Thesis (Ph.D.) - Cairo University - Faculty of Agriculture - Department of Plant Pathology and Physiology

Our results demonstrated that all Egyptian P. infestans isolates were identified as A1 mating type except only one isolate EG_9 was self-fertile (SF), however the majority of Japanese isolates were A2 mating type. Additionally, based on PCR-RFLP approach all Egyptian isolates were the Ia mt-DNA haplotype, whereas the Japanese isolates were IIa. Genome-wide SSR analysis of P. infestans populations revealed that 45 alleles were detected using 16 microsatellite markers. According to presence or absence of P. infestans effector genes AVR1 was absent in all tested samples, however AVR4 effector gene was present in all isolates. Intriguingly, 996 high-quality SNPs marker were detected using double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology. Interestingly, the comparative genomics of P. infestans populations showed that the copy number variation (CNV) percent ranged from 0.4 to 12.5%. The highest late blight resistance was detected in S. habrochaites accessions LA1777, LA1352, LA2855, LA1347, LA1718 and LA1295, with disease severities ranging from 4.5 to 13.5%. Two quantitative trait loci on chromosomes 12 and 6 for resistance to an aggressive two Egyptian isolates of P. infestans EG_11 and EG_12, respectively, were identified. Whole-genome resequencing analysis revealed that two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance

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