Résumé
The black rat (Rattus rattus) is the main reservoir of plague (Yersinia
pestis infection) in Madagascar's rural zones. Black rats are highly
resistant to plague within the plague focus (central highland), whereas
they are susceptible where the disease is absent (low altitude zone). To
better understand plague wildlife circulation and host evolution in
response to a highly virulent pathogen, we attempted to determine genetic
markers associated with plague resistance in this species. To this
purpose, we combined a population genomics approach and an association
study, both performed on 249 AFLP markers, in Malagasy R. rattus.
Simulated distributions of genetic differentiation were compared to
observed data in four independent pairs, each consisting of one population
from the plague focus and one from the plague-free zone. We found 22 loci
(9% of 249) with higher differentiation in at least two independent
population pairs or with combining p-values over the four pairs
significant. Among the 22 outlier loci, 16 presented significant
association with plague zone (plague focus vs. plague-free zone).
Population genetic structure inferred from outlier loci was structured by
plague zone, whereas the neutral loci dataset revealed structure by
geography (eastern vs. western populations). A phenotype association study
revealed that two of the 22 loci were significantly associated with
differentiation between dying and surviving rats following experimental
plague challenge. The 22 outlier loci identified in this study may undergo
plague selective pressure either directly or more probably indirectly due
to hitchhiking with selected loci.