Background: Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode,Haemonchus contortus. Host genetic variation for resistance toH. contortusallows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimateFst outliers in three different breeds of sheep and goats exposed toH. contortus.Results: Our results for sheep populations showed SNPs under selection inC3AR1,CSF3,SOCS2,NOS2,STAT5B,TGFB2andIL2RAgenes using frequentist and Bayesian approaches. For goats, SNPs inCD1D,ITGA9,IL12A,IL13RA1, CD86andTGFB2genes were under selection. Common signatures of selection in both species were observed inNOS2,TGFB2andTLR4genes. Directional selection was present in all SNPs evaluated in the present study.Conclusions: A total of 13 SNPs within 7 genes of our candidate gene panel related toH. contortusexposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance toH. contortusis likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection againstH. contortusinfection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.

Internal parasitism has been the leading cause of morbidity and mortality in small ruminants in many areas such as the southcentral USA. Among the different approaches and management practices to cope with internal parasitism, genetic selection for internal parasite resistance is recognized as one with considerable potential long-term impact. A central performance test with artificial infection of Haemonchus contortus for selection of growing meat goats and hair sheep for breeding to increase resistance to internal parasitism and on-farm selection of females was conducted for 3 years. The results varied considerably among breeds of goats and flocks of sheep. Spanish goats and St. Croix sheep maintained relatively low fecal egg count (FEC) each year, whereas for goats categorized as being of high resistance and Dorper sheep FEC decreased with advancing year. Packed call volume (PCV) and total serum immunoglobulin (Ig) levels were not strongly related to FEC. Genetic parameters varied between the two species, which might be related to previous selection pressure exerted for parasite resistance. Heritability of FEC was higher in goats than sheep. The genetic correlation between FEC and IgM and IgG was negative for both species, which suggests possible genetic association. Genetic and phenotypic correlations between ADG and FEC were nonsignificant for both species. In conclusion, different relationships of FEC and PCV between species require careful attention during selection and the lack of relationship between ADG and FEC suggests that selection of growing male meat goats and hair sheep for resistance to internal parasitism will not adversely affect growth performance.

Assessing infection by a parasite, such as Haemonchus contortus, requires time and experienced personnel. Field-based diagnostics using metagenomic species-specific targeting methods would be beneficial. Here, we examine two helminth control methods, zoledronic acid (ZA), an activator of γ δ T cells, and a neutralizing antibody (AB) against γ δ T cells. We conducted a randomized complete block designed investigation for the effects of Haemonchus contortus (Hc) infection on Alpine wethers (young castrated male goats) to identify if metagenomic methods will provide strong evidence for diagnostics. Different tissues were collected from wethers and the microbiome compositions were identified. The relative proportion of microbial community members in the environments; the richness of the microbial community; and the evenness of distribution in microbial community members were determined. It was hypothesized that numerous parameters that include many data points will provide a more precise means to identify infection or health based on similarity to uninfected control data parameters. We found that samples did not sequence well, when multiplexed with high concentration libraries, giving taxonomic numbers that had residual and unmeasured confounding bias related to analysis or selection that define significance of OTUs in the tissue samples at the phylum or species level.