Allele Specific Expression in Bovine RNA Sequence Data

Gene expression can be regarded as a complex trait phenotype, affected by a number of mechanisms, including cis-regulatory genetic variation. Allele specific expression (ASE) analysis can be used to determine genes undergoing cis-regulatory variation. In this study, using RNAseq data mapped to parental reference genomes, we used a Chi-squared test to test for ASE in 18 tissues taken from a single lactating dairy cow and 2 tissues from 20 lactating dairy cows. 89% of all genes tested (total 7,985) in the single cow contained at least one SNP with significant (p<0.01) ASE, in at least one tissue. The ASE ranged from monoallelic to slight overexpression of the major allele. 83% (6,631) of genes displayed ASE in a tissue specific manner. 58% of ASE genes displayed divergent ASE patterns across tissues. The levels of ASE and tissue specificity were validated in the two tissues from 20 cows. Correlations between individual’s ASE within a tissue were only moderate, suggesting that there is much variation between individuals in which genes display ASE. We conclude that ASE is pervasive in cattle and largely tissue specific with divergent ASE across tissues common.  Identification of ASE SNP will aid in the detection of cis-regulatory variants responsible for phenotypic variation in bovine production traits, which in turn, may lead to improved selection of animals.