Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep

Mohammad Al Kalaldeh,Cedric Gondro,John Gibson,Julius H J Van Der Werf,Sang Hong Lee

doi:10.1186/s12711-019-0479-1

Abstract

BackgroundThis study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped with the high-density 600 K Ovine single nucleotide polymorphism array. This study included 7539 sheep from different locations across Australia that underwent a field challenge with mixed gastrointestinal parasite species. Faecal samples were collected and worm egg counts for three strongyle species, i.e. Teladorsagia circumcincta, Haemonchus contortus and Trichostrongylus colubriformis were determined. Data were analysed using genome-wide association studies (GWAS) and regional heritability mapping (RHM).ResultsBoth RHM and GWAS detected a region on Ovis aries (OAR) chromosome 2 that was highly significantly associated with parasite resistance at a genome-wise false discovery rate of 5%. RHM revealed additional significant regions on OAR6, 18, and 24. Pathway analysis revealed 13 genes within these significant regions (SH3RF1, HERC2, MAP3K, CYFIP1, PTPN1, BIN1, HERC3, HERC5, HERC6, IBSP, SPP1, ISG20, and DET1), which have various roles in innate and acquired immune response mechanisms, as well as cytokine signalling. Other genes involved in haemostasis regulation and mucosal defence were also detected, which are important for protection of sheep against invading parasites.ConclusionsThis study identified significant genomic regions on OAR2, 6, 18, and 24 that are associated with parasite resistance in sheep. RHM was more powerful in detecting regions that affect parasite resistance than GWAS. Our results support the hypothesis that parasite resistance is a complex trait and is determined by a large number of genes with small effects, rather than by a few major genes with large effects.

Highlights

This study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped with the highdensity 600 K Ovine single nucleotide polymorphism array
After weaning, a random faecal sample within a management group exceeded a threshold of 1000 eggs per gram in sites predominated by H. contortus, or 500 epg in sites predominated by other species, faecal samples were collected from all individual animals
The quantile–quantile (Q–Q) plot shows that, for these three significant single nucleotide polymorphism (SNP), the deviation from their expected values is larger, which indicates a strong association between these SNPs and parasite resistance (Fig. 3)

Summary

Introduction

This study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped with the highdensity 600 K Ovine single nucleotide polymorphism array. Gastrointestinal nematode infections (GNI) are one of the most important health problems that affect sheep and other grazing ruminants in Australia and worldwide. Genomic improvement for parasite resistance would benefit from greater knowledge about how sheep are able to mount effective immune responses against parasite infection and the genetic architecture behind the trait. Genome-wide association studies (GWAS) using dense single nucleotide polymorphism (SNP) arrays have been used to identify QTL for most of the economically important traits in livestock species. Minimal consistency has emerged from these studies, probably due to the physiological complexity of the trait, and the fact that these studies are very diverse in terms of methodologies, statistical approaches, sheep breeds and parasite species

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Discussion

Conclusion