Abstract:
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 <0.01) compared to the
two other genetic clusters. FEC breeding values of 114 ± 97, -629 ± 84 and -2 ± 45 were
recorded for Cluster 2, 3 and 4, respectively. The distribution of runs of homozygosity was determined for Clusters 1 to 4. Cluster 4 had the most animals and the highest number of
ROH was observed in this genetic cluster. The results from this study indicated that it should
be possible to select for resistance to H. contortus on the basis of the phenotypic traits.
