Dispersion and evolutionary history of rice yellow mottle virus in Africa: tales of rice and men

Rice has become a pillar of food security in Africa. During the 20^th century, rice cultivation intensified to cope with the rising demand due to demographic changes in West and Central Africa (WCA). Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV is a (+)ssRNA virus transmitted at short distance by beetles and by contact during cultural practices. Six major strains were identified with a marked spatial-based diversity⁽¹⁾. Several sources of resistance against RYMV were identified in rice, but none of them are currently widely deployed in field. Resistance-breaking risk maps were proposed based on the spatial distribution of the strains and their pathogeny in controlled conditions⁽²⁾. However, the validity and the sustainability of these risk maps are strictly dependent on the dispersal and adaptive characteristics of the RYMV in field conditions.

The main objectives of this study are i) to reconstruct the dispersion dynamics of RYMV in WCA, ii) to identify the main drivers of RYMV evolution and dispersion, and iii) to estimate the impact of RYMV evolutionary history on the sustainability of the resistance genes in the fields. Thus, based on the RYMV genetic data collected in WCA since the 1970’s, the phylogeography of RYMV was reconstructed using Bayesian evolutionary inference. These spatio-temporal reconstructions revealed links between RYMV expansion dynamics and the rice cultivation history in Africa. In addition, we demonstrated that the geographic dispersion of the RYMV in WCA shaped genetic evolution, with the emergence of adaptive mutations to new host species and of inter-strain recombination events. In addition, experiments in controlled conditions demonstrated that virulence factors were exchanged in fields, even without selection pressure from resistance genes. Altogether, we partially deciphered the balance and the interplay between genetic determinants and stochasticity in evolution and epidemiology of a plant virus.