Journal of Phytopathology. 2018;1–13. wileyonlinelibrary.com/journal/jph | 1 © 2018 Blackwell Verlag GmbH 1 | INTRODUCTION Tomato (Solanum lycopersicum L.) is the most important solanaceous crop after potatoes. Tomato is cultivated on an area of 216,400 hect- ares in Egypt (Emara, Hafez, El-Shafey, Khattab, & Awad, 2014). One common postharvest disease of this vegetable crop is fruit spoilage, which is caused by fungi. Fruit rot fungi in tomatoes were recorded in several reports (Abdel-Gawaad, 1995; Chinoko & Naqvi, 1989; Cohen, Farkash, Reshit, & Baider, 1997; Mathey & Oriolani, 1985; Samuel & Orji, 2015; Wani, 2011). Due to these pathogens, heavy losses of this crop occur during marketing (Okoli & Erinle, 1989), and considerable changes in the quality of the tomato fruits have been recorded (Efiuvwevwere & Hobson, 1989; Glazener, 1982; Rattan & Saini, 1979). Among these pathogens, Alternaria can cause disease symptoms on all parts of the plant (leaf blight, stem lesions and rot- ting fruits) and results in acute damage during all stages of plant de- velopment (Abada, Mostafa, & Hillal, 2008). Alternaria species are taxonomically challenging. The broad morphological categories within Alternaria have been confirmed by phylogenetic analyses (Peever, Su, Carpenter-Boggs, & Timmer, 2004; Pryor, Robert, & Gilbertson, 2000), and these studies have demonstrated a clear distinction between large- and small-spored Alternaria species (Gannibal & Yli-Mattila, 2005; Peever et al., 2004; Pryor & Bigelow, 2003). Currently, this genus includes 26 sections (Woudenberg et al., 2015). However, the small-spored Alternaria taxa are a category of fungi with few morphological and molecu- lar characteristics that are suitable for unambiguous differentiation among taxa (Andrew, Peever, & Pryor, 2009; Woudenberg et al., Received: 15 December 2017 | Revised: 7 June 2018 | Accepted: 26 June 2018 DOI: 10.1111/jph.12752 ORIGINAL ARTICLE Molecular characterization of Alternaria alternata population isolated from Upper Egyptian tomato fruits Youssuf Gherbawy 1 | Mohamed A. Hussein 1 | Fabian Runge 2 | Otmar Spring 2 1 Botany Department, Faculty of Science, South Valley University, Qena, Egypt 2 Institute of Botany, University of Hohenheim, Stuttgart, Germany Correspondence Mohamed A. Hussein, Botany Department, Faculty of Science, South Valley University, Qena, Egypt. Email: m.hussein@sci.svu.edu.eg Funding information South Valley University, German Academic Exchange Service (DAAD), and University of Hohenheim Abstract Alternaria alternata is the most common fungal pathogen of tomatoes in Upper Egypt. Morphological identification of this fungus is challenging; therefore, this study searched for new classification tools based on molecular techniques. Using a dilution plating method, 67 strains of A. alternata were isolated from 34 samples of rotten tomato fruits representing the Giza 80 and Edkawy cultivars. The collected strains were identified using the amplification products of the internal transcribed spacer (ITS) region, glyceraldehyde 3-phosphate dehydrogenase (Gpd) and Alt a1, which is a gene involved in the production of most of the allergens produced by A. alternata. The screening revealed that A. alternata constituted more than half of the total fungi recovered from rotten tomatoes in this study. According to the phylogenetic analysis using these three loci, the collected strains clustered in accordance with the host cultivar type from which they had been isolated. Specific gene random primer poly- merase chain reaction (SGRP-PCR) techniques indicated that the A. alternata popula- tion in the tested region has a high genetic diversity. The pathogenicity test showed that most of the A. alternata isolates (67.2%) were highly pathogenic, and no correla- tion was found between the phylogenetic analysis and pathogenicity. In addition, the influence of the fungicide Disan 80% on the collected strains showed significant dif- ferences that were attributed to the source of isolation. KEYWORDS diversity, fungicide, pathogenicity, PCR, phylogeny