This study aimed to investigate the potential association between the breeding values for somatic cell scores in milk (SCS) and polymorphisms in genes that encode for cytokines (CXCL8, TGF-β1 and IFN-γ) and CD4. These genes were selected because of their critical roles in immune regulation and their known involvement in mastitis-related inflammatory processes. To gain a comprehensive breeding perspective, the association study was conducted simultaneously with breeding values for productive traits in 558 Italian Simmental cows, a widespread dual-purpose dairy and beef bovine breed that is adaptable to harsh farming and breeding conditions.

The association analysis showed that only three of the nine chosen markers, one in IFN-γ and two in CD4, significantly associated with somatic cell breeding values, without effects on the other dairy traits. Only one of the two CD4 SNPs has been considered, being in linkage disequilibrium. The two remaining SNPs were grouped into three haplotypes (A–G, 88%; A–A, 5%; and T–G, 7%, respectively), and Haplotype-3 significantly affected the breeding values for SCS. The combination of Haplotype-1 with Haplotype-2 resulted in a significant decrease, while with Haplotype-3 led to a considerable improvement in SCS breeding values. It was noted that the functional haplotypic combinations examined did not significantly affect the production breeding values. This research could provide interesting polymorphisms for genomic evaluation of Italian Simmental dairy cows, increasing the accuracy of breeding values, assisting breeders in selecting animals with enhanced immune responses, minimising the economic impact of mastitis, and improving overall herd health and productivity.

Third-stage larvae of the anisakid nematode Contracaecum osculatum infecting cod (Gadus morhua) liver elicit a host immune response involving both innate and adaptive factors, but the reactions differ between liver and spleen. Inflammatory reactions occur in both liver and spleen, but a series of immune effector genes are downregulated in liver infected with nematodes whereas these genes in spleen from the same fish are upregulated. A series of novel primer and probe sets targeting cod immune responses were developed and applied in a real-time quantitative polymerase chain reaction set-up to measure the expression of immune-relevant genes in liver and spleen of infected and uninfected cod. In infected liver, 12 of 23 genes were regulated. Genes encoding cytokines associated with inflammatory reactions (IL-1β, IL-6, IL-8) were significantly upregulated, whereas genes encoding effector molecules, assisting the elimination of pathogens, C-reactive protein (CRP)-PII, hepcidin, lysozyme G1, lysozyme G2, C3 and IgDm, were significantly downregulated. The number of downregulated genes increased with the parasite burden. In spleen, 14 of 23 immune genes showed significant regulation and nine of these were upregulated, including genes encoding CRPI, CRPII, C3, hepcidin and transferrin. The general gene expression level was higher in spleen compared to liver, and although inflammation was induced in nematode-infected liver, the effector molecule genes were depressed, which suggests a worm-induced immune suppression locally in the liver.

All organisms encounter pathogens, and birds are especially susceptible to infection by malaria parasites and other haemosporidians. It is important to understand how immune genes, primarily innate immune genes which are the first line of host defense, have evolved across birds, a highly diverse group of tetrapods. Here, we find that innate immune genes are highly conserved across the avian tree of life and that although most show evidence of positive or diversifying selection within specific lineages or clades, the number of sites is often proportionally low in this broader context of putative constraint. Rather, evidence shows a much higher level of negative or purifying selection in these innate immune genes – rather than adaptive immune genes – which is consistent with birds' long coevolutionary history with pathogens and the need to maintain a rapid response to infection. We further explored avian responses to haemosporidians by comparing differential gene expression in wild birds (1) uninfected with haemosporidians, (2) infected with Plasmodium and (3) infected with Haemoproteus (Parahaemoproteus). We found patterns of significant differential expression with some genes unique to infection with each genus and a few shared between ‘treatment’ groups, but none that overlapped with the genes included in the phylogenetic study.