Abstract
The characterization of T cells in chickens has proven to be challenging, primarily due to the lack of specific markers to differentiate classical Th1, Th2, and Th17 subsets. Furthermore, chickens possess a notably high proportion of γδ T cells, making them a unique model for investigating the poorly understood role of these cells not only in chickens but also in mammals. To gain deeper insights into the functions and characteristics of the αβ and γδ T cell subsets in chickens, whole transcriptome analysis (WTA) on CD3(+) single cells isolated from wild type (WT), TCR Cβ knockout (KO) and TCR Cγ KO chickens at embryonic day (ED) 18, day (d) 3, and d14 post-hatch was conducted. The results indicate that γδ T cells exhibit cytolytic activity in both TCR Cβ KO and WT chickens. A distinct cluster of γδ T cells expressing genes associated with the interferon pathway was revealed in TCR Cβ KO chickens, which may contribute to the severe phenotype in these chickens, which is characterized by severe inflammation of spleen, gut and stomach. Additionally, novel gene markers were identified that precisely define the αβ and γδ T cell subsets. These findings provide new insights into chicken T cell biology and contribute to a better understanding of the mechanisms underlying the severe phenotype observed in TCR Cβ KO chickens. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12741-8.