Allele-Specific Expression (ASE) of CD4+ T Cells in Response to Marek’s Disease Virus Infection

Marek’s disease (MD) is a T cell lymphoma and strictly cell-associated disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. To identify high-confidence candidate genes of MD genetic resistance, high throughput sequencing was used to obtain transcriptomic data in CD4⁺ T cells isolated from MDV non-infected and infected groups of two reciprocal crosses individuals mating by two highly inbred F0 chicken lines (6₃ MD-resistant and 7₂ MD-susceptible). After RNA-seq analysis with two biological replicates in each groups, we identified 61 and 123 SNPs (FDR<0.05) annotated in 39 and 132 genes in each reciprocal across, respectively, which exhibited allele-specific expression (ASE) in response to MDV infection. Similarly, we identified 79 and 62 SNPs annotated in 96 and 66 genes in non-infected and infected groups, respectively. qPCR assay of seven differentially expressed genes further verified our results of RNA-seq. Gene-set enrichment analysis showed that many ASE genes were linked to the T cell activation and T cell receptor signaling pathways. Overall, our results suggested that ASE analysis is a simple and powerful approach to identify specific alleles and genes for genetic resistance to MD and other complex traits, and will provide deep insight into the mechanisms of MD and disease resistance breeding in poultry.