Comparison and contrast of genes and biological pathways responding to Marek’s disease virus infection using allele-specific expression and differential expression in broiler and layer chickens

Abstract

BackgroundMarek’s disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek’s disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is desirable to augment current vaccines and other MD control measures. High throughput sequencing was used to profile splenic transcriptomes from individual F1 progeny infected with MDV at 4 days of age from both outbred broilers (meat-type) and inbred layer (egg-type) chicken lines that differed in MD genetic resistance. The resulting information was used to identify SNPs, genes, and biological pathways exhibiting allele-specific expression (ASE) in response to MDV infection in each type of chicken. In addition, we compared and contrasted the results of pathway analyses (ASE and differential expression (DE)) between chicken types to help inform on the biological response to MDV infection.ResultsWith 7 individuals per line and treatment group providing high power, we identified 6,132 single nucleotide polymorphisms (SNPs) in 4,768 genes and 4,528 SNPs in 3,718 genes in broilers and layers, respectively, that exhibited ASE in response to MDV infection. Furthermore, 548 and 434 genes in broilers and layers, respectively, were found to show DE following MDV infection. Comparing the datasets, only 72 SNPs and 850 genes for ASE and 20 genes for DE were common between the two bird types. Although the chicken types used in this study were genetically different, at the pathway level, both TLR receptor and JAK/STAT signaling pathways were enriched as well as exhibiting a high proportion of ASE genes, especially at the beginning of both above mentioned regulatory pathways.ConclusionsRNA sequencing with adequate biological replicates is a powerful approach to identify high confidence SNPs, genes, and pathways that are associated with transcriptional response to MDV infection. In addition, the SNPs exhibiting ASE in response to MDV infection provide a strong foundation for determining the extent to which variation in expression influences MD incidence plus yield genetic markers for genomic selection. However, given the paucity of overlap among ASE SNP sets (broilers vs. layers), it is likely that separate screens need to be incorporated for each population. Finally, comparison of gene lists obtained between these two diverse chicken types indicate the TLR and JAK/STAT signaling are conserved when responding to MDV infection and may be altered by selection of genes exhibiting ASE found at the start of each pathway.

Transcriptional Profiling of MEq-Dependent Genes in Marek’s Disease Resistant and Susceptible Inbred Chicken Lines

“…Our group has previously demonstrated that Jak-STAT is an important cellular pathway involved in genetic basis of MD resistance [20,30]. Similarly, we also noted that genes in Jak-STAT pathway are transcriptionally up-regulated in susceptible line 7 and not in the resistant line 6.…”

“…However, it is worth noting transcript profiling using spleens and other organs suffers from the potential confounding influence of differences in cellular composition and reagents to properly quantify each cell subtype are limiting in chicken. Thus, the high degree of overlap between our current results, which utilized cultured cells from defined chicken lines, and those from our other studies that used actual birds [11,12,20,30] for the identification of critical pathways suggests that CEF are reasonable models. This agreement also suggests an important contribution of innate immunity towards MD genetic resistance.…”

“…A total of 24 candidate genes exhibited polymorphisms between the two lines in their Meq-binding motifs (e.g., TGACTCA or CACACAGC) located in their proximal promoter region (Table 2). Interestingly, this analysis revealed genes in the MAPK kinase signaling pathway (e.g., BRAF and GPS1), contributing to cell cycle regulation (e.g., FANCA, NDC80, and RB1), or coding for transcription factor subunits (e.g., AP1M1 and OPTN), all of which are known to be connected to response to virus infection and members of pathways previously implicated in our prior studies [19,20]. …”

“…We have previously identified SNPs exhibiting allele-specific expression (ASE) in response to MDV infection using F 1 birds derived by intermating lines 6 and 7 [20]. However, the mechanism for the allelic transcriptional variation in response to MDV infection is unknown.…”

Next generation sequencing technologies: Tool to study avian virus diversity

“…Comprehensive analysis of AIV-infected lung tissue suggested that several microRNA (miRNAs) and mRNAs were likely to be involved in regulating the host response (Wang et al, 2012). Allele-specific expression (SNPs, genes and pathways) that was associated with transcriptional response to Marek´s disease virus (MDV) infection was identified to underlay genetic basis for disease resistance to MDV infection in both broilers and layers (Perumbakkam et al, 2013). Gene expression patterns of normal and duck hepatitis A virus genotype C (DHAV-C) infected duck livers were explored and compared, and new insights into the molecular mechanism of host-DHAV-C interaction were provided .…”