Multi-omics fine-mapping pins pleiotropic pig growth-and-fatness signal to a single enhancer variant

Researchers describe in a bioRxiv preprint a multi-omics fine-mapping exercise that resolves a shared genetic signal influencing average daily gain and backfat thickness in Yorkshire pigs to a single candidate functional variant, rs334769214, located within a 1.59-megabase region on Sus scrofa chromosome 1 (SSC1).

The study integrated genome-wide association data from 7,972 pigs with targeted capture sequencing, linkage-disequilibrium-based fine-mapping, porcine epigenomic annotations, three-dimensional chromatin interaction maps, and functional assays to prioritise the variant. The causal candidate lies within an intestinal enhancer that regulates expression of PMAIP1, a gene encoding a pro-apoptotic BCL-2 family protein. The preprint presents this as an example of pleiotropy — where a single regulatory variant influences multiple biologically distinct traits — resolved through the integration of multiple genomic data layers.

The work is primarily of interest to researchers in agricultural genomics, quantitative genetics, and regulatory genomics. The methods applied here — combining GWAS fine-mapping with single-tissue epigenomic and chromatin conformation data — are increasingly standard approaches for dissecting the regulatory architecture of complex traits across species, and the study may have methodological relevance beyond its livestock context. This is a preprint and has not yet been peer reviewed.