Database resource demonstrates integrated multiomics and graph pangenome analysis in pigs, facilitating trait-associated variant discovery.
Key Points
To overcome the limitations of single linear reference genomes in detecting structural variants and population-specific genetic diversity in pigs by creating a graph-based pangenome multiomics database.
Constructed a graph-based pangenome and variome incorporating 2,598 individuals across 35 pig breeds.
Integrated transcriptomic data from four tissues (liver, loin muscle, abdominal fat, and backfat) along with over 150,000 phenotypic records.
Built online analytical tools for genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and colocalization.
Identified and cataloged 185,759 structural variants, 117 million SNPs, and 6.8 million indels across the multi-breed population.
Provided an interactive multiomics framework that successfully pinpointed trait-associated loci and clarified potential regulatory mechanisms through two proof-of-concept analyses.