Identification and genetic characterization of <i>Spodoptera frugiperda</i> (Lepidoptera: Noctuidae) corn and rice strains in Egypt utilizing <i>Tpi</i> gene and microsatellite marker

Maize is considered a key food crop worldwide. In Africa, the crop yields were severely reduced in 2016 when the fall armyworm (FAW), Spodoptera frugiperda, entered Western Africa and quickly expanded throughout sub-Saharan Africa. Although Egypt is a large corn-growing and consuming country, the genetic divergence of FAW has not been investigated. In order to analyze genetic variance of Corn (C) and Rice (R) strains, FAW larvae were gathered from 3 different governorates (Ismailia, Qalyubia and Assiut) throughout Egypt. The study analyzed genetic polymorphisms within the triosephosphate isomerase (Tpi) gene locus and Sfrugi76 microsatellite motif across the collected samples. The findings showed that the gTpi183 site exhibited polymorphism across all collected samples. Other strain-discriminatory markers, such as gTpi168 and gTpi180, showed clear polymorphism, while gTpi192 and gTpi198 lacked strain specificity. The Microsatellite typing of Sfrugi76 revealed a repeat-length polymorphism without a distinctive pattern within governorates, suggesting ecological or host plant influences. The phylogenetic analysis of Tpi gene sequences showed mixed clustering among governorates, with Assiut samples exhibiting low genetic diversity and tight clustering, likely due to host-specific adaptation or isolation. In contrast, Ismailia samples displayed greater genetic variation, while Qalyubia samples showed intermediate identities, hinting at hybridization or ancestral gene flow. Similar clustering patterns were observed in the microsatellite-based dendrogram, reinforcing the impact of ecological and agricultural influences on strain distribution. This study provides important information on FAW genetic diversity in Egypt, which can be used for effective management of FAW.