This study investigates the impact of whole-genome duplications (WGDs) on the evolution of genomic structural variants (SVs) in the plant genus *Cochlearia*. WGDs, while disruptive, are believed to have played a significant role in eukaryotic evolution, particularly in plants. The authors use long-read sequencing and a graph-based pangenome to analyze SV diversity and their evolutionary dynamics in *Cochlearia*. They find that WGDs lead to both negative and positive interactions with SVs. Specifically, WGDs mask recessive mutations, leading to an accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), which likely reduces the adaptive potential of polyploid populations. However, the study also reveals that more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids, suggesting potential benefits from SV accumulation. The results highlight the complex and contrasting roles of SVs in the evolutionary trajectories of young polyploids, with SVs contributing to both the genetic load and adaptive potential of these organisms. The study provides important insights into the evolutionary relationship between WGDs and SVs, which is crucial for understanding the long-term fate of polyploid species.This study investigates the impact of whole-genome duplications (WGDs) on the evolution of genomic structural variants (SVs) in the plant genus *Cochlearia*. WGDs, while disruptive, are believed to have played a significant role in eukaryotic evolution, particularly in plants. The authors use long-read sequencing and a graph-based pangenome to analyze SV diversity and their evolutionary dynamics in *Cochlearia*. They find that WGDs lead to both negative and positive interactions with SVs. Specifically, WGDs mask recessive mutations, leading to an accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), which likely reduces the adaptive potential of polyploid populations. However, the study also reveals that more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids, suggesting potential benefits from SV accumulation. The results highlight the complex and contrasting roles of SVs in the evolutionary trajectories of young polyploids, with SVs contributing to both the genetic load and adaptive potential of these organisms. The study provides important insights into the evolutionary relationship between WGDs and SVs, which is crucial for understanding the long-term fate of polyploid species.