Population Structure of Aspergillus flavus in Hazelnuts from Azerbaijan: Genetic Diversity, Clonality and Biocontrol Implications

Aflatoxin contamination is a growing concern in hazelnut production across the Caucasus, particularly due to its health risks and the economic impact in markets with strict safety standards, such as the European Union. This study examined the genetic diversity and population structure of Aspergillus flavus, the main source of aflatoxin, in three key hazelnut regions of Azerbaijan: Zaqatala, Qabala, and Khachmaz. It also assessed the presence of genotypes genetically similar to known non-aflatoxigenic biocontrol strains using simple sequence repeat (SSR) markers. A total of 710 A. flavus isolates were analyzed using 17 SSR markers, revealing 377 distinct haplotypes and high genetic diversity across regions, seasons, and production stages. Linkage disequilibrium analysis indicated a primarily clonal reproduction pattern, suggesting that dominant genotypes may persist over time and that introduced non-aflatoxigenic strains could remain stable in the population. Among 477 clone-corrected isolates, several haplotypes closely matched the non-aflatoxigenic biocontrol strains MUCL54911 and AF36, which are the active ingredients of the commercial products AF-X1 and AF36 Prevail, suggesting that genotypes potentially suitable for aflatoxin biocontrol may already be present and adapted to the Azerbaijani hazelnut agroecosystem. These findings establish a genetic baseline for A. flavus in Azerbaijani hazelnut systems and support the potential use of MUCL54911 or AF36 for local biocontrol efforts aimed at reducing aflatoxin contamination.