Epidemiology and genetic characterization of Alternaria alternata causing leaf spot in Fragaria × ananassa

Alternaria leaf spot (ALS), caused by Alternaria alternata, is a major disease threatening strawberry (Fragaria × ananassa) production globally, including in Pakistan. This study investigated the incidence and prevalence of ALS in key strawberry-producing regions of Pakistan and characterized the pathogen using morphological and molecular techniques. Surveys were conducted during the 2014–2015 and 2015–2016 seasons across 182 farms in Punjab, Khyber Pakhtunkhwa, and Islamabad. Disease prevalence was 100% across all regions, with incidence rates ranging from 17.25% in cooler Islamabad to 55% in Mardan, KPK. Pathogenicity tests confirmed A. alternata as the causal agent. Morphological traits and sequencing of the ITS and endoPG genes further validated its identity. Phylogenetic analysis showed close genetic relatedness to known A. alternata isolates. This is the first comprehensive report of ALS in strawberries in Pakistan, confirming A. alternata as the primary pathogen. The widespread occurrence and high incidence highlight the urgent need for effective control measures. Integrated disease management, including resistant cultivars and targeted fungicide use, is strongly recommended. Further research should investigate environmental factors influencing disease spread and severity to support long-term sustainable management of ALS in strawberry cultivation.