Landscape of structural variants reveals insights for local adaptations in the Asian corn borer

Capturing the genetic diversity of different wild populations is crucial for unraveling the mechanisms of adaptation and establishing links between genome evolution and local adaptation. The Asian corn borer (ACB) moth has undergone natural selection during its adaptative evolution. However, structural variants (SVs), which play significant roles in these adaptation processes, have not been previously identified. Here, we constructed a multi-assembly graph pan-genome to highlight the importance of SVs in local adaptation. Our analysis revealed that the graph pan-genome contained 176.60 Mb (∼37.33%) of unique sequences. Subsequently, we performed an analysis of expression quantitative trait loci (QTLs) to explore the impact of SVs on gene expression regulation. Notably, through QTL mapping analysis, we identified the FTZ-F1 gene as a potential candidate gene associated with the traits of larval development rate. In sum, we explored the impact of SVs on the local adaptation of pests, therefore facilitating accelerated pest management strategies. [Display omitted] •A multi-assembly graph pangenome highlights structural variants in local adaptation•More than 50% of SVs are derived from transposable elements•Analysis of expression QTLs to explore the impact of SVs on gene expression regulation•SVs contribute to changes in adaptive traits, such as diapause Most variant analyses depend on a linear reference genome, which is presumed to be missing millions of bases found in the genomes of other populations. Peng et al. utilize a graph pan-genome to highlight the significant impact of structural variants on gene expression and adaptive traits such as diapause.