Résumé
Rice yellow mottle virus (RYMV) is one of the main constraints for rice cultivation intensification in Africa leading to high yield losses [1]. Six major strains, with a well defined geographical distribution, have been identified and were characterized by a large range of pathogenic properties (infection abilities and symptom intensities) on the rice and few wild grasses [2]. Originated from Tanzania, the genetic diversity is maximal in this area where three out of six of the major strains are circulating [3]. It has been demonstrated that some agricultural practices, as seedbed to field transplantation and elimination of the wild rice and grasses, can influence the RYMV prevalence in fields [2]. However, no study has analyzed at the field scale the consequences of these agro-ecological modifications on the diversity and the dynamics of the viral populations. Thus, the main objective of this work is to measure the effects of the rice cultivation intensification (changes of the cultural practices, from traditional to intensive cultivation) and the environmental variability (cultivated and wild host diversity) on the RYMV populations in order to better understand the emergence, the propagation and the maintenance of the viral strains at the field scale. For that, the RYMV prevalence was first investigated in Tanzania in an “intensive” rice plantation and some surrounding “traditional” farms, taking in account the cultivation mode, the irrigation level, the rice phenological stage, the density and the diversity of the hosts (wild and cultivated). A distribution map of the RYMV in this area was build and we observed that the irrigation enhances the RYMV prevalence. Then, the analysis of the genetic diversity identified isolates belonging to the three major strains of East Africa in the same plantation. Finally, while no genetic structure of the virus diversity has been highlight between cultural practices, the analysis of the samples by depth sequencing is on progress in order to characterize and to compare precisely the intra-host genetic diversity and structure depending to the cultivation mode and to the host (wild or cultivated). Altogether, this study will allow us to understand the diversification processes and the flow of the viral populations at the field scale in order to participate to the improvement of the control strategies against the RYMV. (Résumé d'auteur)