Whole-genome duplication (WGD) significantly impacts structural variant (SV) evolution in the plant genus Cochlearia. Using long-read sequencing and a graph-based pangenome, the study reveals both negative and positive interactions between WGDs and SVs. Polyploid populations accumulate more deleterious SVs due to masking of recessive mutations, potentially reducing their adaptive potential. However, ploidy-specific SVs show signals of local adaptation in polyploids compared to diploids. SVs may also contribute to environmental adaptation, with climate-associated SVs identified in Cochlearia. The study highlights the complex role of SVs in polyploid evolution, suggesting that while SVs can increase genetic load, they may also provide adaptive benefits. The results indicate that SVs play diverse roles in the evolutionary trajectories of young polyploids, with implications for understanding the adaptive potential of polyploid organisms. The study also shows that SVs may become more important in future climate change scenarios, particularly in range-edge populations. Overall, the findings provide insights into the evolutionary relationship between WGDs and SVs, emphasizing their significance in polyploid evolution.Whole-genome duplication (WGD) significantly impacts structural variant (SV) evolution in the plant genus Cochlearia. Using long-read sequencing and a graph-based pangenome, the study reveals both negative and positive interactions between WGDs and SVs. Polyploid populations accumulate more deleterious SVs due to masking of recessive mutations, potentially reducing their adaptive potential. However, ploidy-specific SVs show signals of local adaptation in polyploids compared to diploids. SVs may also contribute to environmental adaptation, with climate-associated SVs identified in Cochlearia. The study highlights the complex role of SVs in polyploid evolution, suggesting that while SVs can increase genetic load, they may also provide adaptive benefits. The results indicate that SVs play diverse roles in the evolutionary trajectories of young polyploids, with implications for understanding the adaptive potential of polyploid organisms. The study also shows that SVs may become more important in future climate change scenarios, particularly in range-edge populations. Overall, the findings provide insights into the evolutionary relationship between WGDs and SVs, emphasizing their significance in polyploid evolution.