Singel cell RNA sequencing of an F1 cross of Marek’s disease resistant and susceptible chickens

Marek's disease virus (MDV) is a highly contagious alphaherpesvirus with widespread incidence in the poultry industry. The double stranded DNA virus infects chickens and turkeys causing a lymphoproliferative disease known as Marek's disease (MD). Infected and susceptible birds develop T cell lymphomas that cause peripheral nerve degeneration, partial or complete paralysis and immunosuppression. Previously, our lab performed scRNA seq of splenic-derived cells from MD resistant Line 6 (L6) and MD susceptible Line 7 (L7) during MDV infection to identify major immune cell subsets. In this study we extend this previous analysis by adding scRNA seq of a first-generation (F1) L6 x L7 population to characterize allele specific expression in individual immune cell types. The joint analysis of scRNA seq of the L6, L7 and F1 cross provide a deeper understanding of how genetic variation impacts gene expression variation in immune cell types and identify regulatory mechanism playing a key role in MD resistance. Overall design: The experimental design consisted of 20 L6 x L7 F1 chickens randomly allocated to either an MDV-challenge or control (unchallenged) group, i.e., 10 chicks per condition. The challenged group receive an intra-abdominal injection at two weeks of age with 2,000 pfu JM/102W strain MDV. Birds were housed 6 days post-infection in HB units and humanly euthanized. Splenic derived lymphocytes were collected from each bird for sequencing. Three birds per condition were selected for 10X Genomics scRNA seq.