Population genomics of fall armyworm by genotyping-by-sequencing: Implications for pest management

Authors: ISHIZUKA, TAMYLIN - State University Of Campinas; CORDEIRO, ERIC - University Of São Paulo; ALVES-PEREIRA, ALESSANDRO - State University Of Campinas; BATISTA, CARLOS - University Of São Paulo; MURUA, GABRIELA - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET); PINHEIRO, JOSE - University Of São Paulo; SETHI, AMIT - Corteva Agriscience; Nagoshi, Rodney; ZUCCHI, MARIA - State University Of Campinas; FORESTI, JOSEMAR - Corteva Agriscience

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2023
Publication Date: 4/18/2023
Citation: Ishizuka, T.K., Cordeiro, E.M., Alves-Pereira, A., Batista, C.E., Murua, G., Pinheiro, J.B., Sethi, A., Nagoshi, R.N., Zucchi, M.I., Foresti, J. 2023. Population genomics of fall armyworm by genotyping-by-sequencing: Implications for pest management. PLOS ONE. 18(4):e0284587. https://doi.org/10.1371/journal.pone.0284587.
DOI: https://doi.org/10.1371/journal.pone.0284587

Interpretive Summary: The fall armyworm is a global pest of corn and other crops and is the primary pest of corn South America. Due to the fact that the species can fly long distances and is associated with multiple pesticide resistance traits, it is a challenging pest to control. While the migratory behavior of fall armyworm is described for North America, it remains largely uncharacterized in the Southern Hemisphere. In a collaborative study between South American researchers and a scientist at USDA/ARS Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, a whole genome approach was used to evaluate patterns of genetic diversity of FAW populations across Brazil and Argentina as a first step to study fall armyworm movements in South America. Genotyping-by-sequencing enabled reduced representation of the genome, while identifying a large number of genetic markers using state-of-the-art next generation sequencing. The results found no genetic differentiation between geographical regions in Brazil but in contrast, there was substantial genetic structure in Argentina. These results revealed major regional differences in migration behavior and underscores the importance of phytosanitary barriers between countries for effective fall armyworm management. This approach of monitoring population structure going forward promises to improve the understanding of the risks of pest outbreaks and the spread of resistance genes.

Technical Abstract: The fall armyworm (FAW), Spodoptera frugiperda, is a significant pest of many crops in the world and it is native to the Western Hemisphere, where the species have shown the ability to rapidly evolve resistance to transgenic plants and insecticides. Despite the importance of this species, there is a gap in the knowledge regarding the migration pattern of FAW in South America. Here, we examined the genetic diversity of FAW populations across a wide agricultural area of Brazil and three locations from Argentina using a Genotyping-By-Sequence (GBS) approach. We also characterized samples as their host strain based on mitochondrial COI gene and the Z-linked gene Tpi. The GBS methodology enabled us to discovery 3,309 SNPs, including neutral and outlier markers. The 37 COI haplotypes could not differentiate samples among ecoregions or countries, whereas GBS data revealed significant genetic structure between Brazil and Argentina (FST = 0.067), and also among the Argentinian ecoregions. Populations inside Brazil showed little genetic differentiation indicating high gene flow among locations and confirming that structure is related to the presence of corn and rice strains. Adaptive analysis indicated 456 loci putatively under selection, including proteins related to resistance evolution such as ABC transporter C family and cytochrome P450. Together, our findings point to GBS being a useful tool for population genomics research of challenging pests, as well as the value of genomic studies as regards integrated pest management.