Detection and characterisation of de novo structural variants in pigs

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.