Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2025
Publication Date: 7/2/2025
Citation: Tessnow, A.E., Nagoshi, R.N., Meagher Jr, R.L., Gulligan, T.M., Sadd, B., Carriere, Y., Miller, A.C., Richers, K., Porter, P., Fleischer, S.J., Palumbo, J., Rodrigues, J.V., Sword, G.A. 2025. Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations. BMC Genomics. 26:116. https://doi.org/10.1186/s12864-025-11214-8.
DOI: https://doi.org/10.1186/s12864-025-11214-8

Interpretive Summary: The fall armyworm is a global pest of corn and many other important crops. The species is comprised of two genetically distinct host strains (Corn - and Rice-strain) that while morphologically identical, exhibit differences in their behavior and physiology that impact strategies for their control. Scientists with the USDA-ARS, Center for Medical, Agricultural and Veterinary Entomology in Gainesville, FL in collaboration with researchers with Texas A&M University, USDA-APHIS, Penn State University, University of California-Berkeley, and University of Arizona, conducted laboratory studies to determine the structure of a major sex chromosome and field studies to determine the geographic distribution of the strains. Results suggest that Corn-strain populations in the eastern U.S. may be at increased risk of insecticide control failures relative to Corn- and Rice-strain populations in the rest of the country. Additionally, the differences in the dispersal patterns of the two different fall armyworm strains support consideration of these two strains as two unique pests that require separate consideration when devising and implementing management strategies.

Technical Abstract: Molecular genetic approaches have become key to understanding and controlling insect pests across agricultural landscapes. From mapping the development of resistance to monitoring and predicting pest movement, genomic tools and techniques can inform pest management approaches and allow us to better control pest populations. We utilized a whole genome sequencing population genomics approach to unravel novel patterns of population structure, linkage, and selection across the genome of a notorious agricultural pest, the fall armyworm. Our data strongly supports the identity of two genetically-distinct strains of fall armyworm in North America, which have previously been referred to as the C- strain and the R-strain. Although these strains have genetically diverged, we find that differentiation is not uniform across the genome. Instead, the Z-chromosome appears to be driving divergence between strains with virtually no recombination occurring on this chromosome. This could point to a larger structural rearrangement on the Z-chromosome that results in hybrid incompatibility. Our data also suggests that the two strains differ in their geographic distributions and exhibit distinctly different patterns of geographic sub-structuring. Taken together, these observed patterns indicate that the fall armyworm strains exhibit differences in their dispersal patterns and should be considered as two unique pests. Finally, our data reveals strain-specific patterns of selection on genomic regions containing putative insecticide resistance alleles, indicating that C-strain populations in the eastern US may be at increased risk of chemical control failures relative to C- and R-strain populations in the rest of the US. Our results support the existence of the fall armyworm in the US as a pest dyad with differences in population structure and genomic signatures of selection in response management history that should be separately considered when devising and implementing management strategies.