Population genomics of migratory and resident Spodoptera frugiperda reveals key genes and loci driving migration traits

Abstract Background The fall armyworm ( Spodoptera frugiperda, FAW) is one of the most devastating invasive pests in the world, owing to its extraordinary migration performance. Research has clarified the migratory pathways and external environmental factors affecting FAW migration. However, the internal genes and loci regulating migration or reside in FAW remain largely unknown. Results In this study, we used a tethered flight mill system to distinguish migratory and resident individuals, which exhibit significant differences in flight‐related traits such as flight distance, duration, and maximum speed. Selective sweep analysis of 51 resequencing FAW (23 migratory and 28 resident individuals) identified 652 candidate genes, and genome‐wide association analysis (GWAS) identified 79 functional annotated genes associated with the most significant trait, flight distance. These candidate genes were mainly concentrated in amino acid metabolism, signal transduction, and environmental adaptation. The neuroendocrine convertase 2 gene was crossed between the two analyses, with 65 selective mutation loci in the intron region. Casein kinase I , which reported regulating circadian rhythm by phosphorylating the period, was simultaneously involved in several enriched signaling pathways, and had 11 selective loci in the regulatory region. These selective mutation loci may affect the expression of target genes and regulate the migration behavior of FAW. Conclusion Key loci and genes may determine the migration behavior of FAW by regulating the circadian rhythm and other signaling pathways. These findings provide a new perspective for elucidating the internal driving mechanism of migratory insects, and provide a new possibility for developing eco‐friendly control strategies for migratory pests. © 2025 Society of Chemical Industry.