Gene Flow of Phytophthora infestans Between Refuse Piles, and Organic and Conventional Potato Fields in Southern Flevoland, The Netherlands

Phytophthora infestans causes late blight, a devastating disease of potato and tomato. Previous work in the Netherlands showed that the population is highly diverse due to sexual reproduction and that oospores can overwinter in the soil. We sequenced archived DNA from multiple nuclear and mitochondrial loci from P. infestans sampled in 1994 from 17 conventional and 5 organic potato fields and 7 potato refuse pile sites in the Southern Flevoland. We assessed the genealogical history using sequences from two regions of the single-copy nuclear ras gene (intron 1 and exons 3–6) and several mitochondrial loci (P3-rpl14, rpl5 and tRNAs and P4-cox1) from 83 isolates. There were 10 heterozygous sites in the ras gene and 12 in the mitochondrial genes that were phylogenetically informative. Five nuclear and 5 mitochondrial haplotypes were shared among fields and several unique haplotypes were found. Nucleotide diversity and population mean mutation rates (θW) were higher in samples from refuse piles and organic fields than conventional fields for both nuclear and mitochondrial loci. Subdivision was observed between conventional fields and refuse piles. Migration analysis suggested that gene flow may have occurred first from conventional potato fields to organic fields and then to refuse piles. Recent mutations were found in rare lineages from organic fields. Ancestral mutations in mitochondrial loci were derived from samples from refuse piles documenting the importance of refuse piles as a source of inoculum for late blight epidemics in the organic and conventional fields.