Single-cell transcriptome profiling of peripheral blood mononuclear cells reveals immune cell heterogeneity in chickens

Chickens are economically important animals commonly utilized as model organisms in immunological research, but their immune cell heterogeneity and the subtle relationship between chicken immune cells and inter-breed immune variation remain poorly characterized. To fully understand the heterogeneity of immune cells and immune variation between breeds, single-cell RNA sequencing (scRNA-seq) technology was used to analyze the peripheral blood mononuclear cell (PBMC) of Hy-Line white (HW) and Hy-Line brown (HB) laying hens. This analysis revealed differences in immune cell heterogeneity and gene expression profiles among cell subpopulations between the two breeds. A total of nine immune cell populations were identified using known marker genes. Due to species differences between chickens and mammals such as humans and mice, which rendered some of the markers inapplicable, we identified new marker genes in the classification of cellular subpopulations that applied to chicken PBMC. Cell composition and expression abundance of immune genes underlie differences in immune traits between breeds. HW had a high intrinsic immune cell count, with a significant difference in the cellular proportion of B cells. In the B cell subpopulation, this was specifically demonstrated by the fact that B atypical memory and Plasma occupied a higher cellular proportion in HW. In contrast, the number of adaptive immune cells was higher in HB, with a significant difference in the proportion of conventional dendritic cell (cDC), specifically represented by type 1 conventional dendritic cell (cDC1) occupying a higher proportion of cells in HB and type 2 conventional dendritic cell (cDC2) occupies a higher proportion of cells in HW. In summary, HW can quickly respond to foreign pathogens and has stronger humoral immunity, while HB has advantages in antiviral response and cross-presentation. This study enhances our understanding of chicken immune heterogeneity and immune traits, facilitating the identification and functional analysis of chicken immune cells.