Analysis of the lineage ofPhytophthora infestansisolates using mating type assay, traditional markers, and next generation sequencing technologies

Abstract

AbstractPhytophthora infestans(Mont.) de Bary, a hemibiotrophic oomycete, has caused severe epidemics of late blight in tomato and potato crops around the world since the Irish Potato Famine in the 1840s. Breeding of late blight resistant cultivars is one of the most effective strategies to overcome this disruptive disease. However,P. infestansis able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability amongP. infestansisolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence ofP. infestansisolates. In this study, we analyzed the genomes ofP. infestansisolates collected from Egypt and Japan using various molecular approaches including the mating type assay and genotyping simple sequence repeats, mitochondria DNA, and effector genes. We also analyzed genome-wide single nucleotide polymorphisms using double-digest restriction-site associated DNA sequencing and whole genome resequencing (WGRS). The isolates were classified adequately using high-resolution genome-wide approaches. Moreover, these analyses revealed new clusters ofP. infestansisolates in the Egyptian population. Monitoring the genetic divergence ofP. infestansisolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.