Genetic parameters for fecal egg counts and their relationship with body weights in Katahdin lambs

Genomic Regions Associated with Resistance to Gastrointestinal Parasites in Australian Merino Sheep

The objective of this study was to identify genomic regions and genes associated with resistance to gastrointestinal nematodes in Australian Merino sheep in Uruguay, using the single-step GWAS methodology (ssGWAS), which is based on genomic estimated breeding values (GEBVs) obtained from a combination of pedigree, genomic, and phenotypic data. This methodology converts GEBVs into SNP effects. The analysis included 26,638 animals with fecal egg count (FEC) records obtained in two independent parasitic cycles (FEC1 and FEC2) and 1700 50K SNP genotypes. The comparison of genomic regions was based on genetic variances (gVar(%)) explained by non-overlapping regions of 20 SNPs. For FEC1 and FEC2, 18 and 22 genomic windows exceeded the significance threshold (gVar(%) ≥ 0.22%), respectively. The genomic regions with strong associations with FEC1 were located on chromosomes OAR 2, 6, 11, 21, and 25, and for FEC2 on OAR 5, 6, and 11. The proportion of genetic variance attributed to the top windows was 0.83% and 1.9% for FEC1 and FEC2, respectively. The 33 candidate genes shared between the two traits were subjected to enrichment analysis, revealing a marked enrichment in biological processes related to immune system functions. These results contribute to the understanding of the genetics underlying gastrointestinal parasite resistance and its implications for other productive and welfare traits in animal breeding programs.

Pedigree diversity and implications for genetic selection of Katahdin sheep

The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.

Weighted single-step genome-wide association study and functional enrichment analyses for gastrointestinal nematode resistance traits in Santa Ines sheep

This study aimed to identify genomic regions, pathways, and putative candidate genes associated with resistance to gastrointestinal nematode in Santa Ines sheep. The phenotypic information comprised 5529 records from 1703 naturally infected animals. After genomic data quality control, 37,511 SNPs from 589 animals were available. The weighted single-step approach for genome-wide association study was performed to estimate the SNP effects and variances accounted by 10-SNP sliding windows. Confirming the polygenic nature of the studied traits, 20, 22, 21, and 19 genomic windows that explained more than 0.5% of the additive genetic variance were identified for fecal egg counts (FEC), Famacha© (FAM), packed cell volume (PCV), and total plasma protein (TPP), respectively. A total of 81, 122, 106, and 101 protein-coding genes were found in windows associated with FEC, FAM, PCV, and TPP, respectively. Several protein-coding genes related to the immune system and inflammatory response functions were identified within those genomic regions, such as ADCY9, ADRB2, BRAF, CADM1, CCL20, CD70, CREBBP, FNBP1, HTR4, IL16, IL22, IL26, MAPK8, NDFIP1, NLRC3, PAK5, PLCB1, PLCB4, ROCK1, TEK, TNFRSF12A, and VAV1. Functional enrichment analysis by DAVID tool also revealed many significant (P < 0.05) pathways and Gene Ontology terms that could be related to resistance to gastrointestinal nematode in Santa Ines sheep, such as chemokine signaling pathway (oas04062), cAMP signaling pathway (oas04024), cGMP-PKG signaling pathway (Oas04022), platelet activation (Oas04611), Rap1 signaling pathway (oas04015), and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705). These results contribute to improving the knowledge of the genetic architecture of resistance to gastrointestinal nematode in Santa Ines sheep.

Potential use of garlic products in ruminant feeding: A review

The addition of antibiotics as growth promoters to ruminant feed can result in bacterial resistance and antibiotic residues in ruminant products. Correspondingly, there is serious public concern regarding the presence of antibiotic residue in ruminant products and the consequent threat to human health. As a result, the addition of plants and their products to ruminant feeds, as an alternative to antibiotics, has received much attention recently. Garlic and its products are rich in organosulphur compounds, which have a variety of biological activities and have been widely used as natural additives in animal production. This review presents recent knowledge on the addition of garlic products (powder, skin, oil, leaf and extracts) to the diets of ruminants. In this paper, garlic products are evaluated with respect to their chemical composition, bioactive compounds, and their impacts on the rumen ecosystem, antioxidant status, immune response, parasitic infection, growth performance and product quality of ruminants. This review provides valuable guidance and a theoretical basis for the development of garlic products as green, highly efficient and safe additives, with the aims of promoting ruminant growth and health, reducing methane emissions and improving ruminant product quality. Garlic extracts have the potential to control parasite infections by decreasing the faecal egg count. Garlic powder, oil and allicin are able to reduce the methane emissions of ruminants. Organosulphur compounds such as allicin, which is present in garlic products, have the potential to inhibit membrane lipid synthesis of the archaeal community, thus influencing the population of methanogenic archaea and resulting in a reduction in methane emissions. Some garlic products are also able to increase the average daily gain (garlic skin, water extract, and leaf) and the feed conversion ratio (garlic skin and leaf) of ruminants. Garlic stalk silage fed to sheep has the potential to improve the nutritional value of mutton by increasing the concentrations of linoleic and linolenic acids and essential amino acids. Sheep fed a diet containing garlic powder or oil are able to produce milk with higher concentrations of the conjugated linoleic acids and n-3 fatty acids, which has health benefits for consumers, due to the widely recognized positive impact of n-3 polyunsaturated fatty acids and conjugated linoleic acids on human heart health, improving platelet aggregation, vasodilation and thrombotic tendency. Overall, garlic products have the potential to enhance growth performance and product quality and reduce parasite infections, as well as methane emissions of ruminants.

Genome-Wide Analysis of Sheep Artificially or Naturally Infected with Gastrointestinal Nematodes

The anthelmintic resistance of gastrointestinal nematodes (GINs) poses a significant threat to sheep worldwide, but genomic selection can serve as an alternative to the use of chemical treatment as a solution for parasitic infection. The objective of this study is to conduct genome-wide association studies (GWASs) to identify single nucleotide polymorphisms (SNPs) in Rambouillet (RA) and Dorper × White Dorper (DWD) lambs associated with the biological response to a GIN infection. All lambs were genotyped with a medium-density genomic panel with 40,598 markers used for analysis. Separate GWASs were conducted using fecal egg counts (FECs) from lambs (<1 year of age) that acquired their artificial infections via an oral inoculation of 10,000 Haemonchus contortus larvae (n = 145) or naturally while grazing on pasture (n = 184). A GWAS was also performed for packed cell volume (PCV) in artificially GIN-challenged lambs. A total of 26 SNPs exceeded significance and 21 SNPs were in or within 20 kb of genes such as SCUBE1, GALNT6, IGF1R, CAPZB and PTK2B. The ontology analysis of candidate genes signifies the importance of immune cell development, mucin production and cellular signaling for coagulation and wound healing following epithelial damage in the abomasal gastric pits via H. contortus during GIN infection in lambs. These results add to a growing body of the literature that promotes the use of genomic selection for increased sheep resistance to GINs.

Clustering climate and management practices to define environmental challenges affecting gastrointestinal parasitism in Katahdin sheep

Gastrointestinal nematodes (GIN) negatively affect the performance and well-being of sheep. Due to anthelmintic resistance, GIN are difficult to control leading producers to choose breeds that can exhibit resistance to parasitism. An example is Katahdin sheep. Katahdins are raised in various climates and management systems in the United States. These environmental factors can be combined to form eco-management groupings or clusters. We hypothesized that GIN challenge varies predictably based on the characteristics of these environmental clusters. Forty Katahdin producers from across the United States were surveyed for management information, with body weights (BW), fecal egg counts (FEC), and FAMACHA scores (FAM) available from 17 of the 40 flocks. The performance data included 3,426 lambs evaluated around 90 d of age. Management and climate data were combined into clusters using multiple correspondence and principal component (PC) analysis. Performance data were aligned with their corresponding cluster. Depending on the trait, eco-management cluster, birth-rearing type, sex, and, as a covariate, dam age, were fitted as systematic effects with ANOVA. Clusters also were formed based on climate or management data alone. When compared with fitting the eco-management clusters, they defined less variation in each of the traits based on Akaike and Bayesian information criterion, and adjusted r2 values. To further examine variation defined by eco-management clusters, residuals from an ANOVA model excluding eco-management cluster were retained, and their correlation with PC loadings calculated. All PC loadings were included as potential independent variables and tested for significance using backward stepwise regression. The PC loadings with a correlation |≥0.49| explained significant variation in each trait and were included in the final models chosen; adjusted r2 values for BW, FEC, and FAM were 0.90, 0.81, and 0.97, respectively. When analyzing GIN challenge, eco-management clusters corresponding with hotter temperatures and greater rainfall, and with pasture-born lambs, suffered greater parasitism. Conversely, the eco-management clusters with lambs turned out to pasture at older ages benefited from reduced parasitism. Through the formation of eco-management clusters, an environmental variable can be defined to study interactions of genotypes to their environment, providing a potentially useful tool for identifying parasite-resistant sheep.

Genotype by environment interaction and heteroscedasticity influence the expression of parasite resistance in Katahdin sheep

Increasingly, sheep producers are choosing breeds that express resistance to gastrointestinal parasites due to reduced efficacy of anthelminthic drugs. One such breed is Katahdin. Katahdins are raised in various climates and management systems in the United States, which can be combined into eco-management clusters to describe production environments more holistically. The objectives of this study were to determine if genotype by environment interaction (G × E) and heteroscedasticity existed across these eco-management clusters for traits indicative of parasite resistance. Body weights (BW), FAMACHA scores (FAM), and fecal egg counts (FEC) were collected at around 90 d in 3,527 Katahdin lambs delineated into nine eco-management clusters. A tri-variate animal model including birth-rearing type, sex, and dam age (as a quadratic covariate) as fixed effects, and eco-management cluster, direct additive, uncorrelated maternal environmental (for BW), and residual as random effects, was fitted with ASReml. Heritability estimates for BW, FEC, and FAM were 0.36 ± 0.07, 0.31 ± 0.07, and 0.26 ± 0.05, respectively. The genetic (additive) correlation between BW with FEC was -0.26 ± 0.08 and with FAM was -0.16 ± 0.08, and thereby favorable. Heritabilities were also estimated univariately within eco-management clusters and ranged from 0.30 ± 0.05 to 0.37 ± 0.05 for BW, 0.18 ± 0.12 to 0.50 ± 0.13 for FEC, and 0.07 ± 0.06 to 0.40 ± 0.19 for FAM. Significant genetic and phenotypic heteroscedasticity among eco-management clusters was detected in FEC and FAM. A sire by eco-management cluster interaction term was added to the initial model fitted to evaluate G × E. This interaction defined substantial variation (P < 0.01) in all traits and explained 12% (FEC) to 20% (BW) of the phenotypic variation. Accounting for G × E and heteroscedasticity in the design and implementation of breeding programs may introduce operational challenges. Still, doing so would improve the efficacy of selection programs to improve parasite resistance.

EVALUATION OF PELIBUEY LAMBS BORN TO MOTHERS PHENOTYPICALLY SEGREGATED ACCORDING TO RESISTANCE TO GASTROINTESTINAL NEMATODES IN THE HUMID TROPICS OF MEXICO

The objective was to evaluate the effect of the resistance of ewes to gastrointestinal nematodes (GIN) on the parasitologic and productive performance of their lambs during preweaning and postweaning periods. Offspring from 44 Pelibuey ewes classified as resistant or susceptible to GIN were evaluated. During the preweaning period, birth weight (BW), live weight (LW) at 35 and 70 days of age, and live weight changes (LWC) were determined in 73 lambs. During the postweaning period, 20 lambs to susceptible or resistant ewes were evaluated. The lambs were challenged under natural GIN infections and artificial infection with L3 of Haemonchus contortus. The fecal egg count (FEC), hematocrit (HT), peripheral eosinophil count, plasma protein, LW, and LWC were determined. There were no differences among parameters evaluated during preweaning (P > 0.05). The type of lambing (single or multiple) affected the BW, LW, and LWC (P < 0.01). The sex (male) of the lamb had a positive effect on BW at 35 and 70 days of age (P < 0.05). After weaning, lambs of susceptible ewes showed higher FEC than resistant ewes (P < 0.05). The HT of lambs to resistant ewes was higher than those the susceptible group (P < 0.01). In conclusion, offspring of resistant ewes show low FEC compared with those susceptible during the postweaning stage.

Genetic parameters for resistance to gastrointestinal nematodes in sheep: a meta-analysis

Gastrointestinal nematodes (GINs) are damaging parasites of global sheep populations. The key weapons in fighting GINs have been anthelmintic drugs, but the emergence of drug-resistant parasites has meant that alternative control methods are needed. One of these alternatives is to breed for enhanced host resistance to GINs, and decades of research have estimated the genetic contribution to different measures of resistance to GINs and their genetic correlations with other desirable performance traits. It is clear that parasite resistance is a heritable trait that can be selected for. Despite this consensus, estimates of both heritability of resistance and genetic correlations with other traits vary widely between studies, and the reasons for this variation have not been examined. This study provides a comprehensive and quantitative meta-analysis of genetic parameters for resistance to GINs in sheep, including measures of worm burden (faecal egg counts, FECs), anti-parasite immunity (GIN-specific antibodies), and parasite-induced pathology (FAMACHA© scores). Analysis of 591 heritability estimates from 121 studies revealed a global heritability estimate for resistance to GINs of 0.25 (95% confidence interval (CI) = 0.22-0.27) that was stable across breeds, ages, geographical location and analytical methods. Meanwhile, analysis of 559 genetic correlations from 54 studies revealed that resistance to GINs overall has a positive genetic correlation of +0.10 (95% CI = 0.02-0.19) with performance traits, and that this was consistent across breeds, ages, sexes and analytical methods. Importantly, the direction of the genetic correlation varied with the resistance trait measured: while FECs and FAMACHA© scores were favourably correlated with performance traits, adaptive immune markers were unfavourably correlated, suggesting that selection for enhanced immune responses to GINs could reduce animal performance. Overall, the results suggest that breeding for resistance to GINs should continue to form part of integrated management programs to reduce the impact of parasites on health and performance, but that selection for enhanced immune responses should be avoided.

Advances in diagnosis and control of anthelmintic resistant gastrointestinal helminths infecting ruminants

Infection with gastrointestinal helminths is widely spread among ruminant causing severe losses and adversely affects the livestock husbandry. Synthetic chemotherapeutics have been utilized throughout years, as a means of combating helminthiasis. Anthelmintic resistance (AR) has a serious concern on livestock industry which, mainly arises as outcome of misuse, improper dosing and frequent utilization of the synthetic drugs.Various gastrointestinal helminths have the capability to survive the therapeutic dose of anthelmintics and become resistant to the major anthelmintic classes. Early diagnosis might delay or reduce the risk of AR. Conventional phenotyping methods were commonly used for detection of anthelmintic resistant helminths, but appeared to lack of sensitivity, especially when the frequency of resistant allele is very low. Several molecular assays were carried out to detect the AR with greater accuracy. Sustainable effective preventive and control measures for gastrointestinal helminths infection remain the corner stone to overcome AR. Rational use of anthelmintics with keeping unexposed proportion of worm populations, could have the potentiality to maintain and prolong the efficacy of anthelmintics. Several alternative anthelmintic treatments might offer valuable solutions either alone or adjunct to synthetic drugs to dilute the spread of resistance alleles among the helminths population. This article reviews current status of various diagnostic methods and control measures for anthelmintic resistant gastrointestinal helminths infecting ruminants and tries to present a practical protocol to avoid or delay the development of AR.

Response of Rambouillet Lambs to an Artificial Gastrointestinal Nematode Infection

Gastrointestinal nematodes (GIN) threaten the productivity and health of sheep worldwide, prompting the need for genetic selection to reduce GIN susceptibility. Fecal egg count (FEC), packed-cell volume (PCV), and various production traits were examined in parasitized Rambouillet sheep and compared to sire FEC estimated breeding value (EBV). Rambouillet lambs (n = 77) were inoculated with 10,000 H. contortus L3 larvae. Subsequently, FEC, PCV, and body weight (BW) were captured at seven-day intervals for six weeks. Lambs were sired by one of two rams with post-weaning FEC EBV of −9% or +9%. Mean FEC differed (p = 0.0132) with lambs from the lower EBV sire (“Sire L”) being reduced, versus those from the higher EBV sire (“Sire H”), being 2135 ± 211 vs. 2912 ± 207 eggs per gram, respectively. Males and females did not differ for FEC, but females exhibited a higher mean PCV than males, (33.74 vs. 29.65%, p < 0.0001). Lambs were shorn ~120 d post artificial infection and wool measurements were captured. A negative correlation between FEC and grease fleece weight was observed. Our results describe the response of Rambouillet lambs to artificial H. contortus infection and suggest FEC EBV can reduce susceptibility to GIN in this breed.

Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires

Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and 91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations between markers and FEC EBV were initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70 Mb, with LD among these SNP of r² ≤ 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9 Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mb codes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.

Variants Within Genes EDIL3 and ADGRB3 are Associated With Divergent Fecal Egg Counts in Katahdin Sheep at Weaning

Gastrointestinal nematodes (GIN) pose a severe threat to sheep production worldwide. Anthelmintic drug resistance coupled with growing concern regarding potential environmental effects of drug use have demonstrated the necessity of implementing other methods of GIN control. The aim of this study was to test for genetic variants associated with resistance or susceptibility to GIN in Katahdin sheep to improve the current understanding of the genetic mechanisms responsible for host response to GIN. Linear regression and case-control genome-wide association studies were conducted with high-density genotype data and cube-root transformed weaning fecal egg counts (tFEC) of 583 Katahdin sheep. The case-control GWAS identified two significant SNPs (P-values 1.49e-08 to 1.01e-08) within introns of the gene adhesion G protein-coupled receptor B3 (ADGRB3) associated with lower fecal egg counts. With linear regression, four significant SNPs (P-values 7.82e-08 to 3.34e-08) were identified within the first intron of the gene EGF-like repeats and discoidin domains 3 (EDIL3). These identified SNPs were in very high linkage disequilibrium (r² of 0.996–1), and animals with alternate homozygous genotypes had significantly higher median weaning tFEC phenotypes compared to all other genotypes. Significant SNPs were queried through public databases to identify putative transcription factor binding site (TFBS) and potential lncRNA differences between reference and alternate alleles. Changes in TFBS were predicted at two SNPs, and one significant SNP was found to be within a predicted lncRNA sequence with greater than 90% similarity to a known lncRNA in the bovine genome. The gene EDIL3 has been described in other species for its roles in the inhibition and resolution of inflammation. Potential changes of EDIL3 expression mediated through lncRNA expression and/or transcription factor binding may impact the overall immune response and reduce the ability of Katahdin sheep to control GIN infection. This study lays the foundation for further research of EDIL3 and ADGRB3 towards understanding genetic mechanisms of susceptibility to GIN, and suggests these SNPs may contribute to genetic strategies for improving parasite resistance traits in sheep.

Genetic × environment variation in sheep lines bred for divergent resistance to strongyle infection

Drug-resistant parasites threaten livestock production. Breeding more resistant hosts could be a sustainable control strategy. Environmental variation linked to animal management practices or to parasite species turnover across farms may however alter the expression of genetic potential. We created sheep lines with high or low resistance to Haemonchus contortus and achieved significant divergence on both phenotypic and genetic scales. We exposed both lines to chronic stress or to the infection by another parasite Trichostrongylus colubriformis, to test for genotype-by-environment and genotype-by-parasite species interactions respectively. Between-line divergence remained significant following chronic stress exposure although between-family variation was found. Significant genotype-by-parasite interaction was found although H. contortus-resistant lambs remained more resistant against T. colubriformis. Growth curves were not altered by the selection process although resistant lambs were lighter after the second round of divergence, before any infection took place. Breeding for resistance is a sustainable strategy but allowance needs to be made for environmental perturbations and worm species.

Genetic Selection for Resistance to Gastrointestinal Parasitism in Meat Goats and Hair Sheep through a Performance Test with Artificial Infection of Haemonchus contortus

Simple Summary

Internal parasitism has been an important constraint to small ruminant production and anthelmintic resistance has become a worldwide issue. This study evaluated a 3-year genetic selection program through activities on-farm and a centralized performance test and also provided estimates of genetic parameters of growth and response to artificial infection with Haemonchus contortus by goats and sheep in the southcentral USA. Considerable species as well as breed differences were found in average daily gain and response to parasite infection. Average daily gain was greater for Boer than for Kiko and Spanish goats and slightly greater for Dorper than for St. Croix sheep. Infection level (number of eggs found in feces) of Spanish and St. Croix were relatively low each year, whereas that of Kiko and Dorper was lower after selection. An indicator of anemia (packed cell volume) did not always reflect infection level, which is probably reflective of differences among animals in resilience and susceptibility to haemonchosis. Moderate to high heritabilities were found for growth performance and response to parasite infection for growing meat goat and hair sheep males under a standardized environment that suggests considerable potential for genetic improvement through selection.

Abstract

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.

Quebracho tannins aid in the control of Eimeria spp. and gastrointestinal nematodes in lambs and goat kids

The objective was to examine the effects of supplementary quebracho on control of coccidiosis and gastrointestinal nematodes in lambs and kids. In Exp. 1, naturally infected lambs weaned (87.8 ± 0.4 days of age; day 0) in January (winter) were blocked by sex and randomly assigned (n = 10/treatment) to receive supplement with or without 100 g/lamb of quebracho for 28 days. In Exp. 2, single or twin rearing ewes were randomly assigned into two groups, and naturally infected lambs were fed control (n = 28) or quebracho (100 g/lamb of quebracho tannins in feed; n = 27) between -28 and 21 days (weaning = day 0; 70.8 ± 0.1 days of age). In Exp. 3, weaned doe kids (57.6 ± 2.0 days of age) were randomly assigned to receive alfalfa (Medicago sativa) supplement with (n = 9) or without (n = 8) 50 g/kid quebracho or sericea lespedeza (Lespedeza cuneata) with quebracho (n = 8) for 21 days. Fecal oocyst count (FOC), nematode egg counts (FEC), fecal score, dag score (soiling around rear quarters), and blood packed cell volume (PCV) were determined every 7 days. Data were analyzed as repeated measures using mixed models. In Exp. 1, FOC decreased in quebracho-fed lambs (diet × time, P < 0.001) but FEC was similar between treatments during the feeding period (P = 0.19). Packed cell volume (P = 0.19) and fecal score (P = 0.42) were similar between groups. Quebracho-fed lambs had a greater dag score initially (diet × time, P = 0.02), but were similar by day 42 (P = 0.72). In Exp. 2, FOC remained low (P = 0.02), PCV tended to decrease (P = 0.06), but FEC increased on days 14 and 21 (diet × time; P < 0.001) in quebracho compared with control-fed lambs. Quebracho-fed lambs had lower fecal score (diet × time; P = 0.005) but higher dag score (diet × time; P < 0.001). In Exp. 3, FOC of kids fed quebracho (alfalfa or sericea lespedeza supplement) was lower than control (P < 0.001). Fecal score of kids fed sericea lespedeza compared with alfalfa were lower regardless of quebracho (P = 0.01). There were no differences among treatments for dag, FEC, PCV, or body weight (P> 0.10). Quebracho was effective in reducing FOC but not clinical signs of coccidiosis in both lambs and kids, and may not be highly digestible in lambs as it caused loose stools.

Evaluating the relationship between fecal egg count, FAMACHA score, and weight in dewormed and non-dewormed Katahdin rams during a parasite challenge

The objective of this study was to evaluate and to estimate the relationship between fecal egg counts (FECs) and FAMACHA score and the body weight of growing Katahdin rams during a parasite challenge. One of the largest factors negatively influencing reproduction and economics in the sheep industry is gastrointestinal nematode (GIN) parasites. Due to anthelmintic resistance of these parasites, animals are selected for parasite resistance using FEC and FAMACHA scores. Data were used from the Virginia Tech Southwest Agricultural Research and Extension Center Ram Test in Glade Spring, VA, from the year 2012 to 2018 in which animals were tested in 14-d intervals for 70 d. Mixed models for repeated weight measurements were made from backward stepwise selection to evaluate the relationships between weight and GIN FEC. A total of 576 animals within 23 contemporary groups derived from test year and pasture group were analyzed. Ram, contemporary group, and consignor were considered random effects, and fixed effects were birth type, test day, age, age squared, starting weight, FEC, and FAMACHA score. Pairwise contrasts were used in the statistical analysis of parameters and their interactions. Weight and age were found to have a quadratic relationship. Increased FEC was associated with weight loss at a rate of 0.00030 kg/FEC (P < 0.0001). Animals dewormed at any point during the trial weighed less than those that were not and increased with test day to a maximum difference of 4.66 kg (P < 0.001). FAMACHA score was found to be significant (P < 0.05), but a direct relationship with weight was not conclusive. Overall, rams with severe enough parasite load to require deworming had lesser weights, which could impact the profitability of sheep production and reinforced the need to select animals that had greater innate parasite resistance.

Test positivity for Maedi-Visna virus and Mycobacterium avium ssp. paratuberculosis in Sarda ewes: Effects on milk composition and coagulation traits and heritability estimates for susceptibility

Maedi-Visna virus (MVV) and Mycobacterium avium ssp. paratuberculosis (MAP) are two pathogens that cause chronic, production-limiting diseases in dairy sheep. Although they are present worldwide, there are no detailed reports on their actual effects on milk traits in the literature. This study was designed to investigate the effects of test positivity to MVV and MAP on ovine milk yield, composition and coagulation properties, and curd-firming over time (CF_t) variables in clinically healthy animals at the field level. The additive genetic variation and heritabilities of MVV and MAP positivity were also estimated. Milk samples were collected from 1,079 Sarda sheep kept on 23 farms, and pedigree information was obtained from the flock book. Milk yield was also recorded on the sampling date. Positivity for MVV and MAP was determined from milk samples using indirect ELISA test kits. Milk composition traits were measured by spectroscopy, milk coagulation properties were measured with a Formagraph (Foss Italia, Padua, Italy), and CF_t traits were calculated using the data from the Formagraph diagram. The effects of MVV and MAP positivity on milk traits were determined through a set of mixed linear models, which took into account various sources of variation, such as days in milk, parity, and flock effects, and included the effects (positive or negative) of the 2 pathogens. A Bayesian threshold sire model with sire relationship was used to estimate genetic variation and heritability. The overall animal prevalence of MVV-positive ewes was 43.6%; on only 1 farm of the 23 tested were all sampled ewes negative. An overall animal prevalence of 10.6% was recorded for MAP, with 4 farms at 0%. Positivity for MVV significantly affected the logarithmic score of the bacterial count, curd firmness after 30 min and 45 min, and the curd-firming instant rate constant. We found significant effects of MAP infection on milk composition, pH, and rennet coagulation time. The mean of the posterior distributions of heritability estimates on the liability scale was 0.15 for MAP and 0.07 for MVV. Our results demonstrate that only a few traits are negatively affected by MVV and MAP positivity, and that there is exploitable genetic variation in MVV and MAP susceptibility in dairy sheep.

Sustainable Approaches to Parasite Control in Ruminant Livestock

It is increasingly difficult to manage and control gastrointestinal nematode parasites in pasture-based ruminant livestock operations because of the high prevalence of anthelmintic resistance. Anthelmintics should be combined with alternative forms of control. Sustainable tools include copper oxide wire particles and condensed tannin-rich plants, which target primarily Haemonchus contortus in small ruminants. Nematophagous fungi reduce larvae on pasture and target nematode larvae in feces of most livestock species. In addition, and perhaps most importantly, genetic selection focuses on parasite resistance. Producers should use as many tools as possible to minimize the need for pharmaceutical interventions and optimize animal production.

Identification of potential functional variants underlying ovine resistance to gastrointestinal nematode infection by using RNA-Seq

In dairy sheep flocks from Mediterranean countries, replacement and adult ewes are the animals most affected by gastrointestinal nematode (GIN) infections. In this study, we have exploited the information derived from an RNA-Seq experiment with the aim of identifying potential causal mutations related to GIN resistance in sheep. Considering the RNA-Seq samples from 12 ewes previously classified as six resistant and six susceptible animals to experimental infection by Teladorsagia circumcincta, we performed a variant calling analysis pipeline using two different types of software, gatk version 3.7 and Samtools version 1.4. The variants commonly identified by the two packages (high-quality variants) within two types of target regions - (i) QTL regions previously reported in sheep for parasite resistance based on SNP-chip or sequencing technology studies and (ii) functional candidate genes selected from gene expression studies related to GIN resistance in sheep - were further characterised to identify mutations with a potential functional impact. Among the genes harbouring these potential functional variants (930 and 553 respectively for the two types of regions), we identified 111 immune-related genes in the QTL regions and 132 immune-related genes from the initially selected candidate genes. For these immune-related genes harbouring potential functional variants, the enrichment analyses performed highlighted significant GO terms related to apoptosis, adhesion and inflammatory response, in relation to the QTL related variants, and significant disease-related terms such as inflammation, adhesion and necrosis, in relation to the initial candidate gene list. Overall, the study provides a valuable list of potential causal mutations that could be considered as candidate causal mutations in relation to GIN resistance in sheep. Future studies should assess the role of these suggested mutations with the aim of identifying genetic markers that could be directly implemented in sheep breeding programmes considering not only production traits, but also functional traits such as resistance to GIN infections.

Genome-wide association study to identify genetic loci associated with gastrointestinal nematode resistance in Katahdin sheep

Resistance to gastrointestinal nematodes has previously been shown to be a moderately heritable trait in some breeds of sheep, but the mechanisms of resistance are not well understood. Selection for resistance currently relies upon faecal egg counts (FEC), blood packed cell volumes and FAMACHA visual indicator scores of anaemia. Identifying genomic markers associated with disease resistance would potentially improve the selection process and provide a more reliable means of classifying and understanding the biology behind resistant and susceptible sheep. A GWAS was conducted to identify possible genetic loci associated with resistance to Haemonchus contortus in Katahdin sheep. Forty animals were selected from the top and bottom 10% of estimated breeding values for FEC from a total pool of 641 sires and ram lambs. Samples were genotyped using Applied Biosystems™ Axiom™ Ovine Genotyping Array (50K) consisting of 51 572 SNPs. Following quality control, 46 268 SNPs were included in subsequent analyses. Analyses were conducted using a linear regression model in plink v1.90 and a single‐locus mixed model in snp and variation suite. Genome‐wide significance was determined by a Bonferroni correction for multiple testing. Using linear regression, loci on chromosomes 2, 3, 16, 23 and 24 were significantly associated at the genome level with FEC estimated breeding values, and we identified a region on chromosome 2 that was significant using both statistical analyses. We suggest a potential role for the gene DIS3L2 for gastrointestinal nematode resistance in Katahdin sheep, although further research is needed to validate these findings.

Across and within breed differences in the relationship between packed cell volume and fecal egg count in growing meat goat and hair sheep males naturally and artificially infected with gastrointestinal nematodes

The relationship between packed cell volume (PCV) and fecal egg count (FEC) in different breeds of meat goats and hair sheep infected with gastrointestinal nematodes, including Haemonchus contortus, was characterized. Growing males from eight commercial and two research farms (one Kiko, Spanish, Dorper, and St. Croix; three Boer; four Katahdin) in the southcentral United States were evaluated in a central performance test with ad libitum intake of a 50% concentrate pelleted diet. There were 84 Boer, 55 Kiko, and 57 Spanish goats and 52 Dorper, 129 Katahdin, and 49 St. Croix sheep. During adaptation, animals were dewormed then dosed with 10,000 infective H. contortus larvae. PCV and FEC were determined before deworming (i.e., natural infection potentially with multiple internal parasites) and 21, 28, 35, 42, and 49 days after artificial infection. Effects of species, breed, and year were analyzed with mixed effects models including day of sampling post dosing as a repeated measure and FEC and FEC × breed as covariates. Moreover, differences in correlation coefficients between PCV and logarithmic FEC (lnFEC) among species, breed, year, and day of sampling were evaluated. Breed affected (P ≤ 0.001) PCV in goats (24.8, 27.2, and 26.0% for Boer, Kiko, and Spanish, respectively; SEM = 0.42) and sheep (29.8, 26.7, and 31.0% for Dorper, Katahdin, and St. Croix, respectively; SEM = 0.28). There were effects of FEC × breed (P ≤ 0.029) on PCV for Boer, Kiko, Dorper, Katahdin, and St. Croix (-0.31, -0.33, -0.46, -0.46, and - 0.49% per 1000 eggs, respectively) but not for Spanish goats (P = 0.451). With all data, PCV and lnFEC with natural infection were highly correlated (P < 0.001) for Boer and Kiko goats and Dorper and Katahdin sheep (r = -0.59, -0.67, -0.77, and - 0.84, respectively) but not for Spanish goats or St. Croix sheep (P ≥ 0.323). Correlation coefficients for artificial infection with H. contortus were significant (P ≤ 0.002) except for Spanish goats, although values were lower (-0.40, -0.21, -0.23, -0.47, and - 0.28 for Boer, Kiko, Dorper, Katahdin, and St. Croix, respectively) compared with natural infection. In conclusion, PCV was not related to FEC in Spanish goats infected either naturally or artificially, and the nature of the relationship varied among breeds of goats and sheep. Based on the magnitude of the FEC × breed coefficient, sheep incurred a relatively greater reduction in PCV as FEC increased, and correlation coefficients indicate stronger relationships with natural than artificial infection.

Genetic parameter estimates for fecal egg counts and their relationship with growth in Avikalin and Malpura sheep

Breeding for resistance against nematodes has become the need of the hour due to emergence of anthelmintic resistant strains of major pathogenic nematodes of economic importance and rising demand for chemical residue free food by consumers. ICAR-Central Sheep and Wool Research Institute Avikanagar (Rajasthan) has developed Haemonchus contortus resistant lines of sheep in Avikalin and Malpura breeds by harvesting benefits of over-dispersion in fecal egg counts (FEC) through executing a breeding program since year 2004. Aim of the present study was to assess the genetic parameters for nematode resistance in these lines and also to develop suitable criteria for selection targeting resistance as well as growth improvement in these two lines. The data on 1240 Avikalin and 2172 Malpura sheep generated over 13 years (2004-16) for FEC along with deep pedigree and growth records for live weight at 6 (6WT) and 12 month were used for study. Data were analyzed using Average Information Restricted Maximum Likelihood (AIREML) approach. Results revealed moderate heritability (h2) for pre-drench log transformed fecal egg count (LFEC) in Avikalin (0.21±0.06) and Malpura (0.18±0.04) sheep. The post-drench h2 for LFEC was low in Avikalin (0.04±0.03) and Malpura (0.11±0.03) sheep. Effective selection program can be carried out for further improving the resistance against H. contortus in both the breeds using pre-drench LFEC estimates. The genetic correlation between the pre-drench LFEC and growth traits was not in the desired direction. Existence of substantial genotype × environment (G×E) interaction was seen in Malpura sheep, where major shift in ranks of sheep based on pre-drench LFEC as that of post-drench LFEC was observed owing to genetic correlation of 0.65±0.15. The G×E was absent in Avikalin sheep. Unreliable genetic correlation between growth and LFEC does not warrant a multi trait selection index development and its utilization in breeding program. The independent selection for LFEC followed by corrected 6WT can precisely help in achieving the goal of improving growth in nematode resistant sheep.

Variation in phenotypic resistance to gastrointestinal nematodes in hair sheep in the humid tropics of Mexico

The objective of the study was to evaluate phenotypic resistance against gastrointestinal nematodes in Blackbelly, Pelibuey and Katahdin ewes before pregnancy in the humid tropics of Mexico. Individual faecal and blood samples were taken in 59 Pelibuey, 69 Blackbelly and 73 Katahdin ewes. The egg count per gram of faeces (EPG) of gastrointestinal nematodes (GINs) was determined. The percentage of packed cell volume (PCV) and body condition score (BCS) of each animal were also recorded. The ewes were segregated as susceptible, intermediate or resistant based on the EPG using the quartile method. The data were analysed using the general linear method, and the means between breeds were compared by Tukey's test. The relationships between the EPG, PCV and BCS were evaluated by Spearman correlation. The Katahdin ewes showed the highest EPG counts (3613.6 ± 5649) compared to the Blackbelly and Pelibuey ewes (576.1 ± 1009 and 56.8 ± 187, respectively, P < 0.01). The PCV values between breeds were similar (P > 0.05). The susceptible ewes had the highest EPG counts and the lowest PCV percentage (5069 ± 6404 and 22.8% ± 8.1% respectively) compared to the resistant ewes (P < 0.01). A higher percentage of Katahdin ewes were susceptible compared to the other breeds (P < 0.05). The main GIN species were Haemonchus contortus, Trichostrongylus colubriformis and Cooperia curticei. In conclusion, Katahdin ewes showed susceptibility to GIN compared to Blackbelly and Pelibuey ewes before the pregnancy period in the humid tropics of Mexico.

Genetic parameters for ewe reproductive performance and peri-parturient fecal egg counts and their genetic relationships with lamb body weights and fecal egg counts in Katahdin sheep

This study estimated genetic parameters for ewe reproductive traits [number of lambs born (NLB) and weaned (NLW) per ewe lambing] and fecal egg counts (FEC) during the peri-parturient rise (PPR) for use in genetic evaluation of Katahdin sheep. Data included NLB and NLW for 23,060 lambings by 9,295 Katahdin ewes, 1,230 PPR at lambing (PPR0) for 750 ewes, 1,070 PPR at approximately 30 d postpartum (PPR30) for 611 ewes, BW at birth, weaning, and (or) post-weaning for 12,869 lambs, and FEC at weaning and (or) post-weaning for 4,676 lambs. Direct additive, permanent environmental, and residual (co)variances were estimated in univariate and bivariate animal models. Fixed effects included effects of ewe management group and ewe age for all traits, and, for PPR, a continuous effect of days between lambing and measurement. Effects of litter size on PPR0 and number of lambs suckled on PPR30 were included in univariate models but excluded from bivariate models for PPR and NLB or NLW. Heritability estimates in univariate models for NLB, NLW, PPR0, and PPR30 were 0.09 ± 0.01, 0.06 ± 0.01, 0.35 ± 0.06, and 0.24 ± 0.07, respectively. Estimates of permanent environmental variance as a proportion of total phenotypic variance were 0.02 ± 0.01 for NLB, 0.03 ± 0.01 for NLW, 0.05 ± 0.06 for PPR0, and 0.13 ± 0.07 for PPR30. Direct additive, phenotypic, permanent environmental, and residual correlations between NLB and NLW were 0.88 ± 0.03, 0.74 ± 0.004, 0.54 ± 0.15, 0.74 ± 0.003, respectively; corresponding correlations between PPR0 and PPR30 were 0.96 ± 0.07, 0.46 ± 0.03, 0.98 ± 0.50, 0.18 ± 0.05, respectively. The additive genetic correlation (rd) between ewe reproductive traits and PPR ranged from 0.12 to 0.18. Estimates of rd between lamb BW and subsequent ewe NLB and NLW ranged from 0.07 to 0.20, and those between PPR and lamb BW ranged from -0.03 to 0.29. The rd between ewe reproductive traits and lamb FEC ranged from 0.27 to 0.40, and those between PPR and lamb FEC ranged from 0.56 to 0.77. Correlations between maternal additive effects on BW and direct additive effects on PPR were low (-0.08 to 0.10), and those between maternal additive effects on BW and direct additive effects on ewe reproductive traits were variable (-0.36 to 0.11). We conclude that FEC in growing lambs and peri-parturient ewes are controlled by similar genes and that modest, but manageable, genetic antagonisms may exist between FEC and ewe productivity.