Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle

The response of the abomasal transcriptome to gastrointestinal parasites was evaluated in parasite-susceptible and parasite-resistant Angus cattle using RNA-seq at a depth of 23.7 million sequences per sample. These cattle displayed distinctly separate resistance phenotypes as assessed by fecal egg counts. Approximately 65.3% of the 23,632 bovine genes were expressed in the fundic abomasum. Of these, 13,758 genes were expressed in all samples tested and likely represent core components of the bovine abomasal transcriptome. The gene (BT14427) with the most abundant transcript, accounting for 10.4% of sequences in the transcriptome, is located on chromosome 29 and has unknown functions. Additionally, PIGR (1.6%), Complement C3 (0.7%), and Immunoglobulin J chain (0.5%) were among the most abundant transcripts in the transcriptome. Among the 203 genes impacted, 64 were significantly over-expressed in resistant animals at a stringent cutoff (FDR < 5%). Among the 94 224 splice junctions identified, 133 were uniquely present: 90 were observed only in resistant animals, and 43 were present only in susceptible animals. Gene Ontology (GO) enrichment of the genes under study uncovered an association with lipid metabolism, which was confirmed by an independent pathway analysis. Several pathways, such as FXR/RXR activation, LXR/RXR activation, LPS/IL-1 mediated inhibition of RXR function, and arachidonic acid metabolism, were impacted in resistant animals, which are potentially involved in the development of parasite resistance in cattle. Our results provide insights into the development of host immunity to gastrointestinal nematode infection and will facilitate understanding of mechanism underlying host resistance.