Revisiting Alternaria-host interactions: New insights on its pathogenesis, defense mechanisms and control strategies

Necrotrophic fungal pathogens of the genus Alternaria are globally recognized as one of the most destructive plant pathogens in most of the industrially and agriculturally important crops inflicting myriad crop yield and economic losses. In addition, they have recently attracted global attention because of their capacity to produce abundant mycotoxins, rendering them a major food safety concern. Most of the economically important crops lack adequate disease resistance to pathogenic Alternaria species, and the development of durable resistant cultivars through traditional breeding is arduous owing to the scarcity of Alternaria-resistant germplasms. Moreover, application of fungicides, which is one of the common methods of Alternaria disease control, is noxious to the environment and a major cause of fungicide resistance in the pathogenic species. In view of the innumerable perils that the pathogenic Alternaria spp. pose to agriculturally and industrially important crops it is important to use a holistic approach to understand the molecular, physiological, and biochemical pathogenesis mechanisms of Alternaria and related regulatory networks to develop precise and sustainable biotechnological preventive measures. In the present review, we elucidate the advances in Alternaria infection pathogenesis, host immune signaling responses and biotechnology-based control strategies (transgenics, RNA interference, artificial microRNA, and genome editing). This review also addresses the importance of deep learning in the diagnosis of Alternaria infection. Finally, we discuss how next-generation sequencing and multi-omics can be used to explore new frontiers in Alternaria–host interactions to identify key target genes, which underpin disease resistance in economically significant crops, using genome editing.