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 mammals and is associated with healthy and economically relevant traits. ASE is often used to support the identification of variants related to gene expression (cis-eQTLs). Thus, profiling ASE represents a significant step in elucidating the mechanism underlying gene expression regulation. In this study, we developed an ASE pipeline using public available RNA-seq data and open-source software. Using this pipeline, we were 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 genotype or whole genome sequence data. ASE was widely, but not evenly, spread across the genome. We also observed considerable variation in ASE profiles among various tissues, in which the ASE fraction ranged from 1.3% to 54.1%. ASE tends to be highly tissue-specific, and the overlap across tissues is limited. The functional analysis of tissue-specific ASE sites indicates that they are involved in the critical maintenance of these tissues. Our ASE pipeline can be readily applied to other RNA-seq data sets for livestock, thereby significantly 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.