Identification of quantitative trait loci affecting gastrointestinal parasite resistance in an experimental Angus population

A journey through 50 years of research relevant to the control of gastrointestinal nematodes in ruminant livestock and thoughts on future directions

This review article provides an historical perspective on some of the major research advances of relevance to ruminant livestock gastrointestinal nematode control over the last 50 years. Over this period, gastrointestinal nematode control has been dominated by the use of broad-spectrum anthelmintic drugs. Whilst this has provided unprecedented levels of successful control for many years, this approach has been gradually breaking down for more than two decades and is increasingly unsustainable which is due, at least in part, to the emergence of anthelmintic drug resistance and a number of other factors discussed in this article. We first cover the remarkable success story of the discovery and development of broad-spectrum anthelmintic drugs, the changing face of anthelmintic drug discovery research and the emergence of anthelmintic resistance. This is followed by a review of some of the major advances in the increasingly important area of non-pharmaceutical gastrointestinal nematode control including immunology and vaccine development, epidemiological modelling and some of the alternative control strategies such as breeding for host resistance, refugia-based methods and biological control. The last 50 years have witnessed remarkable innovation and success in research aiming to improve ruminant livestock gastrointestinal nematode control, particularly given the relatively small size of the research community and limited funding. In spite of this, the growing global demand for livestock products, together with the need to maximise production efficiencies, reduce environmental impacts and safeguard animal welfare - as well as specific challenges such as anthelmintic drug resistance and climate change- mean that gastrointestinal nematode researchers will need to be as innovative in the next 50 years as in the last.

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

Parasitological and immunological response to Haemonchus contortus infection: Comparison between resistant Garole and susceptible Sahabadi sheep

Parasitological and immunological responses to the experimentally induced Haemonchus contortus infection were compared between Garole and Sahabadi breeds of sheep. The experiment was conducted in a 2 (breed) × 2 (infection status) factorial arrangement with a completely randomised design. Two breeds of sheep were divided into infected (n = 10) and control (n = 6) groups, and the infected groups were orally infected with H. contortus (500 stage 3 larvae per kilogram of body weight). Faecal egg counts (FEC) were determined from 18 days post infection (DPI) at 3-day intervals until 42 DPI. Average daily body weight gain, packed cell volume (PCV), concentrations of serum immunoglobulin (Ig) G₁, IgG₂, IgE and peripheral eosinophil count were measured at 14-day intervals from 0 to 42 DPI. Lymphocyte proliferation in response to somatic antigen of H. contortus was determined by in vitro lymphoproliferation assay, and concentrations of interferon gama (IFN-γ) and interleukin 4 (IL-4) in lymphocyte culture supernatant were measured at 14-day intervals until 42 DPI. Variables were analysed using the repeated measures mixed model procedure over DPI. Faecal egg count was significantly (p < 0.01) lower in Garole sheep than Sahabadi sheep and no faecal eggs were detected in the infected Garole sheep on 30 DPI. Infected Garole sheep had significantly (p < 0.05) higher body weight gain and PCV% than the infected Sahabadi sheep. In the infected Garole sheep, serum Ig except IgE increased significantly (p < 0.05) compared to infected Sahabadi sheep. On 28 DPI, peripheral eosinophil number, in vitro lymphoproliferation as well as concentrations of IFN-γ and IL-4 in culture supernatant were significantly (p < 0.05) higher in the infected Garole sheep than in the infected Sahabadi sheep. Parasitological observations indicated that Garole sheep were resistant to H. contortus and they exhibited greater cellular as well as humoral immune responses compared to Sahabadi sheep.

Quantification of differences in resistance to gastrointestinal nematode infections in sheep using a multivariate blood parameter

Breeding for resistance to gastrointestinal nematodes (GIN) in sheep relies largely on the use of worm egg counts (WEC) to identify animals that are able to resist infection. As an alternative to such measures of parasite load we aimed to develop a method to identify animals showing resistance to GIN infection based on the impact of the infection on blood parameters. We hypothesized that blood parameters may provide a measure of infection level with a blood-feeding parasite through perturbation of red blood cell parameters due to feeding behaviour of the parasite, and white blood cell parameters through the mounting of an immune response in the host animal. We measured a set of blood parameters in 390 sheep that had been exposed to an artificial regime of repeated challenges with Trichostrongylus colubriformis followed by Haemonchus contortus. A simple analysis revealed strong relationships between single blood parameters and WECs with correlation coefficients -0.54 to -0.60. We then used more complex multi-variate methods based on supervised classifier models (including Bayesian Network) as well as regression models (Lasso and Elastic Net) to study the relationships between WECs and blood parameters, and derived algorithms describing the relationships. The ability of these algorithms to classify sheep GIN resistance status was tested using the WEC and blood parameters collected from a different group of 418 sheep that had acquired natural infections of H. contortus from pasture. We identified the most resistant and most susceptible animals (10% percentiles) of this group based on WECs, and then compared the identities of these animals to the identities of animals that were predicted to be most resistant and most susceptible by our algorithms. The models showed varying abilities to predict susceptible and resistant sheep, with up to 65% of the most susceptible animals and 30% of the most resistant animals identified by the Elastic Net model algorithms. The prediction algorithms derived from female sheep data performed better than those for male sheep in some cases, with the predicted animals accounting for up to 50-60% of the actual resistant and susceptible female animals. Heritability values were calculated for blood parameters and the aggregate trait descriptions defined by the novel prediction algorithms. The aggregate trait descriptions were moderately heritable and may therefore be suitable for use in genetic selection strategies. The present study indicates that multivariate models based on blood parameter data showed some ability to predict the resistance status of sheep to infection with H. contortus.

Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle

BACKGROUND

Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites.

METHODS

Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 genotyped dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic effects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were available for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals.

RESULTS

Genomic regions for F. hepatica-damaged liver were located on Bos taurus autosomes (BTA) 1, 8, 11, 16, 17 and 18; each region included at least one SNP with a p value lower than 10^-6. Five SNPs were identified as significant (q value < 0.05) for antibody response to N. caninum and were located on BTA21 or 25. For antibody response to F. hepatica and O. ostertagi, six and nine quantitative trait loci (QTL) regions that included at least one SNP with a p value lower than 10^-6 were identified, respectively. Gene set enrichment analysis revealed a significant association between functional annotations related to the olfactory system and QTL that were suggestively associated with endo-parasite phenotypes.

CONCLUSIONS

A number of novel genomic regions were suggestively associated with endo-parasite phenotypes across the bovine genome and two genomic regions on BTA21 and 25 were associated with antibody response to N. caninum.

Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle

Background

Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are associated with reduced milk production and detrimental impacts on female fertility, contributing to economic losses in affected farms. In quantitative-genetic studies, the heritabilities for GIN and F. hepatica were moderate, encouraging studies on genomic scales. Genome-wide association studies (GWAS) based on dense single nucleotide polymorphism (SNP) marker panels allow exploration of the underlying genomic architecture of complex disease traits. The current GWAS combined the identification of potential candidate genes with pathway analyses to obtain deeper insights into bovine immune response and the mechanisms of resistance against endoparasite infections.

Results

A 2-step approach was applied to infer genome-wide associations in an endangered dual-purpose cattle subpopulation [Deutsches Schwarzbuntes Niederungsrind (DSN)] with a limited number of phenotypic records. First, endoparasite traits from a population of 1166 Black and White dairy cows [including Holstein Friesian (HF) and DSN] naturally infected with GIN, F. hepatica and D. viviparus were precorrected for fixed effects using linear mixed models. Afterwards, the precorrected phenotypes were the dependent traits (rFEC-GIN, rFEC-FH, and rFLC-DV) in GWAS based on 423,654 SNPs from 148 DSN cows. We identified 44 SNPs above the genome-wide significance threshold (p_Bonf = 4.47 × 10^− 7), and 145 associations surpassed the chromosome-wide significance threshold (range: 7.47 × 10^− 6 on BTA 1 to 2.18 × 10^− 5 on BTA 28). The associated SNPs identified were annotated to 23 candidate genes. The DAVID analysis inferred four pathways as being related to immune response mechanisms or involved in host-parasite interactions. SNP effect correlations considering specific chromosome segments indicate that breeding for resistance to GIN or F. hepatica as measured by fecal egg counts is genetically associated with a higher risk for udder infections.

Conclusions

We detected a large number of loci with small to moderate effects for endoparasite resistance. The potential candidate genes regulating resistance identified were pathogen-specific. Genetic antagonistic associations between disease resistance and productivity were specific for specific chromosome segments. The 2-step approach was a valid methodological approach to infer genetic mechanisms in an endangered breed with a limited number of phenotypic records.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5659-4) contains supplementary material, which is available to authorized users.

Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle

To elucidate the molecular mechanism of host resistance, we characterized the jejunal transcriptome of Angus cattle selected for parasite resistance for over 20 years in response to infection caused by the intestinal worm Cooperia oncophora. The transcript abundance of 56 genes, such as that of mucin 12 (MUC12) and intestinal alkaline phosphatase (ALPI), was significantly higher in resistant cattle. Novel splicing variants, exon skipping events, and gene fusion events, were also detected. An algorithm for the reconstruction of accurate cellular networks (ARACNE) was used to infer de novo regulatory molecular networks in the interactome between the parasite and host. Under a combined cutoff of an error tolerance (ϵ = 0.10) and a stringent P-value threshold of mutual information (1.0 × 10(-5)), a total of 229,100 direct interactions controlled by 20,288 hub genes were identified. Among these hub genes, 7651 genes had ≥ 100 direct neighbors while the top 9778 hub genes controlled more than 50% of total direct interactions. Three lysozyme genes (LYZ1, LYZ2, and LYZ3), which are co-located in bovine chromosome 5 in tandem and are strongly upregulated in resistant cattle, shared a common regulatory network of 55 genes. These ancient antimicrobials were likely involved in regulating host-parasite interactions by affecting host gut microbiome. Notably, ALPI, known as a gut mucosal defense factor, controlled a molecular network consisting 410 genes, including 14 transcription factors (TF) and 10 genes that were significantly regulated in resistant cattle. Several large regulatory networks were controlled by TF, such as STAT6, SREBF1, and ELF4. Gene ontology (GO) processes significantly enriched in the regulatory network controlled by STAT6 included lipid metabolism. Our findings provide insights into the immune regulation of host-parasite interactions and the molecular mechanisms of host resistance in cattle.

Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC

Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI) nematode fecal egg count (FEC) data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS) based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log₁₀ p=4.3) with Box-Cox transformed mean FEC (BC-MFEC). DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection.

A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle

Gastrointestinal (GI) nematode infections are a worldwide threat to human health and animal production. In this study, we performed a genome-wide association study between copy number variations (CNVs) and resistance to GI nematodes in an Angus cattle population. Using a linear regression analysis, we identified one deletion CNV which reaches genome-wide significance after Bonferroni correction. With multiple mapped human olfactory receptor genes but no annotated bovine genes in the region, this significantly associated CNV displays high population frequencies (58.26 %) with a length of 104.8 kb on chr7. We further investigated the linkage disequilibrium (LD) relationships between this CNV and its nearby single nucleotide polymorphisms (SNPs) and genes. The underlining haplotype blocks contain immune-related genes such as ZNF496 and NLRP3. As this CNV co-segregates with linked SNPs and associated genes, we suspect that it could contribute to the detected variations in gene expression and thus differences in host parasite resistance.