Uncovering functional INDELs responsible for splice sites in sheep with different immune profiles naturally exposed to gastrointestinal nematode infection

Gastrointestinal nematodes (GINs) are responsible for high morbidity and mortality rates in the sheep industry. This study aimed to identify functional INDELs responsible for splice sites using RNA-Sequencing from the liver tissue of sheep with different innate immune responses after being naturally exposed to GIN infection. Two GIN-naïve groups of lambs with divergent cortisol levels (high stress responders - HSR and medium stress responders - MSR) were naturally exposed to GIN during grazing. The animals were euthanized, and six HSR and six MSR, in addition to four immunological control animals (GIN-unexposed), were selected for RNA sequencing from liver tissue. Variant INDELs were identified, and variant consequences analysis was performed to identify INDELs responsible for splice site (SS). A total of 34,168 and 39,380 INDELs were identified for the HSR and MSR, respectively. From those, 1,614 and 2,980 INDELs were responsible for possible SS. The location of the INDELs yielded a list of 514 and 855 genes for HSR and MSR, respectively. Among these genes, the STAT6 and CFI genes were identified. The CFI gene was previously identified as differentially expressed in resistant lines of sheep exposed to GIN, and the STAT6 gene appears to play an important role in the immune response to helminths. The Terminal pathway of complement was enriched (FDR > 0.05) and could be playing a role in building an innate immune response to GIN infection. This study identified novel INDELS responsible for possible SS in genes that could be modulating the immune response to GIN in sheep. Furthermore, enriched immune-related pathways were discovered, suggesting previously uncharacterized components in the inflammatory response to GIN in sheep.