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.

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 ±â€…0.07, 0.31 ±â€…0.07, and 0.26 ±â€…0.05, respectively. The genetic (additive) correlation between BW with FEC was -0.26 ±â€…0.08 and with FAM was -0.16 ±â€…0.08, and thereby favorable. Heritabilities were also estimated univariately within eco-management clusters and ranged from 0.30 ±â€…0.05 to 0.37 ±â€…0.05 for BW, 0.18 ±â€…0.12 to 0.50 ±â€…0.13 for FEC, and 0.07 ±â€…0.06 to 0.40 ±â€…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.

Sheep producers increasingly rely on breeds that express resistance to gastrointestinal parasites because anthelminthic drugs are often ineffective. An example is Katahdin sheep, which are raised in various climates and management systems in the United States. These factors can be combined into eco-management clusters to describe production environments more holistically. Our objective was to determine if a genotype by eco-management cluster (environment) interaction (G × E) affected performance levels, particularly for traits indicative of parasite resistance. Body weights (BW), fecal egg counts (FEC), and FAMACHA scores (FAM) were collected at around 90 d in 3,527 Katahdin lambs delineated into nine eco-management clusters. Heritabilities of BW, FEC, and FAM were 0.36, 0.31, and 0.26, respectively. Genetic correlations of BW with FEC and FAM were low to moderate and favorable (negative). When estimated within eco-management cluster, heritabilities were 0.30 to 0.37 for BW, 0.18 to 0.50 for FEC, and 0.07 to 0.40 for FAM. For FEC and FAM, these differences corresponded with heterogenous variances (heteroscedasticity) across environments. Furthermore, G × E explained 13% (FAM) to 20% (BW) of the variation in a trait. In genetic evaluation of parasite resistance, G × E and heteroscedasticity should be incorporated to improve the efficacy of the breeding program.

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.

Katahdin sheep are a popular maternal hair breed that can exhibit resistance to gastrointestinal nematodes (GIN). Still, the consequences of GIN infection on performance levels, even in this breed, depend on the climatic and management conditions in which they are raised. Information on management practices in 40 U.S. Katahdin flocks was collected with an online survey. Climate data corresponding with these flock's locations were gathered from the National Weather Service. Using multivariate analysis to combine these data, nine distinct eco-management groupings or clusters were identified. These clusters differed in temperature, rainfall, grain supplementation, and the age at which the lambs were introduced to pasture. In 17 of these flocks, traits indicative of GIN parasitism­body weight, fecal egg count, and FAMACHA score­were measured in 90-d old Katahdin lambs. Eco-management cluster explained more variation in performance in all three traits than climate or management alone. Based on fecal egg counts, eco-management clusters corresponding with hotter temperatures and greater rainfall, and with pasture-born lambs, suffered greater parasitism. Conversely, eco-management clusters with lambs turned out to pasture at older ages benefited from reduced parasitism. Eco-management clusters provide a holistic approach to combine environmental factors that predispose lambs to parasitism.

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 r 2 ≤ 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 (r 2 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 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.

Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry.

Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing importance of hair sheep in the Americas their genetic origins have remained speculative. Prior to this report no genetic studies were able to identify a unique geographical origin of hair sheep in the New World. Our study clarifies the African and European ancestry of Caribbean hair sheep. Whole-genome structural analysis was conducted on four established breeds of hair sheep from the Caribbean region. Using breeds representing Africa and Europe we establish an objective measure indicating Caribbean hair sheep are derived from Iberian and West African origins. Caribbean hair sheep result from West African introgression into established ecotypes of Iberian descent. Genotypes from 47,750 autosomal single nucleotide polymorphism markers scored in 290 animals were used to characterize the population structure of the St. Croix, Barbados Blackbelly, Morada Nova, and Santa Ines. Principal components, admixture, and phylogenetic analyses results correlate with historical patterns of colonization and trade. These patterns support co-migration of these sheep with humans.

Changes in plasma concentrations of luteinizing hormone, progesterone, and estradiol-17beta in peripubertal turkey hens under constant or diurnal lighting.

Possible circadian fluctuations and long-term changes in concentrations of reproductive hormones in peripubertal female birds is poorly documented in comparison with mammalian species. Our objective was to document changes in concentrations of several reproductive hormones the several days before and after initial pubertal preovulatory surges of LH in turkey hens photostimulated with either constant (24L:0D) or diurnal (14L:10D) lighting. The hens were cannulated for hourly blood sampling, starting 10 days after photostimulation and continuing until all hens had laid at least two eggs. First eggs were oviposited between 16 and 24 days after photostimulation, and egg production ranged from two to nine eggs/hen during the experimental period. With both lighting treatments, concentrations of LH declined slightly, concentrations of progesterone (P(4)) increased, and concentrations of estradiol-17beta (E(2)) were constant the 3-4 days prior to initial LH surges with no circadian fluctuations in hormone concentrations. Most (10 of 13) initial preovulatory surges of LH were coupled with ovulations, and all LH surges were coupled with P(4) surges. Those LH and P(4) surges not coupled with ovulations (blind surges) occurred with both lighting treatments, but the incidence of blind surges was higher with diurnal lighting. The interval between LH and P(4) surges was longer between the first and second surges than between subsequent surges, when the interval was approximately 26 h. The duration of LH surges (7.4 +/- 3.0 h) was shorter than that of P(4) surges (10.0 +/- 2.0 h). We conclude that, in the peripubertal female turkey, 1) prior to puberty (first LH-P(4) surges), there are no circadian fluctuations in concentrations of LH, P(4), and E(2), 2) 3 days prior to initial LH surges, E(2) concentrations are stable, LH concentrations decline slightly, and P(4) concentrations increase, and 3) surges of LH are coupled to surges of P(4) but LH-P(4) surges are not always coupled to ovipositions (blind surges), possibly because of internal ovulations.