The population genetics and gene editing of Spodoptera frugiperda (Lepidoptera: Noctuidae) in South Africa

Abstract

The fall armyworm, Spodoptera frugiperda, is invasive polyphagous pest native to the Americas, which has become invasive to Africa and rapidly spread across sub- Saharan Africa since it was first reported in West Africa in 2016. This dissertation explores aspects of S. frugiperda biology, population genetics, the application of gene editing tools, and strategies to manage resistance to Bacillus thuringiensis (Bt) toxins in agricultural systems, with a focus on the African context. The research presented reports on the populations genetics of S. frugiperda in South Africa, using mitochondrial COI sequences and five microsatellite markers. The study reveals high genetic diversity, extensive gene flow, and a lack of population structure across Limpopo, Mpumalanga, and KwaZulu-Natal provinces. The findings underscore the extensive migratory behaviour of S. frugiperda and the potential for rapid dissemination of traits such as Bt resistance across maize-producing regions. The study highlights the utility of employing both mitochondrial and microsatellite markers in population genetics analyses and provides valuable insights in S. frugiperda population dynamics in South Africa, which will inform the implementation of effective management strategies. The study furthermore outlines the design and in vitro testing of single-guide RNAs (sgRNAs) for CRISPR/Cas9 gene editing in S. frugiperda. Targeting three marker genes (SfAbd, BLOS2, and ebony) the study successfully demonstrates the cleavage efficiency of sgRNAs for SfAbd and BLOS2, justifying the use of CRISPR/Cas9 in this species. This proof-of-concept study establishes the foundation for future research into understanding the genetic mechanisms underlying Bt resistance and the potential use of CRISPR-based approaches, including gene drives, to enhance pest management strategies in South African agriculture.