PS1-24. Transcriptome-wide Identification of INDEL Variants with Potential Splice-site and Coding Effects in Nematode-challenged Sheep.

Abstract Gastrointestinal nematode (GIN) infections severely impact the global sheep industry, causing economic losses through reduced productivity and raising animal health and welfare concerns due to increased morbidity and mortality in affected animals. Insertions and deletions (INDELs) are a common form of genetic variation that can influence gene function through alterations in coding sequences or splice sites. This study aimed to identify INDEL variants with potential splice-site (SSE) and coding-sequence (CSE) effects in sheep with differing resistance to GIN infections. Publicly available RNA-seq data were obtained from the NCBI Gene Expression Omnibus database (Accession: GSE63547), comprising 20 abomasal lymph node samples collected from the most resistant (R; n = 10) and most susceptible (S; n = 10) Scottish Blackface lambs experimentally challenged with the Teladorsagia circumcincta nematode. Sequence quality control and alignment to the Oar_rambouillet_v3.0 reference genome were performed using CLC Genomics Workbench v20.0.4. INDEL discovery was conducted using the fixed ploidy variant detection tool to identify variants uniquely fixed in the R and S groups. Identified INDELs were annotated to determine their potential splice-site and coding effects using Ensembl Variant Effect Predictor (VEP). Genes associated with these INDEL variants were further analyzed for functional enrichment using the DAVID bioinformatics tool to explore their potential roles in host response to GIN infections. A total of 154 insertions with SSE or CSE were uniquely fixed in the R group, while 147 insertions were uniquely fixed in the S group. Similarly, 96 deletions with SSE or CSE were uniquely fixed in the R group, whereas 87 deletions were uniquely fixed in the S group. Functional enrichment analysis of genes associated with insertions in the R group revealed enrichment of signaling pathways involved in cell proliferation and survival, including PI3K–Akt, Rap1, and MAPK signaling pathways, along with processes related to cellular senescence and autophagy. In contrast, insertions in the S group were primarily associated with immune-related pathways, including T cell receptor signaling and natural killer cell–mediated cytotoxicity, as well as cellular signaling pathways such as phosphatidylinositol and phospholipase D signaling. For deletions, genes associated with variants uniquely fixed in the R group were enriched for processes related to RNA processing and mRNA splicing, as well as nuclear and cytoskeletal components. Conversely, deletions identified in the S group were enriched for pathways involved in DNA repair and genome maintenance, including base excision repair and DNA damage response processes. Overall, these findings suggest that INDEL variants with potential splice-site and coding effects may influence immune signaling and transcriptional regulation pathways associated with resistance or susceptibility to GIN infections in sheep.