Ochratoxin A (OTA) production and genetic structure of Aspergillus niger isolates causing ear rot in maize fields of Southern Botswana

Fungi are among the principal causes of deterioration and yield losses affecting maize farmers in Southern Africa, especially Botswana. Maize is one of Botswana’s staple crops attacked by more than sixty diseases, and several species of insect pests with maize ear rot as the most damaging in the region. Among the field fungal potential pathogens, Aspergillus niger is one of the most predominant species causing maize ear rot. However, the genetic diversity and pathogenic potential of A. niger under field conditions of Botswana is still deficient. This study aimed to investigate the occurrence and genetic diversity of A. niger strains associated with maize ear rot in monoculture fields of southern Botswana (Ramotswa, Ramaphate and Kopong). The presence of A. niger was detected in 64% of maize ear rot isolates sampled from the monoculture fields. Thin layer chromatography and ANPKS primer pair indicated 71.4% of the strains to be potentially orchratoxigenic (i.e., positive test for Ochratoxin A). While internal transcribed spacer (ITS) gene sequences, assessed through UPGMA, principal component analysis (PCA) and Bayesian techniques revealed the Ramotswa population to be genetically divergent from Kopong and Ramaphatle populations. Our preliminary data suggests a possible infraspecific split of natural A. niger populations in Botswana, with probable implications for pathogen control related traits such as susceptibility to antifungal agents. This study also observed the occurrence of A. niger putative hybrids which could be detected with machine learning algorithms like Kernel-SVM (Kernel – Support Vector Model) as the main classifier, while Grid search and XGBoost (eXtreme gradient boosting) can be used to search for the optimal model. Since ochratoxin A poses significant food safety and human health issues, this study provided valuable insight into potential control of maize ear rot in Botswana. Understanding this genetic variation is crucial for developing effective strategies to control fungal outbreaks and reduce the risk of ochratoxin contamination, ultimately helping to protect both food security and public health. • Aspergillus niger was found to cause maize ear rot in monoculture fields of southern Botswana (Ramotswa, Ramaphatle and Kopong). • Thin layer chromatography and ANPKS primer pair indicated 71.4% of the strains to be potentially ochratoxigenic. • Genetic analyses through UPGMA, principal component analysis (PCA) and Bayesian techniques revealed the Ramotswa population to be genetically divergent from Kopong and Ramaphatle populations. • This study also observed the occurrence of A. niger putative hybrids which could be detected with machine learning algorithms. • The findings of this study could provide a pathway towards managing both the field Aspergillus infections and intoxication.