Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep (PRJCA046372)
This study represents the first comprehensive whole genome sequencing-based copy number variation (CNV) analysis comparing Haemonchus contortus-resistant and susceptible Rideau Arcott sheep. Using controlled parasite challenge with 5,000 third-stage H. contortus larvae, we identified 16 animals with extreme resistance/susceptibility phenotypes from 78 ewe lambs. Whole genome sequencing at 6.75X coverage was performed using Illumina NovaSeq 6000 platform. Consensus CNV calling across three algorithms (CNVpytor, DELLY, and Manta) identified 22,184 high-confidence CNVs consolidated into 3,751 CNV regions. Analysis revealed 503 differential/candidate CNVRs between resistant and susceptible groups, with resistant animals showing enhanced mucosal barrier genes (CLCA1 duplication) and susceptible animals exhibiting metabolic dysfunction markers (PIK3CA, AGXT duplications). These findings provide novel genomic targets for selective breeding programs to enhance parasite resistance and reduce anthelmintic dependence in sheep production.