Coccidiosis is an economically important intestinal parasitic disease in poultry production characterized primarily by intestinal damage and bleeding [1]. In chickens, coccidial infection affects intestinal digestion and absorption, leading to a reduction in body weight gain and feed conversion [2,3], inflammation, suppression of the immune system, and increased mortality [4]. These deleterious effects seriously jeopardize poultry productivity and welfare, thus hindering the development of the poultry industry globally [4,5]. Demand for chicken meat and eggs is likely to increase in the future, highlighting the need for effective measures to prevent and control coccidiosis in poultry.

MicroRNAs (miRNAs) are a class of small, non-coding RNA molecules with lengths of approximately 20–22 nucleotides [6]. MiRNAs are evolutionarily conserved in animals. They exert their functions through the post-transcriptional regulation of messenger RNA (mRNA) [7]. MiRNAs act mainly by binding to the 3′-untranslated region (3′UTR) of target mRNAs, thereby inducing their degradation or inhibiting their translation [7,8]. Their biological functions include important roles in immune and inflammatory responses, such as in immune cell differentiation and activation, cytokine responses, and relevant intracellular signaling pathways [9,10]. Several studies have shown that miRNAs participate in the regulation of the immune response to pathogen infection [11,12]. Tim et al. [13] analyzed the expression of miRNAs in fast-growing broiler chickens infected with Eimeria maxima and Eimeria acervuline and found that gga-miR-122-5p, gga-miR-205b, and gga-miR-144-3p could serve as diagnostic markers for sub-clinical coccidiosis. Additionally, 24 miRNAs were found to be differentially expressed between different stages (endogenous and exogenous) of the E. tenella life cycle and were likely to be involved in the development of coccidian oocysts [14]. The miRNA expression profile in the small intestine of chickens during Eimeria necatrix infection has also been reported [15].

However, relatively few studies have investigated the expression profiles, functions, and regulation of miRNAs in poultry during coccidial infection. In the present study, we used transcriptome sequencing to delineate the expression profiles of miRNAs in the cecal tissue of control, resistant, and susceptible broiler chickens following infection with E. tenella and conducted functional and molecular experiments of the key differentially expressed miRNAs. The purpose of this research was to further understand the inflammatory response of chickens against E. tenella infection from the perspective of miRNA.