune.

In certain rare traditional varieties of the Asian species of rice, Oryza sativa, and of the African variety, O. glaberrima, RYMV infection does not generally produce leaf symptoms, or have any impact on the harvest production. However, these varieties do not have the agronomic characteristics sought after for intensive irrigated cultivation or growing on low-lying land, where the disease provokes most damage. IRD geneticists have for several years been applying their research to the genetic bases of this resistance in order to facilitate its transfer to varieties that are agronomically useful yet susceptible to the virus with a view to optimizing their use.

Standard genetic studies first found evidence that resistance was controlled by a single recessive gene. Subsequent genetic mapping identified a fragment of chromosome 4 containing the resistance gene. Data from rice genome sequencing have been extremely useful for research on this fragment to find out if one gene rather than another could confer resistance to RYMV. Data from the literature indicates that gene eIF(iso)4G, involved in cellular RNA translation and named Rymv1, appeared to be the best candidate. Validation of the function of this resistance gene was performed by genetic transformation. For this, a line of resistant rice was modified by transgenically introducing the allele for susceptibility of this gene. The descendents of transformed plants that manifested restored susceptibility always showed the presence of the transgene.

Viruses are built with a small genome coding for a limited number of proteins (5 in the RYMVs). They therefore need their host’s proteins in order to accomplish each stage of their infection cycle. One of the proteins that the RYMV requires appears to be the eIF(iso)4G translation initiation factor coded by the Rymv1 gene which is probably involved in viral protein translation, but also perhaps in other processes such as the virus’s movement within the cell.

The research team discovered mutations of the gene they analysed in three different resistant varieties. These are distinct but are situated in the same domain of the gene in a patch on the surface favourable for interaction with the virus. In these varieties, the mutation does not appear to alter the protein’s role in its primary biological functions, but can prevent its interaction with the virus which is then blocked in one of the stages of its infectious cycle.

In parallel, a team of IRD virologists showed that it was possible to carry out laboratory selection of RYMV strains that break the gene’s resistance and that the process involved was determined by mutations in one of the viral proteins. The two approaches are now being combined in order to determine the molecular mechanisms of resistance or susceptibility on the basis of direct interactions between the rice protein and that of the virus. Understanding of these mechanisms will give clues as to the best ways of making long-term use of this resistance gene.

Another strategy developed by the IRD for combating this virus involves introducing part of the viral genes into the plant genome by transgenesis, as has been done in other plant/virus interactions, with the aim of inducing resistance to RYMV. The results show that the transgenic plants have only partial resistance, and for only a short time, and can even end up with a heightened susceptibility. In the particular case of the rice/RYMV interaction, the strategy of introducing a viral gene by transgenic techniques does not bring any advantages compared with the use of natural resistance.

This research can find applications in ways of improving rice production in countries hit by RYMV. Already, the IRD has transferred the gene Rymv1, by crossing, into some agronomically important varieties. The corresponding lineages have been given to various national (Ivory Coast, Senegal, Madagascar) and international research institutions such as the African Rice Centre (Warda, Benin) for them to use in variety selection programmes.

Aude Sonneville
Translation : Nicholas Flay
Glossaire :
(1) Messenger RNA: a ribonucleic acid transcribed from the DNA of a gene and which serves as a model for translation of a protein.

(2) Allele: each of the different possible forms of the same gene.

Marie Guillaume | alfa
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