RNA-Seq Analyses Reveals High Frequency of Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken

Epigenetic and genetic cis-regulatory elements in diploid organisms may cause allele specific expression (ASE) – unequal expression of the two autosomal gene copies. An intriguing type of ASE is that some genes are expressed monoallelically from either the paternal allele or maternal allele, i.e. genomic imprinting. Imprinted genes have been identified in several animal species and are frequently associated with embryonic growth. Yet whether genomic imprinting exists in chickens is still debatable, as previous studies have reported conflicting evidence. Albeit no genomic imprinting has been reported in the chicken embryo as a whole, we investigated whether certain individual embryonic tissues exhibit genomic imprinting. In this study we interrogated the existence or absence of genomic imprinting in chicken embryonic brain and liver by examining the mRNA expression of parental alleles in an F1 generation. Eggs from two inbred chicken lines (Fayoumi and Leghorn) and their reciprocal crosses were collected and incubated for 12 days; then brain and liver were harvested from embryos for cDNA library preparation. To establish the genotypes of the inbred lines and their F1 hybrids and to minimize reference bias of RNA-Seq sequence alignment, genomic DNA from inbred Fayoumi and Leghorn chickens was pooled separately and each pool was sequenced at 20X coverage. Our results indicate that 34% and 30% of genes show ASE pattern in chicken 12-day embryonic brain and liver, respectively. But, there was no evidence detected of genomic imprinting in chicken 12-day embryonic brain and liver.