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Early blight (EB) disease is one of the most devastating threats of potato production. Alternaria alternata and A. solani are the main causative species of the EB disease globally. Thus, in this study, we investigated the response of a diverse collection of ten potato cultivars to EB at pre and post-flowering stages to both species, and their colony growth rates, as well as leaf cuticular wax thickness associated with EB resistance and biomass parameters. We also analysed genetic diversity of the related cultivars using eleven simple sequence repeat (SSR) markers accordingly. Based on the mean disease severity percentage (DSP), A. alternata was more pronounced than A. solani on the related potato cultivars at both growth stages, significantly. The highest DSP to A. alternata was on "Burren" (80 %) and "White Desiree" (77 %), and the lowest one on "Agria" (7 %). Whereas, the highest DSP to A. solani was on "Burren" (52 %), and the lowest one on "Agria" (17 %). The wax thickness of the adaxial cuticle on the fifth leaf varied from 0.9 μ to 1.5 μ and for abaxial cuticle varied from 0.6 μ to 1.4 μ. The highest epicuticular wax layer was of partially resistant "Agria" and moderately resistant "Santana" (1.3–1.5 μ), and the lowest one on susceptible "White Desiree", "Milva" and "Burren" (0.8, 0.9 μ, respectively). Biomass analysis showed lower values of growth parameters in the susceptible cultivars than the resistant ones, significantly. According to primer polymorphism analysis, eleven SSR primers were polymorphic. The selected SSR primers showed significant genetic diversity with the polymorphism information content ranging from 0.1 to 0.5 (mean 0.4), effective multiplex ratio from 0.7 to 12.3 (mean 4.3), marker index from 0.04 to 6 (mean 2), and resolving power from 0.6 to 12.8 (mean 5). Cluster analysis of SSR data revealed considerable genetic diversity between the related potato cultivars, suggesting a significant genetic variation between resistant and susceptible ones. This work may improve our understanding of genetic diversity and wax thickness as markers for identifying resistant potato cultivars to EB disease. Above; A: early blight lesions on potato leaves, B: Colony of Alternaria solani on PDA, C: Conidia. (Scales bars = 10 μm). Below; A: early blight lesions on potato leaves, B: Colony of Alternaria alternata on PDA, C: Conidia (Scales bars = 10 μm). [Display omitted] • 'Agria' was a partially resistant potato cultivar to both Aternaria alternata and Aternaria solani. • Cuticular wax thickness had an important role in potato resistance to Alternaria spp. • The polymorphic SSR marker could differentiate the potato cultivars into distinct groups significantly. • Genetic diversity and EB resistance level categorized potatoes into 5 main groups. [ABSTRACT FROM AUTHOR]