De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots

The Duroc × (Landrace × Yorkshire) (DLY) pig is a cornerstone of three-way crossbreeding system. Nevertheless, advances in commercial crossbred performance have been constrained by the dearth of high-resolution genomic resources for this key population. Here, we report the sequencing and assembly of 16 haplotype-resolved, chromosome-level genome assemblies derived from eight DLY pigs. These assemblies exhibited high continuity (contig N50: 18.17–29.54 Mb) and completeness (BUSCO: 99.3–99.4%), with sequences successfully localized to the 19 chromosomes. Genome annotation revealed an average of 21,922 protein-coding genes and 44.66% repetitive sequences per assembly. Comparative genomic analysis against the current reference genome Sscrofa11.1 enabled the construction of a non-redundant SV catalog comprising 130,416 variants, nearly half of which (48.99%) were novel relative to existing pig pan-genome SV panel. These SVs clustered non-randomly into 231 “SV hotspots” that were significantly enriched in protein-coding genes and putative regulatory elements. Functional analyses further linked these SV hotspots to quantitative trait loci (QTLs) associated with economically important traits. A focused analysis of a 3.43 Mb hotspot on chromosome 1, overlapping a known QTL for average daily gain, revealed eight high-frequency SVs in open chromatin regions near candidate genes (NCS1, HMCN2, FUBP3, ABL1, and FIBCD1), suggesting a cis-regulatory mechanism that may influence gene expression. Collectively, this work provides the first haplotype-resolved genomic resource for commercial crossbred pigs, and establishes a foundational framework for deciphering the genomic architecture of hybrid vigor and advancing precision breeding in swine.