Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep.

Rising drug resistance necessitates genomic selection to enhance parasite resistance in sheep. Copy number variations (CNVs) constitute structural genomic alterations that influence livestock traits by modifying gene dosage. This study aimed to identify candidate CNVs that differentiate between Haemonchus contortus-resistant and susceptible Rideau Arcott ewe lambs through comprehensive whole genome sequencing (WGS) analysis. Fecal egg count (FEC) analysis of 32 inoculated animals across five time points (days 21, 28, 35, 42, and 56 post-infection) identified 16 individuals with consistent extreme parasite response phenotypes. The resistant group (n = 9) showed a 10.5-fold lower FEC at day 21 post-infection and maintained 3- to 14-fold lower FEC (p < 0.05) across multiple time points than the susceptible group (n = 7). Consensus calling across CNVpytor, DELLY, and Manta algorithms yielded 22,184 high-confidence CNVs from WGS data at 6.75X genome coverage. These CNVs were consolidated into 3,751 CNV regions (CNVRs) encompassing 65.0 Mb (2.63%) of the sheep autosomal genome. Group-wise comparison identified 329 resistant-only and 133 susceptible-only differential CNVRs. The resistant group harboured 3.5-fold more gain category CNVRs and 13-fold more associated duplicated genes than susceptible animals. A 2.3 Mb duplication containing CLCA1 appeared exclusively in resistant sheep, which is associated with mucus production. Functional enrichment analysis also confirmed that calcium-gated chloride channel activity was exclusively in the resistant group, which is associated with regulating mucus production. Additional resistance-associated gain CNVRs encompassed LTC4S, ROBO1, RASGRP1, PRKCQ, and MBL2. Conversely, susceptible animals exhibited metabolic dysfunction potentially due to PIK3CA and AGXT duplications, with an enrichment of pathways associated with diabetic cardiomyopathy and prion disease. The study suggests associations between resistance-linked CNVRs and genes involved in mucosal barriers, immune cell trafficking, and T-cell responses. In contrast, susceptible group-linked CNVRs are associated with metabolic disruption, suggesting that metabolic disturbance is a key factor in susceptibility. The first WGS-based CNV analysis successfully identified novel structural variants distinguishing resistant from susceptible Rideau Arcott ewe lambs. The discovery of resistance- and susceptibility-specific gene duplications and metabolic pathways offers new targets for genetic selection. However, the candidate CNVRs warrant validation in larger populations for implementation in breeding programs aimed at improving parasite resistance.