Morphological, Molecular, and Pathogenic Characterization of Alternaria Associated with Apple Fruit Rot in China

Alternaria fruit rot is one of the most prevalent postharvest diseases of apples in China. To clarify the species associated with this disease, we characterized Alternaria isolates from symptomatic fruit using morphological traits and multi-gene phylogenetic analyses, and further assessed their pathogenicity on apple. A total of 373 isolates were obtained from decayed apples collected in major production and storage regions, including Shandong, Shaanxi, Gansu, and Beijing. Based on colony characteristics and sporulation patterns, isolates were assigned to two groups resembling A. alternata and A. tenuissima. Phylogenetic analyses of Histone 3 (H3), Alternaria major allergen Alt a1 (Alt a1), Calmodulin (CaM), and plasma membrane ATPase (PMA) genes, however, failed to separate the two groups, and all isolates morphologically identified as A. tenuissima clustered within A. alternata. Single nucleotide polymorphism (SNP) network analysis further showed that although some isolates shared haplotypes or formed intermixed clusters, most grouped according to geographic origin or host, forming distinct Chinese, Chilean and U.S. lineages. Pathogenicity tests demonstrated that all tested isolates caused fruit rot, with virulence varying among isolates. These results indicate that A. alternata is the causal agent of postharvest Alternaria fruit rot of apples in China.