Survey of the pathogen of Alternaria late blight reveals different levels of carboxamide fungicide resistance in the main pistachio producing regions of California

Alternaria late blight (ALB), caused mainly by the fungal pathogen Alternaria alternata, is an important pistachio disease that causes severe tree defoliation and fruit shell staining. Its control relies on multiple fungicide sprays, including carboxamide fungicides. In 2015, we surveyed 35 orchards representing nine pistachio producing counties of California to determine the current situation of Alternaria resistance to four widely used carboxamide fungicide active ingredients. This survey showed that isolates collected in the northern (Tehama, Glenn and Colusa counties) and southern (Tulare, Kings and Kern counties) Central Valley presented higher frequencies of carboxamide resistance than isolates collected from orchards in the central region (Fresno, Madera and Merced counties). The number of carboxamide usages in a year is the main factor determining elevated resistance. By extracting the A. alternata DNA and sequencing the carboxamide target genes, we evaluated the prevalence of specific molecular alterations (mutations) associated with carboxamide fungicide resistance. Finally, we identified cross-resistance patterns among different carboxamide fungicides, leading to recommendations about combinations to avoid.