PSVRP: a pig structural variant reference panel for complex trait genomics and precision breeding

Pigs are not only a key source of animal protein worldwide, but also serve as important models in biological research. With the rapid development of short- and long-read sequencing technologies, genetic studies in pigs have advanced considerably. Although extensive research has been conducted on single-nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), which has provided important insights into pig domestication, evolution, and trait formation, structural variants (SVs) remain underexplored due to technical limitations in sequencing resolution, challenges in variant detection, and insufficient population-scale sampling.

In this study, we constructed the Pig Structural Variant Reference Panel (PSVRP) by integrating 21 long-read and 1,193 short-read whole-genome resequencing datasets from globally diverse pig populations. A total of 319,058 high-confidence SVs were identified, comprising 196,620 insertions and 122,438 deletions. Phylogenetic and ADMIXTURE analyses revealed clear divergence between Asian and European pigs, consistent with results derived from SNPs and indels data. Selection scans highlighted candidate genes associated with key traits, such as EPAS1 and NOVA1 for high-altitude adaptation, and PLAG1 and MIB1 for body size regulation.

The PSVRP provides a high-resolution, population-scale pig SVs genotyping resource. This comprehensive panel deepens our understanding of genetic variation, facilitates the discovery of functional variants underlying adaptive and economic traits, and offers new insights for precision pig breeding.