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Spatial genetic structure and dispersal of the cacao pathogen Moniliophthora perniciosa in the Brazilian Amazon

Moniliophthora perniciosa is the causal agent of witches’ broom in Theobroma cacao (cacao). Three biotypes of M. perniciosa are recognized, differing in host specificity, with two causing symptoms on cacao or Solanaceae species (C- and S-biotypes), and the third found growing endophytically on lianas (L-biotype). Our objectives were to clarify the genetic relationship between the three biotypes, and to identify for the C-biotype, those regions in the Brazilian Amazon with the greatest genetic diversity. Phylogenetic reconstruction based on the rRNA ITS regions showed that the C-and S-biotypes formed a well-supported clade separated from the L-biotype. Analysis of 131 isolates, genotyped at 11 microsatellite loci found that S- and especially L-biotypes showed a higher genetic diversity. A significant spatial genetic structure was detected for the C-biotype populations in Amazonia for up to 137 km, suggesting isolation by distance mode of dispersal. However, in regions containing extensive cacao plantings, C-biotype populations were essentially ‘clonal’, as evidenced by high frequency of repeated multilocus genotypes. Among the Amazonian C-biotype populations, Acre and West Amazon displayed the largest genotypic diversity and might be part of the center of diversity of the fungus. The pathogen dispersal may have followed the direction of river flow downstream from Acre, Rondonia and West Amazon eastward to the rest of the Amazon valley, where cacao is not endemic. The Bahia population exhibited the lowest genotypic diversity, but high allele richness, suggesting multiple invasions, with origin assigned to Rondonia and West Amazon, possibly through isolates from the Lower Amazon population. 
 
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