Abstract
The Rice yellow mottle virus (RYMV) causes severe yield losses in rice fields in Africa and became a model in plant virus molecular epidemiology. However, the patterns disease incidence and viral diversity of small geographical scale were much less investigated to date in spite of their critical importance for the deployment of efficient control methods. Indeed, both identification of disease hotspot and genetic characterization of circulating viral isolates are critical for information-based deployment of crop resistant varieties.We performed a five-years monitoring of RYMV incidence in six sites in western Burkina Faso (three georgraphical zones each consisting of one irrigated area and one neighboring rainfed lowland site) and characterized RYMV genetic diversity (Coat Protein Sanger sequencing) over time in one of the site identified as a disease hotspot.In accordance with symptom observations, we found that the repartition of yellow mottle disease is not affected by rice growing system (irrigated vs rainfed lowland rice production) but instead highly site-specific, with the identification of one disease hotspot. Within-field disease aggregation is evidenced statistically, as expected because mechanical transmission is a major transmission mode for RYMV.Five-years monitoring of RYMV genetic diversity in the disease hotspot reveals a high viral diversity, with the co-occurrence of four genetic lineages at small geographic scale. The relative frequencies of these four genetic groups fluctuates over the period (2015-2019).Our data consequently suggest that high viral incidence and high viral diversity promotes rapid evolution of viral population, with modifications in the relative frequencies of each genetic lineage. However, the drivers of this rapid evolution remain un-identified in this study. We hypothesize that the fluctuations of viral genetic compositions are caused by modifications in the frequency of rice cultivars grown locally. The perspectives consequently include experimental inoculations of local rice cultivars by the different RYMV genetic lineages to get fitness estimations for each viral lineage in controlled settings.