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