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Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

ABSTRACT: BACKGROUND:Dagginess (faecal soiling of the perineum region) and host nematode parasite resistance are important animal welfare traits in New Zealand sheep. Genomic prediction (GP) estimates the genetic merit, as a molecular breeding value (mBV), for each trait based on many SNPs. The additional information the mBV provides (as determined by its accuracy) has led to its incorporation into breeding schemes. Some GP methods give SNP effects, which provide additional information to identify genome-wide associations (GWAS) for a trait of interest. Here we report results from a GP and GWAS study for dagginess and host nematode parasite resistance in a New Zealand sheep industry resource. RESULTS:Genomic prediction analysis was performed using 50K SNP chip data and parent average-removed, de-regressed BVs for five traits, from a resource of 8705 pedigree recorded animals. The five traits were dag score at three and eight months (DAG3, DAG8) and nematode faecal egg count in summer (FEC1), autumn (FEC2) and as an adult (AFEC). The resource consisted of Romney, Coopworth, Perendale, Texel and various breed crosses (designated: CompRCP, CompRCPT and CompCRP). The pure breeds, apart from Texel, plus CompRCP were used to develop the GP. The resulting SNP effects were used to identify genetic regions associated with dagginess and parasite resistance. Accuracies of the weighted correlation between mBV and true BV ranged between -0.07 (Texel) and 0.56 (Coopworth) for DAG3 and DAG8. For FEC1, FEC2 and AFEC accuracies ranged between -0.22 (CompRCPT) and 0.69 (Coopworth). The weighted average individual accuracy (calculated from theory) ranges were 0.13 (Texel) to 0.52 (Coopworth) and 0.11 (Texel) to 0.55 (Coopworth) respectively, for dagginess and parasite traits. There was one SNP for DAG8 that reached Bonferroni significance threshold (P < 1 × 10(-6)) on OAR15, the same two SNPs for each of the parasite traits (OAR26) and none for DAG3. A notable peak was also observed on OAR7 for all the parasite traits, however, it did not reach the Bonferroni significance threshold. CONCLUSIONS:This study presents the first results of a GWAS on dagginess and faecal egg count traits in New Zealand sheep. The results suggest that there are quantitative trait loci on OAR 15 for dagginess and on OAR26 and seven for faecal egg count.

SUBMITTER: Pickering NK

PROVIDER: S-EPMC4650926 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

Pickering Natalie K NK Auvray Benoit B Dodds Ken G KG McEwan John C JC

BMC genomics 20151117

<h4>Background</h4>Dagginess (faecal soiling of the perineum region) and host nematode parasite resistance are important animal welfare traits in New Zealand sheep. Genomic prediction (GP) estimates the genetic merit, as a molecular breeding value (mBV), for each trait based on many SNPs. The additional information the mBV provides (as determined by its accuracy) has led to its incorporation into breeding schemes. Some GP methods give SNP effects, which provide additional information to identify ...[more]

PMID: 26576677

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Project description:BackgroundThe integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control.MethodsEggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content.ResultsThe heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep.ConclusionsThe present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep.

Dataset Information

Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

Publications

Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

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