An Anas pangenome graph reveals the role of structural variations in duck domestication

Despite the significant phenotypic divergence between domestic ducks and their wild progenitors, the structural variants (SVs) underlying this differentiation remain largely unexplored due to the limitations of linear references in capturing genetic diversity across the genus Anas. Current pangenome efforts either lack base-level resolution or are constrained by genomic anchoring, hindering the exploration of genetic signatures of domestication. Here, we assembled chromosome-level genomes for a mallard (Anas platyrhynchos) and an eastern spot-billed duck (Anas zonorhyncha) that retained substantial domestic components. By integrating these with 14 high-quality Anas assemblies, we constructed a base-level resolution pangenome graph encompassing 243.4 Mb of non-reference sequences. Our graph-based pipeline demonstrated superior mapping performance and identified 67,165 population-level SVs, representing a five-fold increase in detection sensitivity compared to linear-based methods. Notably, SVs explained more genetic variance (PC1: 8.75% vs. 3.25%) and provided finer resolution of local ancestry than single nucleotide polymorphisms (SNPs), highlighting the unique advantage of SVs in resolving duck population structure. Leveraging the graph, we recovered 163 ancestral SVs that are prevalent in distant species but persist at low frequencies in domestic and wild populations. The loss of these ancestral sequences in gravity sensing and cilium assembly likely provided the physiological plasticity necessary for domestication. Moreover, highly divergent exonic SVs exhibited a non-random distribution, preferentially accumulating in UTRs over CDS regions. Specifically, highly divergent SVs located in UTRs of TMEM123 and FAM13A may be associated with viral resistance and the regulation of adipogenesis. Similarly, we identified a highly divergent 75 bp insertion located 3.66 kb upstream of the FAM184B gene, which may be associated with changes in muscle growth during duck domestication. In conclusion, the study establishes a comprehensive base-resolution pangenome resource for the Anas. Our findings reveal that SVs are essential for resolving complex evolutionary histories and suggest that SV-mediated regulatory evolution is an important driver of rapid phenotypic change during duck domestication.