RNA-Seq Based Genome-Wide Analysis of Genomic Imprinting in Chicken Lungs

Genomic imprinting is non-Mendelian, autosomal inheritance resulting from mono-allelic gene expression from one parent-of-origin and it has been observed in viviparous vertebrates, insects and plants but not yet reported in oviparous vertebrates including birds. The objective of this study was to identify potential genomic imprinting genes in chickens. High-throughput RNA-seq is recently being used as a novel strategy to identify imprinted genes at whole-genome level by utilizing single nucleotide polymorphism (SNP) information in the transcriptome from highly inbred parental lines and their F1 reciprocal crosses. Our previous studies revealed that parent-of-origin effects of disease resistance and allele-specific expression were observed in the lungs of avian influenza virus infected inbred chicken lines and their F1 crosses (Leghorn and Fayoumi). These two genetically distinct, highly inbred chicken lines were used to maximize the efficiency of identification of the parent-of-origin of each transcript from their F1 reciprocal crosses. Whole transcriptome of lungs from three individuals of each parent line and four individuals of each F1 reciprocal cross were sequenced and a total of 270 million (M) and 300M 100 bp pair-end reads were generated, respectively. An average of 68.7% of RNA-seq reads were uniquely mapped against galGal4 chicken reference genome using the Bowtie2 and 339±97K SNPs were called by Samtools from each individual. Average 94% of SNPs were homozygous in parental lines and F1 reciprocal crosses had high heterozygosity of SNPs. Allelic expression bias and the significance of parent-of-origin effect will be analyzed and further verification of candidate imprinted genes is warranted.