The influence of structural variants from 2445 pigs on gene expression and complex traits

The impact of structural variants on gene regulation and complex traits in pigs remains poorly understood. Here, we present a resource comprising 60 long-read sequencing and 2445 high-quality short-read sequencing samples from 120 pig breeds/populations worldwide. These samples include 293 high-depth short-read sequencing samples and three long-read samples generated in this study. Integrating two graph-based genotyping approaches, we construct a structural variant map encompassing 158,288 deletions, 137,493 insertions, 660 inversions, and 10,063 duplications. We perform eQTL mapping in liver, skeletal muscle, backfat, and intramuscular fat tissues from an F6 hybrid pig family, finding that 49.01% of expressed genes are significantly associated with cis-region structural variants. We further explore the contribution of structural variants to domestication and population differentiation. We find a 53 bp insertion on chromosome 11 that significantly down-regulates GPC6 expression in liver tissue, potentially contributing to adaptive selection in northern Chinese pig populations. Additionally, FST analyses between miniature and commercial pig breeds identify candidate structural variant loci associated with body size. We next integrate results from structural variant-eQTL and GWAS to find a 50 bp deletion at chr4:75,613,295 that significantly reduces PLAG1 expression in skeletal muscle tissue and is associated with body weight at 240 days of age. Structural variation in pigs remains poorly understood. Here, the authors analyse the genomes from 2,445 pigs to create a map of structural variation in pigs and explore how these variants affect gene activity, domestication and body size.