Systems genetics approach reveals candidate genes for parasite resistance from quantitative trait loci studies in agricultural species

Genomic integration to identify molecular biomarkers associated with indicator traits of gastrointestinal nematode resistance in sheep

This study aimed to integrate GWAS and structural variants to propose possible molecular biomarkers related to gastrointestinal nematode resistance traits in Santa Inês sheep. The phenotypic records FAMACHA, haematocrit, white blood cell count, red blood cell count, haemoglobin, platelets and egg counts per gram of faeces were collected from 700 naturally infected animals, belonging to four Brazilian flocks. A total of 576 animals were genotyped using the Ovine SNP12k BeadChip and were imputed using a reference population with Ovine SNP50 BeadChip. The GWAS approaches were based on SNPs, haplotypes, CNVs and ROH. The overlapping between the significant genomic regions detected from all approaches was investigated, and the results were integrated using a network analysis. Genes related to the immune system were found, such as ABCB1, IL6, WNT5A and IRF5. Genomic regions containing candidate genes and metabolic pathways involved in immune responses, inflammatory processes and immune cells affecting parasite resistance traits were identified. The genomic regions, biological processes and candidate genes uncovered could lead to biomarkers for selecting more resilient sheep and improving herd welfare and productivity. The results obtained are the start point to identify molecular biomarkers related to indicator traits of gastrointestinal nematode resistance in Santa Inês sheep.

Differential responses of abomasal transcriptome to Haemonchus contortus infection between Haemonchus-selected and Trichostrongylus-selected merino sheep

Haemonchus contortus is the most prevalent and pathogenic gastrointestinal nematode infecting sheep and goats. The two CSIRO sheep resource flocks, the Haemonchus-selected flock (HSF) and Trichostrongylus-selected flock (TSF) were developed for research on host resistance or susceptibility to gastrointestinal nematode infection. A recent study focused on the gene expression differences between resistant and susceptible sheep within each flock, with lymphatic and gastrointestinal tissues. To identify features in the host transcriptome and understand the molecular differences underlying host resistance to H. contortus between flocks with different selective breeding and genetic backgrounds, we compared the abomasal transcriptomic responses of the resistant or susceptible animals between HSF and TSF flocks. A total of 11 and 903 differentially expressed genes were identified in the innate infection treatment in HSF and TSF flocks between resistant and susceptible sheep respectively, while 52 and 485 genes were identified to be differentially expressed in the acquired infection treatment, respectively. Among them, 294 genes had significantly different gene expression levels between HSF and TSF flock animals within the susceptible sheep by both the innate and acquired infections. Moreover, similar expression patterns of the 294 genes were observed, with 273 genes more highly expressed in HSF and 21 more highly expressed in the TSF within the abomasal transcriptome of the susceptible animals. Gene ontology enrichment of the differentially expressed genes identified in this study predicted the likely differing function between the two flock's susceptible lines in response to H. contortus infection. Nineteen pathways were significantly enriched in both the innate and adaptive immune responses in susceptible animals, which indicated that these pathways likely contribute to the host resistance development to H. contortus infection in susceptible sheep. Biological networks built for the set of genes differentially abundant in susceptible animals identified hub genes of PRKG1, PRKACB, PRKACA, and ITGB1 for the innate immune response, and CALM2, MYL1, COL1A1, ITGB1 and ITGB3 for the adaptive immune response, respectively. Our results offered a quantitative snapshot of host transcriptomic changes induced by H. contortus infection between flocks with different selective breeding and genetic backgrounds and provided novel insights into molecular mechanisms of host resistance.

Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations

Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

Single nucleotide polymorphisms from candidate genes associated with nematode resistance and resilience in Corriedale and Pampinta sheep in Argentina

Selective breeding of genetically resistant animals is considered a promising strategy to face the problem of nematode resistance to anthelmintics and mitigate concerns about the presence of chemical residues in animal food products and the environment. Gastrointestinal nematode resistance is a complex, multifactorial trait related to host immunity. However, the mechanisms underlying host resistance and response to infection remain to be fully elucidated. In this context, the objective of this study was to provide insight into the chromosomal regions determining nematode resistance and resilience in Corriedale and resistance in Pampinta sheep breeds. A total of 170 single nucleotide polymorphisms (SNP) from 76 candidate genes for immune response were studied in 624 Corriedale and 304 Pampinta animals. Lambs underwent artificial or natural challenges with infective larvae mainly from Haemonchus contortus. Fecal egg counts, estimated breeding values for fecal egg counts, and rate of packed cell volume change and FAMACHA© score change over the challenge were used, when available, as indicators of host parasite resistance or resilience. Phenotype-genotype association studies were conducted and significance values obtained were adjusted for multiple testing errors. Eight SNPs, located on OARs 3, 6, 12, and 20, reached significance in Corriedale sheep under artificial challenge. Those SNP represent allelic variants from the MHC-Ovine Lymphocyte Antigen-DRA, two C-type lectin domain families, the Interleukin 2 receptor β, the Toll-like receptor 10, the Mannan binding lectin serine peptidase 2, and the NLR family, CARD domain containing 4 genes. On Pampinta lambs under natural challenge, we found three significant SNPs, located in the TIMP metallopeptidase inhibitor 3, the FBJ murine osteosarcoma viral oncogene homolog, and the Interleukin 20 receptor alpha genes, on OARs 3, 7, and 8, respectively. The results obtained herein confirm genomic regions previously reported as associated with nematode resistance in other sheep breeds, reinforcing their role in host response to parasites. These findings contribute to gain knowledge on parasite resistance and resilience in Corriedale sheep and report for the first time SNPs associated with resistance to gastrointestinal parasite infections in Pampinta breed.

Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso

A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76 % of the phenotypic variance for PCV, 21.24 % for lnFEC, and 34.38 % for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125 kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype-environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

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.

Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance

Gastrointestinal nematodes are a serious cause of morbidity and mortality in grazing ruminants. The major ovine defence mechanism is acquired immunity, with protective immunity developing over time in response to infection. Nematode resistance varies both within and between breeds and is moderately heritable. A detailed understanding of the genes and mechanisms involved in protective immunity, and the factors that regulate this response, is required to aid both future breeding strategies and the development of effective and sustainable nematode control methods. The aim of this study was to compare the abomasal lymph node transcriptome of resistant and susceptible lambs in order to determine biological processes differentially expressed between resistant and susceptible individuals. Scottish Blackface lambs, with divergent phenotypes for resistance, were challenged with 30,000 Teladorsagia circumcincta larvae (L3), and abomasal lymph nodes recovered at 7 and 14days post-infection (dpi). High-throughput sequencing of cDNA from the abomasal lymph node was used to quantitatively sample the transcriptome with an average of 32 million reads per sample. A total of 194 and 144 genes were differentially expressed between resistant and susceptible lambs at 7 and 14 dpi respectively. Differentially expressed networks and biological processes were identified using Ingenuity Pathway Analysis. Genes involved in the inflammatory response, attraction of T lymphocytes and binding of leukocytes were more highly expressed in resistant animals at 7 dpi and in susceptible animals at 14 dpi indicating that resistant animals respond to infection earlier than susceptible animals. Twenty-four Single Nucleotide Polymorphisms (SNP) within 11 differentially expressed genes, were tested for association with gastrointestinal nematode resistance in the Scottish Blackface lambs. Four SNP, in 2 genes (SLC30A2 and ALB), were suggestively associated with faecal egg count. In conclusion, a large number of genes were differentially expressed in the abomasal lymph node of resistant and susceptible lambs responding to gastrointestinal nematode challenge. Resistant Scottish Blackface lambs appear to generate an earlier immune response to T. circumcincta. In susceptible lambs this response appears to be delayed. SNP in 2 differentially expressed genes were suggestively associated with faecal egg count indicating that differentially expressed genes may be considered candidate loci for mediating nematode resistance.

Genome-Wide Specific Selection in Three Domestic Sheep Breeds

BACKGROUND

Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.

RESULTS

We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study.

CONCLUSIONS

Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

Exploiting ovine immunology to improve the relevance of biomedical models

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Sheep make a valuable contribution to immunology research.

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Lessons to be learned from studying infections in the natural host.

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Factors to consider when selecting biomedical models.

Animal models of human disease are important tools in many areas of biomedicine; for example, in infectious disease research and in the development of novel drugs and medical devices. Most studies involving animals use rodents, in particular congenic mice, due to the availability of a wide number of strains and the ease with which they can be genetically manipulated. The use of mouse models has led to major advances in many fields of research, in particular in immunology but despite these advances, no animal model can exactly reproduce all the features of human disease. It is increasingly becoming recognised that in many circumstances mice do not provide the best model and that alternative species may be more appropriate. Here, we describe the relative merits of sheep as biomedical models for human physiology and disease in comparison to mice, with a particular focus on reproductive and respiratory pathogens.

Current status for gastrointestinal nematode diagnosis in small ruminants: where are we and where are we going?

Gastrointestinal nematode (GIN) parasites pose a significant economic burden particularly in small ruminant production systems. Anthelmintic resistance is a serious concern to the effective control of GIN parasites and has fuelled the focus to design and promote sustainable control of practices of parasite control. Many facets of sustainable GIN parasite control programs rely on the ability to diagnose infection both qualitatively and quantitatively. Diagnostics are required to determine anthelmintic efficacies, for targeted treatment programs and selection of animals for parasite resistant breeding. This review describes much of the research investigated to date to improve the current diagnostic for the above practices which is based on counting the number of parasite eggs in faeces.

Candidate gene approach for parasite resistance in sheep--variation in immune pathway genes and association with fecal egg count

Sheep chromosome 3 (Oar3) has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs) within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF) did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05) in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have potential for future large scale association studies in naturally exposed sheep populations.

Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. The candidate gene approach has been applied to studies of a number of traits in various species, in an attempt to elucidate their genetic basis. Here, we test the application of the candidate gene approach to identify the loci involved in variation in gastrointestinal parasite burden, a complex trait likely to be controlled by many loci, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources between cattle and sheep were used to generate a list of candidate genes. In a pilot study, these candidates, along with 50 random genes, were then sequenced in two pools of Soay sheep; one with low gastrointestinal nematode burden and the other high, using a NimbleGen sequence capture experiment. Further candidates were identified from single nucleotide polymorphisms (SNPs) that were highly differentiated between high- and low-resistance sheep breeds. A panel of 192 candidate and control SNPs were then typed in 960 individual Soay sheep to examine whether they individually explained variation in parasite burden, as measured as faecal egg count, as well as two immune measures (Teladorsagia circumcincta-specific antibodies and antinuclear antibodies). The cumulative effect of the candidate and control SNPs were estimated by fitting genetic relationship matrices (GRMs) as random effects in animal models of the three traits. No more significant SNPs were identified in the pilot sequencing experiment and association study than expected by chance. Furthermore, no significant difference was found between the proportions of candidate or control SNPs that were found to be significantly associated with parasite burden/immune measures. No significant effect of the candidate or control gene GRMs was found. There is thus little support for the candidate gene approach to the identification of loci explaining variation in parasitological and immunological traits in this population. However, a number of SNPs explained significant variation in multiple traits and significant correlations were found between the proportions of variance explained by individual SNPs across multiple traits. The significant SNPs identified in this study may still, therefore, merit further investigation.