Copy number variation regions in sheep resistant, resilient and susceptible to gastrointestinal nematode infection

Gastrointestinal nematode (GIN) infection in sheep is a major cause of production losses, and the inappropriate use of anthelmintics has promoted drug resistance and environmental contamination, highlighting the need for alternative control strategies. Copy number variations (CNVs) are important structural variations that can influence gene expression, adaptation, and disease susceptibility. Therefore, this study detected copy number variation regions (CNVRs) in resistant, resilient, and susceptible Santa Ines sheep, and identified genes associated with resistance to GIN. The estimated breeding values of 573 genotyped animals for packed cell volume, fecal egg count, and FAMACHA© score obtained with single-trait animal models were used in cluster analysis to identify resistant, resilient, and susceptible animals based on the additive genetic pattern of each trait. CNVs were detected using PennCNV v1.0.5 and CNVRs were inferred by concatenation of individual CNVs. The resistant, resilient, and susceptible clusters contained 93, 172 and 197 CNVRs, respectively. The concatenation of CNVRs revealed 25 genomic regions shared among all three clusters, 43 genomic regions shared between the resilient and susceptible clusters, 18 genomic regions shared between the resistant and resilient clusters, and 16 genomic regions shared between the susceptible and resistant clusters. Concatenation also identified 34, 86 and 113 genomic regions exclusively in the resistant, resilient and susceptible clusters, respectively. Functional enrichment analysis revealed several terms related to immunity, inflammation, tissue repair, vesicular trafficking, and cell adhesion. This study contributes to improving our understanding of the mechanisms that underlie resistance, resilience, and susceptibility to GIN in sheep.