Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies.

Mohamed T. Rakha,Olfat M. Moussa,Nour Elden K. Soliman,Said M. Kamel,Tzen-Yuh Chiang,Kenta Shirasawa,Ramadan A. Arafa

doi:10.1371/journal.pone.0221604

Abstract

Phytophthora 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. infestans is able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability among P. infestans isolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence of P. infestans isolates. In this study, we analyzed the genomes of P. infestans isolates 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 of P. infestans isolates in the Egyptian population. Monitoring the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.

Highlights

Phytophthora infestans (Mont.) de Bary is a hemibiotrophic oomycete that causes late blight disease in tomato (Solanum lycopersicum) and potato (Solanum tuberosum)
A total of 80 P. infestans isolates were used in this study; these included 62 isolates collected from seven counties in Egypt, and 18 isolates obtained from the National Institute of Agrobiological Sciences (NIAS) in Japan, which were collected from three prefectures (S1 Table)
All three mating types were identified among the 18 isolates obtained from the NIAS, whereas only the A1 mating type was observed among the 62 isolates collected from Egypt (Fig 1 and S1 Table)

Summary

Introduction

Phytophthora infestans (Mont.) de Bary is a hemibiotrophic oomycete that causes late blight disease in tomato (Solanum lycopersicum) and potato (Solanum tuberosum). Many epidemics of tomato and potato late blight have been reported since the end of the 19th century, among which the Irish Potato Famine in the 1840s was probably the worst. P. infestans is reported to have originated either in South America [1, 2] or in central Mexico [3, 4]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Objectives

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Conclusion