A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown

Several studies reported the rapid evolution of avirulence (Avr) genes to
escape R-mediated plant immunity and identified a variety of mechanisms
leading to virulence. The poplar rust fungus Melampsora larici-populina is
the most damaging pathogen of poplars. A major adaptive event occurred in
1994 with the breakdown of RMlp7 resistance gene in poplar. Population
genomics studies identified a locus in the genome of M. larici-populina,
which likely corresponds to the AvrMlp7 candidate avirulence gene. We used
a population genetics approach combined with dedicated qPCR assays on a
comprehensive set of 281 isolates, covering 27 years (encompassing the
resistance breakdown event), to validate the candidate locus and to assess
its polymorphism. We found two mechanisms, a point mutation and a
deletion, that allowed the pathogen to escape RMlp7-mediated resistance.
Six diploid genotypes were thus characterized at the candidate locus
(three avirulent and three virulent). In addition, a temporal analysis
revealed that the two virulence alleles pre-existed (harboured as
avirulent heterozygous genotypes) since the early samplings and were found
in association (as virulent genotypes) at the time of the resistance
breakdown.These molecular analyses were complemented by a population
genetic analysis of those temporal samples, using 22 microsatellite
markers.