Genomic evaluation of resistance to Haemonchus contortus in a South African Dohne Merino flock

Abstract

The aim of this study was to use genome-wide SNP data to investigate phenotypic and genetic differences in resistance to Haemonchus contortus between resistant and susceptible South African Dohne Merino sheep. The participating farm (Wauldby) 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 annually on lambs from weaning in January until the end of June from 2011 to 2014. Animals with FAM scores of ≥ 2.5 or BCS scores < 1.5 were subjected to anthelmintic treatment and recorded as “Dosed” animals. Animals (196) were selected for genotyping based on EBV for FEC and classified into Case and Control groups on the basis of whether they were dosed or not. The Grootfontein Dohne Merino flock has never been subjected to selection for resistance to gastrointestinal parasites and 48 animals were selected on FEC for genotyping. DNA obtained from blood samples were genotyped using the Illumina® Ovine SNP50 BeadChip. Principal component analysis (PCA) resulted in four distinct genetic clusters, with the Grootfontein sheep population clustering separately. The Wauldby animals in Cluster 3 had significantly lower FEC and higher BCS than the animals in Clusters 2 and 4. FEC breeding values of 114 ± 97, -629 ± 84 and -2 ± 45 were recorded for PCA-based Genetic cluster 2, 3 and 4 animals, respectively. The majority (88%) of animals in Cluster 3 were the progeny of sires from the resistant line. The average number of runs of homozygosity (ROH) was 44, 46, 54 and 47 per animal for Clusters 1, 2, 3 and 4 respectively. The highest number of ROHs was found on chromosomes 1, 2, 3, 4, 6, 9 and 10, on which QTL for resistance traits have been identified previously. Sires in Genetic cluster 3 were highly resistant and can be used in a breeding program to develop H. contortus resistant sheep. The results indicated genetic variation in host resistance against H. contortus in the Wauldby flock and breeding for resistance against nematodes is feasible.