De novo mutations arising in the germline add to genetic variation. The number of de novo mutations occurring every generation, especially structural variants, has not been well studied in most species, including livestock. We used whole-genome sequencing from 46 pig trios from two commercial lines to identify de novo structural variants (dnSVs) present in the offspring. We characterised these dnSV by identifying their parent-of-origin, predicting their causal mechanisms, and identifying their functional annotations. We identified four dnSVs, including two clusters of mutations. One of these clusters contained a deletion, and three duplications, one of which was inverted. This cluster was the only dnSV that could be phased and was located in the paternal haplotype of the proband. All four identified dnSVs were located within the introns of genes. Our study is the first of its kind to identify and characterise dnSVs using whole genome shotgun sequence data in pigs.

Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.