ArticleBMC genomics2025
Unlocking the genetic code: a comprehensive Genome-Wide association study and gene set enrichment analysis of cell-mediated immunity in chickens.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Genome-wide association study reveals putative genetic determinants of longitudinal immune responses to avian influenza and Newcastle disease in chickens.Genetics, selection, evolution : GSE · 2026Article
- Mechanistic insights into probiotic modulation of the gut-immune axis and their role as sustainable antibiotic alternatives in poultry production: An integrative review.Veterinary world · 2026Article
- Genome-wide association study reveals loci associated with cytokine levels in chicken serum.Poultry science · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Role of PI3K gene family as a molecular hub for regulation of growth and immunity: Potential implications for sustainable poultry production.Poultry science · 2026Review
- An Integrative Genetic Strategy for Identifying Causal Genes at Quantitative Trait Loci in Chickens.Animals : an open access journal from MDPI · 2026Review
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Authors and funding
5 authors.
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Abstract
backgroundThe poultry immune system is essential for protecting against infectious diseases and maintaining health and productivity. Cell-mediated immune responses (CMIs) protect organisms against intracellular pathogens. This study aimed to enrich the findings of genome-wide association studies (GWAS) by including several systematic gene set enrichment analyses (GSEA) related to cell-mediated immune responses in chickens.
methodsTo investigate the function of the cellular immune system, phenotypic data were collected based on the differences in skin thickness before and after impregnation with dinitrochlorobenzene (DNCB) solution. Additionally, 312 hybrid birds of the F2 generation of Arian broiler chickens and Urmia native chickens were genotyped using the Illumina 60k SNP BeadChip. A general linear model (GLM) with an FDR < 5% was used for the association analysis. Functional enrichment analysis of the identified candidate genes was performed using the Enrichr database. A protein‒protein interaction (PPI) network was constructed using the STRING database. In addition, colocalization analysis was applied to identify QTLs related to the immune system.
resultsGWAS revealed 147 SNPs associated with the CMI trait, which were related to 1363 genes. These genes were significantly enriched in eight KEGG pathways, 22 Reactome pathways, and 18 biological processes. PPI network analysis led to the identification of 26 hub genes. The three hub genes PSMA3, PSMC2 and PSMB4 were enriched in almost all pathways related to cellular immunity, including the proteasome, interleukin-1 signaling, and programmed cell death pathways, which makes them important candidates involved in CMI. In addition, the MAP3K8, NLRC5, UBB, CASP6, DAPK2, TNFRSF6B, TNFSF15, and PIK3CD genes were identified as key genes in several functional pathways. A total of 10 SNPs were found in interferon-gamma QTLs, and two SNPs were found in the cell-mediated immune response QTL region, leading to the identification of 12 cellular immune response-related genes that were reported as important candidates in previous studies.
conclusionThe post-GWAS analysis in this study led to the identification of key genes that regulate the biological processes of cellular immunity in chickens. Therefore, selecting birds that excel in expressing such genes can improve immunity in chickens.
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