Mapping the landscape of allele-specific expression in porcine genomes

Allele-specific expression (ASE) is the imbalanced expression of two alleles of the same locus. It is quite pervasive among many species and is associated with health and economically relevant traits. ASE is often used to support the identification of variants related to gene expression (cis-eQTL). Thus, profiling allele-specific expression represents a significant step in elucidating the mechanism underlying gene expression regulation.

In this study, we developed an ASE pipeline using publicly available RNA-seq data and open-source software. Using this pipeline, we are able to profile pervasive allelic imbalance across 42 tissues and 34 breeds from the Farm-GTEx-pig consortium at both SNP and gene levels without the need for parental genotypes or whole genome sequence data. We find that ASE is widely, but not evenly, spread across the genome. We also observe considerable variation in ASE profiles across various tissues, where the site fraction ranged from 1.3% to 54.1%. ASE tends to be highly tissue-specific, with limited overlap across tissues. The functional analysis of tissue-specific ASE sites indicates that they are involved in important biological functions of these tissues. Our ASE pipeline can be readily applied to other RNA-seq datasets for livestock and other species, thereby expanding its potential utility.

The wealth of available ASE resources provides a solid foundation for identifying regulatory elements within the genome that drive complex traits in livestock, making our pipeline and results valuable resources for researchers in this field.