A case-control study to evaluate resistance to Haemonchus contortus in SA Dohne Merino sheep

Gastrointestinal parasitism is a major problem to livestock productivity worldwide and small ruminant production is affected the most. Resistance of gastrointestinal nematodes (GIN) to anthelmintics is a widespread problem. Breeding animals resistant to nematode infestation has been proposed as a sustainable alternative. The aim of this study was to use highthroughput genome-wide SNP data to investigate the genetic background of GIN resistance in SA Dohne Merino sheep. The farm Wauldby in the Stutterheim district of South Africa has a history of heavy H. contortus challenge and implemented a selection strategy for resistance to H. contortus in 2011. Faecal egg count (FEC), body condition scores (BCS) and FAMACHA scores (FAM) were recorded on all lambs from weaning in January until the end of June annually. Lambs were only drenched if they had a FAM of 2.5 or higher. Breeding values (EBV) for FEC were estimated for the Wauldby animals born from 2011 to 2014. The GADI Dohne Merino flock is kept at the Grootfontein Agricultural Development Institute and has never been subjected to selection for resistance to GIN. FEC ranged from 0 to 52 500 among animals, recordings and years. Wauldby lambs that were not dosed had an overall lower FEC and FAM and higher BCS than lambs that were dosed once or more. Wauldby animals that were selected for genotyping based on EBV for FEC. Within years, animals with the highest (n= 48) and lowest (n=48) EBV for FEC were selected among the Dosed (Cases), as well as the Not dosed (Controls) (Low EBV FEC (n=52) and High EBV FEC (n=48). DNA obtained from blood samples were genotyped using the Illumina® Ovine SNP50 BeadChip. Principal component analysis (PCA) plot was performed using SNP & Variation Suite (SVS) from Golden Helix. Four distinct genetic clusters were observed, with the GADI Dohne Merino sheep population clustering separately. The Wauldby Dohne Merino population differentiated into 3 distinct clusters. ADMIXTURE version 1.23 was used to investigate population genetic structure. Fixation index (FST) was estimated between genetic clusters and ranged from low to moderate (0.040563 to 0.091004). The genetic diversity between the populations was assessed and observed heterozygosity (Ho), values of 0.3733 ± 0.1341 and 0.3736 ± 0.1468 were observed for the Wauldby Dohne Merino and GADI Dohne Merino sheep populations, respectively. The Wauldby animals in the different clusters were compared. Cluster 3 had lower FEC, lower FAM and higher BCS (P