Alternaria alternata causing inner black rot of lemon (Citrus limon) fruits in Turkey: Genetic diversity and characterisation

Abstract

The market sales of symptomless lemons in 2020 revealed a persistent and severe internal black rot with browning of the membrane wall and juice sac. To investigate the causal agent, externally symptom-free lemons from Mediterranean locations were sampled from supermarkets, local markets, and bazaars in three southeastern Turkish provinces. Internal black rot symptoms were observed in 13.69% of the 1300 externally symptomless fruits, and Alternaria was isolated from 96.63% of those exhibiting these symptoms. Morphological analysis confirmed the identity of Alternaria alternata in 26 representative isolates collected from various markets and bazaars. To examine genetic diversity or polymorphisms, start codon targeted (SCoT) markers were used. Species identification was based on the sequences of translation elongation factor 1-alpha (TEF 1-α), RNA polymerase second largest subunit (RPB2), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). SCoT 29 exhibited the highest amount of polymorphic amplicons, with 18 polymorphic bands scored when compared to the other six scoreable markers. The 26 representative isolates from various markets and bazaars were divided into four clades by SCoT 29. However, multilocus sequence analyses confirmed the identification of a single species, A. alternata. In terms of virulence and the impact of temperature on growth, representative isolates from four SCoT clusters were evaluated. Data suggests that SCoT markers can be used to evaluate virulence-based polymorphism in A. alternata; nonetheless, all clades showed comparable temperature responses, with 25 °C being the optimum. There was also no association between individual morphotypes and SCoT clade membership. Due to the lack of obvious signs on lemon fruits, producers, merchants, and consumers are unable to identify black rot, and the widespread presence of A. alternata in lemons may pose a significant risk that must be avoided at all costs.