National Sheep Improvement Program Research Articles

Adding gastrointestinal parasite resistance to the breeding objective in hair sheep: initial steps.

The U.S. Maternal Hair index was designed by the National Sheep Improvement Program (NSIP) to increase total weight of lamb weaned per ewe lambing (TW). Producers are interested in adding gastrointestinal nematode (GIN) resistance to this breeding objective since parasitism causes substantial economic losses. The NSIP provides producers with estimated breeding values (EBV) for post-weaning fecal egg count (PFEC), an indicator of GIN resistance. Our objective was to gauge the effects of including PFEC as another selection criterion and goal trait. Selection index theory was used to construct 11 indexes. First was a benchmark index with TW as the goal. Weaning weight, and number of lambs born and weaned, were selection criteria. An index was then designed with PFEC added as a selection criterion. In 9 more indices, PFEC was also included as a goal trait, where the economic value of TW was scaled relative to that of PFEC. PFEC received a scaled economic value of -1 with that of TW increasing from +1 to +5 at +0.5 increments. Selection criteria were modelled as EBV or phenotypes. Annual genetic responses in goal traits were predicted. The top 3% of males and 26% of females were selected. Breeding values and phenotypes were simulated for 200 lambs by Cholesky decomposition and used to generate index scores, with 100 replicates run. Concordances with the animals selected in the benchmark scenario were determined. Using EBV as selection criteria, TW increased by 1.46kg/yr in the benchmark scenario. However, unfavorably, PFEC increased by 2.24%/yr. When using phenotypic criteria, TW increased by 0.52kg/yr and PFEC by 0.28%/yr. Once added as a goal trait, PFEC decreased regardless of the scaled economic value of TW. However, responses in TW were also reduced, although less so as its scaled economic value increased. A scaled economic value of +3 for TW appeared reasonable over other choices with 79% of the emphasis placed on TW in the breeding objective. With EBV as selection criteria, PFEC declined by 7.96%/yr with 98% of the response in TW retained. Also, on average, 64% of males and 80% of females were chosen in common with the benchmark. With phenotypic selection criteria, PFEC declined by 5.13%/yr and 94% of the response in TW was retained; 61% of males and 80% of females were chosen in common with the benchmark. Implementing an index with scaled economic values of +3 for TW and -1 for PFEC would balance gains in TW with reductions in PFEC.

PSX-7 Heritability estimates for longevity-related traits in U.S. Katahdin ewes

Abstract Genetic selection for increased ewe longevity can directly contribute to improved flock profitability and welfare. Therefore, this study aimed to estimate heritabilities for eight longevity-related traits in 12,149 Katahdin ewes. The ewes were daughters of 1,157 sires and 6,147 dams and were born between 1989 and 2020 in 58 flocks located across the U.S. The National Sheep Improvement Program provided the data. Age at last lambing (ALL); productive life (PL; number of days between the first and last lambing), total number of litters (TLI), lambs born (TNB), and lambs weaned (TNW) over the lifetime of the ewe; total litter weight at lambing (TLB) and weaning (TLW) over the lifetime of the ewe, and TLW divided by the weight of the ewe adjusted for 120 d (TLWadj) were evaluated (Table 1). Body weights (BW) at lambing and weaning (WW) were adjusted for sex effect, while WW was also adjusted for 60 d old. Ewes with lambing interval and age at the first lambing greater than 720 d and 1,095 d, respectively, were excluded. Moreover, only flocks that reported lambing records across at least 7 consecutive years and an average of 20 or more lambing records over the yr were evaluated. Fixed effects of contemporary group (flock, year, and season of birth of the ewe), the combined effect of the birth type and rearing type of the ewe, and age class at first lambing, as well as the animal random effect, were included in the animal model fitted. Contemporary groups with less than three ewes were excluded. Moreover, we excluded records deviating ± ± 3.0 SD from the mean. Variance components were estimated by restricted maximum likelihood based on pedigree (by fitting the A matrix) and genomic information [by fitting an H matrix including pedigree and genomic relationships from 10,032 animals genotyped with a 50K single nucleotide polymorphisms (SNP) chip]. The criteria used to exclude SNP were MAF < 0.05, call rate < 0.95 (for both SNP and animals), and a maximum difference of 0.15 between the observed and expected heterozygosity (Hardy-Weinberg equilibrium). After quality control, 31,182 SNP were used for the analyses. The analyses were performed using the BLUPF90+ programs. The pedigree-based heritability estimates were: ALL (0.10 ± 0.017), PL (0.11 ± 0.023), TLI (0.10 ± 0.017), TNA (0.11 ± 0.017), TNW (0.11 ± 0.018), TLB (0.12 ± 0.020), TLW (0.10 ± 0.024), and TLWadj (0.07 ± 0.031). The genomic-based heritability estimates were: ALL (0.13 ± 0.018), PL (0.14 ± 0.024), TLI (0.13 ± 0.018), TNB (0.13 ± 0.018), TNW (0.14 ± 0.018), TLB (0.15 ± 0.021), TLW (0.11 ± 0.024), and TLWadj (0.07 ± 0.032). The relative standard error (RSE) of the estimates obtained with the A matrix ranged from 15.5% (TNB) to 44.3% (TLWadj) and from 12.9% (TNW) to 45.7% (TLWadj) when fitting the H matrix. In conclusion, longevity-related traits in U.S. Katahdin ewes are heritable, and estimates are slightly greater (with reduced RSE) when incorporating genomic information to estimate variance components.

117 Population structure and genetic diversity of U.S. Polypay Sheep in the National Sheep Improvement Program

Abstract The development of the Polypay breed focused on improving the lifetime productivity of the Western range ewe with the objective of ewes lambing twice a year starting at 1 yr of age. The Polypay was developed at the U.S. Sheep Experiment Station (USSES) in 1968 as a four-breed composite with 25% each of Dorset, Rambouillet, Targhee, and Finnsheep. The breed is versatile and rugged enough to be used extensively in Western sheep production and throughout the Central and Eastern U.S. in intensive accelerated lambing systems. Our objective was to define the current population structure and genetic diversity in this breed using pedigree- and genomic-based methods as the industry adopts genomic selection. Pedigree records from Polypay breeders participating in the National Sheep Improvement Program representing 193 flocks were combined with pedigree records from USSES (n = 162,997) tracing back to the origins of the breed. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip (n = 1,856). Quality control measures were applied for marker and animal call rates and to remove markers in high linkage disequilibrium. Pedigree completeness and quality was 9.6, 2.3, and 4.6 for mean maximum, mean complete, and mean equivalent generations, respectively. Pedigree-based inbreeding for the full data was 2.19%; for the subset of pedigreed animals also genotyped, it was 2.94%. The rate of inbreeding was consistently 0.07%/yr across years (P = 0.88). Measures of genomic inbreeding for genotyped sheep were 1.26% for Wright’s inbreeding coefficient, measured as heterozygote deficiency, and 2.90% for inbreeding based on runs of homozygosity. Ten rams from 8 flocks contributed up to 20.3% of the current gene pool. Pedigree-based measures of effective population size ranged from 70 to 249 while the genomic estimate was 118. Fixed and rare (≤ 0.01) alleles accounted for 3.2% and 1.4% of the markers, respectively. The majority of runs of homozygosity (72.1%) were less than 6 Mb, indicative of founder effects and ancient inbreeding rather than recent inbreeding. Based on principal component (PC) analysis, PC 1 suggested a separation of USSES sheep from the rest. Model-based population structure showed differentiation among flocks as did Wright’s Fixation Index (FST) values with a mean of 0.07. High levels of genetic diversity exist in the Polypay as demonstrated by low inbreeding, high heterozygosity, and large effective population sizes. Population substructure exists in the population as shown by PC analysis, model-based population structure, and FST values. These parameters indicate that sufficient genetic diversity is present to move forward with genomic selection. Genetic diversity measures should be revisited periodically once genomic selection is implemented in the breed. USDA is an equal opportunity provider and employer.

PSVII-8 Survival analyses of the productive life in U.S. Katahdin ewes

Abstract Ewe productive life (PL), defined as the number of days between the first and last lambing, is a common indicator of longevity. This study aimed to analyze the PL of 10,276 Katahdin ewes, of which 69.3% were uncensored and 30.7% were right-censored records. Ewes were daughters of 1,188 sires and 6,312 dams, born between 1989 and 2021 in 58 flocks located across the U.S., and the National Sheep Improvement Program provided the data. Ewes with lambing interval and age at first lambing greater than 720 d and 1,095 d, respectively, were excluded. Moreover, flocks that did not report lambing records across at least 7 consecutive years or did not have an average of 20 or more lambing records over the year were also left out of the analyses. Survival functions were analyzed using the Kaplan-Meyer (KM) and Cox models, while the Hazard function was analyzed using the Cox model. For the Cox model, contemporary group (concatenation of flock, year, and season of ewe’s birth) was fitted as a random effect; the ewe’s BR class (combined effect of birth/rearing types: 1/1, 2/1, 2/2, 3/2, 3/3, with digit-3 including counts ≥ 3), ewe’s age class at first lambing (≤ 378d; 379 to 700d; and > 700 d), and the ewe’s dam’s age class (A: < 713 d; B: 713 to 1,486 d; C: > 1486 d) were fitted as fixed effects. All survival analyses were performed using the Survival R-package. All factors included in the Cox model were highly significant (P < 0.001), except dam age class (P > 0.05). The proportional hazard assumption was checked using a graphical diagnostic based on the scaled Schoenfeld residuals, and there was no failure in the assumption. Moreover, there was no evidence of influential or outlier records in the graphical analysis of the residuals. The Cox survival curve overlapped with the KM survival curve (Figure 1), indicating a good survival prediction with the Cox model. The median PL was 1,036 d (95%CI: 1001 to 1,056 d) with the KM model and 1,056 d (95%CI: 984 to 1,078 d) with the Cox model. The hazard ratio indicated BR levels 2/2 and 3/3 showed less hazards than group 1/1 (Figure 2), and thereby longer PL; no significant difference was observed between 1/1 and the other two levels (2/1 and 2/3). Ewes that first lambed before 378 d had less hazard than those with the first lambing after this age (Figure 2). There was no significant difference between the dam age classes. In conclusion, over 50% of Katahdin sheep have less than 3 yr PL. Moreover, U.S. Katahdin ewes born from larger litters and having the first lambing before 378 d are likelier to have a greater PL.

Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection.

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed's origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020-2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright's inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed.

78 Estimates of genetic parameters for weight, wool, and carcass traits of Rambouillet sheep

Abstract The Rambouillet sheep breed is the foundation to most western range sheep in the U.S. Through the National Sheep Improvement Program (NSIP), Rambouillet breeders seek to improve economically relevant traits. However, the parameters used in the NSIP genetic evaluation were last estimated two decades ago. Our aim was to re-estimate genetic parameters for body weight (BW), carcass, and wool traits. Data were provided by NSIP, which included BW at birth (BWT; n = 28,817), weaning [WWT; n = 5,633; age: 68 (SD 16) day], early post-weaning [PWTE; n = 23,303; 128 (SD 22) d], late post-weaning [PWTL; n = 7,689; 201 (SD 45) d] and as yearlings [YWT; n = 5,830; 375 (SD 33) d]. Yearling ultrasound scans of 12th rib backfat depth (YCF; n = 2,447) and eye muscle depth (YEMD; n = 2,457) were also available. Yearling wool traits were fiber curvature (YFC; n = 6,009), fiber diameter (YFD; n = 9,880), fiber diameter coefficient of variation (YFDCV; n = 8,803), greasy fleece weight (YGFW; n = 11,859) and staple length (YSL; n = 11,270). The pedigree consisted of 36,297 individuals. Animals with phenotypic records were progeny of 333 sires and 1,727 dams. A succession of univariate animal models was fitted. The most comprehensive model included direct and maternal additive genetic effects, their genetic covariance, and maternal permanent environmental and residual effects. Phenotypes were pre-adjusted for birth-rearing type category and, as covariates, dam age and age at recording. Contemporary group—a concatenation of flock, year, season, management group, sex, and, excluding BWT, recording date—was the only fixed effect fitted in the model. Model selection was based on the log-likelihood ratio test, and Akaike and Bayesian information criteria. The data structure, namely dams and their daughters and granddaughters contributing data, allowed reliable testing of the maternal effect terms. The direct-maternal genetic covariance did not explain variation for any trait (P > 0.18). The most parsimonious model for BW traits included direct and maternal additive genetic, and maternal permanent environmental, effects. For carcass and wool traits, only direct additive genetic effects were included in the final model. Such was unsurprising, as maternal effects often diminish as animals age. For the final models fitted (Table 1), direct heritabilities (± SE) for body weights ranged from 0.14 ± 0.01 (BWT) to 0.38 ± 0.04 (PWTL); the maternal heritabilities ranged from 0.04 ± 0.02 (PWTL; YWT) to 0.13 ± 0.01 (BWT). For carcass traits, direct heritabilities were 0.13 ± 0.04 (YCF) and 0.31 ± 0.05 (YEMD). For wool traits, they ranged from 0.37 ± 0.02 (YSL) to 0.58 ± 0.02 (YFD). These re-estimated parameter values are consistent with those used by NSIP, with the exception of PWTL (greater) and YSL (lower). With genomic data accumulating in Rambouillet, further refinements in parameter estimation are planned.

98 Adding parasite resistance to the breeding objective in hair sheep

Abstract Economic selection indexes provide the best method to achieve genetic gain for multiple traits simultaneously. Hair sheep enterprises, particularly in environments with substantial gastrointestinal nematode challenge, may benefit from incorporating parasite resistance in a selection index. However, obtaining the relative economic value (REV) for parasite resistance is challenging; information on its impact on productivity is incomplete, as are the costs of treatment given anthelmintic resistance. The National Sheep Improvement Program (NSIP) currently provides producers with an index designed to increase total weight of lamb weaned per ewe lambing (TW). Our objective was to assess the effects of including fecal egg count, an indicator of parasite resistance, as an additional goal trait. Including the benchmark scenario with TW as its sole objective, 10 indexes were constructed using standard index theory. Post-weaning fecal egg count (PFEC) was added to this breeding objective with a REV of -1 and the REV for TW was varied from +1 to +5 at +0.5 increments. Weaning weight, number of lambs born and weaned, and PFEC were the selection criteria, modelled as either phenotypes or estimated breeding values (EBV). Phenotypes and EBV were simulated for 1,000 lambs by Cholesky decomposition and used to generate index scores. Ten replicates were run and the top 3% of males and 26% of females were retained on index scores. Annual responses in the goal traits were estimated. Responses in PFEC were expressed as a percentage, assuming a mean PFEC of 2,089 eggs/g as in NSIP. Concordances with those selected in the benchmark scenario were determined. Using EBV as selection criteria, TW increased by 1.7 kg/yr in the benchmark scenario (Table 1). However, unfavorably, PFEC increased by 2.3%/yr. When phenotypic criteria were used, TW increased by 0.5 kg/yr, and PFEC by 0.3%/yr. Once added to the breeding objective, PFEC decreased regardless of the REV of TW. However, response in TW also reduced, although less so as its REV increased. With EBV as the criteria, the REV of +3 for TW appeared preferable: PFEC reduced by 7.1%/yr with 98% of the response in TW retained. With phenotypic selection criteria, PFEC reduced by 5.2%/yr with 94% of the response in TW retained. With +3 REV for TW and EBV as the selection criteria, on average 65% and 82% of males and females, respectively, were chosen in common with the benchmark. When phenotypic criteria were used, those percentages were 60% and 80%, respectively. Implementing a more holistic index with REV of +3 for TW and -1 for PFEC would result in reasonable responses in both traits. However, producers will need to decide if reduced gains in TW is acceptable to improve parasite resistance in a hair sheep breeding program.

225 Genomic diversity of Katahdin sheep and impacts on genomic prediction

Abstract In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With its increasing popularity and the recent adoption of genomic prediction in the Katahdin breeding program, evaluating the genetic diversity in this breed is necessary. Prediction accuracies rely on the strength of genetic relationships. That strength often increases with selection using genomically-enhanced estimated breeding values; however, it carries the risk of decreasing diversity. We aim to characterize the genetic diversity present in the breed and the subsequent impact on the accuracies of genomic predictions. Genotypes on Katahdin sheep from member flocks in the National Sheep Improvement Program were used. Data from two medium density 50k bead chips and one high density 600k bead chip were merged and limited to shared autosomal single nucleotide polymorphisms (SNP). After quality control, there were 9,705 animals and 31,984 SNP remaining. Only for analyses of inbreeding and heterozygosity, linkage disequilibrium (LD) pruning was performed; variants with an LD score exceeding 0.8 were removed with 29,904 SNP remaining. To determine the extent of population structure, principal component (PC) analysis was conducted with PC one and PC two explaining 4.9% and 3.8% of the variation in the population, respectively. When examining subpopulations, a single ancestral population explained 99.9% of the genetic variation among animals. When clustered by identity-by-state, all animals were placed in a single cluster. Inbreeding coefficients were estimated with four methods: method of moments, variance-standardized relationship minus one, excess homozygosity, and correlation between uniting gametes. Across methods, average inbreeding coefficients ranged from 1.14% to 1.20% with Pearson and Spearman correlations ranging from -0.51 to 0.91 (Table 1). Historical effective population sizes (Ne) were estimated for earlier generations, and a linear regression fit to predict more recent Ne. At the founding of the breed, historical Ne was estimated to be 310, and the current Ne was estimated to be 150. Effects of Ne on the accuracy of genomic predictions were examined for reference population sizes ranging from 1k to 25k for traits of low (0.1), moderate (0.3), and high (0.5) heritabilities. The corresponding number of effective chromosomal segments were 2NeL, where L was the length of the genome in morgans (26M). Accuracies of genomic predictions increased as the reference population size grew, with only marginal gains once the population exceeded 15k. Overall, there were no detectable genetic subpopulations in the Katahdin breed. Current levels of inbreeding were low. With a small Ne the breed can achieve high accuracy for genomic predictions by aiming for a reference population of 15k animals. Negative impacts on genetic diversity due to genomic selection are not of immediate concern.

Genetic impact of external Targhee sires at the U.S. Sheep Experiment Station: a case study of introgression.

Sheep breeders requested that the U.S. Sheep Experiment Station (USSES) to participate in national genetic evaluation through the National Sheep Improvement Program (NSIP). The reasons included the need for (1) a comparison of the productivity of industry and United States Department of Agriculture (USDA) lines, (2) transparency of USDA flocks, (3) genetic ties for NSIP by sampling of industry flocks, and (4) development of premium genetic lines for public release. In response, USSES began to incorporate external sires from NSIP participating flocks into the USSES Targhee flock. Our objective, based on a pedigree analysis, was to test if introgression of external genetics into the flock was achieved. The pedigree included 13,189 animals with mean maximum generations, mean complete generations, and mean equivalent complete generations of 4.2, 1.8, and 2.6, respectively. The mean generation interval was 3.1 yr. The reference population was defined as lambs born from 2021 to 2023 (n = 792). Two additional populations were defined as the current mature ewe flock (n = 123) and the current mature rams (n = 14). The Genetic Conservation Index averaged 7.7 for the full population and 25.7 for the reference population. Overall inbreeding was 0.003 for the full population and 0.006 for the reference population. The rate of inbreeding was 0.0003 per generation. Average relatedness was 0.015 for the full population and 0.018 for the reference population. The effective number of founders, effective number of ancestors, and founder genome equivalents contributing to the reference population were 60, 39, and 19.1, respectively. The ratio of the effective number of founders to the effective number of ancestors was 1.5, indicating the presence of genetic bottlenecks. Measures of effective population size ranged from 102 to 547. Of the 704 offspring produced by external sires, 17 ram lambs and 132 ewe lambs were retained for breeding. The USSES sires produced 299 offspring with 2 ram lambs and 51 ewe lambs retained. Incorporating external sires resulted in a cumulative percentage of genetic variance of 48.8, 49.1, and 44.2 of external genetics for the reference population, current mature ewe flock, and current mature rams, respectively. Stakeholder needs were addressed by introgression of external sires and participation in NSIP, but future selection practices need to be modified to maintain a minimum of 50% USSES core genetics in the flock.

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.

140 Targhee Sire Benchmarking at the U.S. Sheep Experiment Station

Abstract The Targhee breed was developed at the U.S. Sheep Experiment Station (USSES) starting in 1926, and has become an established range breed used commercially in the Western U.S. Our objective was to benchmark the performance of industry-based (external) Targhee sires with those currently in use at USSES. Nineteen Targhee sires from 12 flocks were incorporated into the USSES breeding flock starting with the 2015 breeding season. Data were measured through 2022 for 3 production and 12 wool traits with a range of 180 to 1,967 records per trait. Externally sourced sires averaged 38.3 progeny (7 to 78), with 0 to 4 ram lambs (15 total) and 0 to 15 (106 total) ewe lambs retained per sire in the flock. They were ancestors of 984 grand-progeny. USSES sires averaged 25.0 progeny (5 to 52), with 0 to 1 ram lambs (2 total) and 0 to 8 (53 total) ewe lambs retained per sire. They had 275 grand-progeny. Pedigree data was used to compute the marginal genetic contributions for each sire to the current flock using ENDOG. External sires had a cumulative contribution of 31.9 percent (0.4 to 3.9) while the USSES sires contributed 1.4 percent (0.0 to 0.9). Using R, fixed effects examined were age of dam, lamb sex, lamb birth year, grazing group, and type of birth/rearing. Significant variation explained in a trait by main effects (P < 0.005), and their two-way interactions (P < 0.001), were included in the final linear mixed models fitted. Externally sourced and USSES sires were assigned to separate genetic groups to account for the anticipated differences in genetic base. Using WOMBAT, a univariate animal model was fitted to estimate variance components and predict estimated breeding values for each lamb trait. Selection of random effects was based on log-likelihood ratio tests. Final models fitted and estimated heritabilities are summarized in Table 1. Total litter weight at 120 days per ewe lambing (TW120) was evaluated using a repeated measures model with direct additive and permanent environmental random effects of the ewe. Genetic group solutions were not significantly different (P > 0.05) for any traits evaluated. Since both sire groups originated from the same population, this suggests significant selection divergence had not occurred between industry and USSES flocks. Incorporation of external Targhee sires increased the genetic diversity of the USSES flock. It also strengthened industry ties to the USSES flock, which will benefit the commercial genetic evaluation conducted by the National Sheep Improvement Program. USDA is an equal opportunity provider and employer.

PSVII-3 The Impact of Genotyping Strategies on Accuracy of Genomic Prediction in Sheep Populations: Preliminary Results of a Simulation Study

Abstract Genomic predictions provide more accurate estimated breeding values (EBV) in younger animals, enabling greater rates of genetic gains over time. However, genomic selection in U.S. sheep is still incipient due to the higher genotyping cost relative to animal cost. Our objective was to compare genotyping strategies differing in the proportion of animals genotyped and the extent of pedigree error on prediction accuracy. These genetic evaluations were based on single-step Genomic Best Linear Unbiased Prediction. We used the AlphaSimR package to simulate a composite sheep population mimicking the Katahdin breeds’ formation. We then simulated four further generations based on the structure of Katahdin flocks engaged in the National Sheep Improvement Program. Thirty-five flocks were simulated with an effective population size of 170. Flock size ranged from 31 to 680 animals and, by design, was skewed towards smaller flocks. Average ram to ewe ratio, mortality rate per generation, and number of lambs born per ewe lambing was 1:16, 10%, and 1.8 lambs, respectively. We simulated a 50k SNP panel for a moderately heritable (0.30) trait. Flocks had low genetic connectedness. Selection criteria differed among flocks: 3 selected randomly, 10 selected based on highest EBV, and 22 selected based on highest phenotypes. All combinations of 5, 40, or 100% of males or females genotyped, 5 or 20% of animals missing pedigree, and 5 or 20% of sires misidentified were compared. We also considered a scenario with no pedigree errors (i.e., no missing pedigree or misidentified sires). Animals with the best phenotype were chosen for genotyping. The first three generations were used as the reference population (7,317 animals) to validate the 4th generation (2,055 animals). Each scenario was replicated 5 times. A linear model was used to estimate differences in prediction accuracy between scenarios, tested with Tukey’s test (alpha 0.05). For the scenario without pedigree errors, prediction accuracy ranged from 0.50 ± 0.06 for 5% of males and females genotyped to 0.75 ± 0.03 for 100% of animals genotyped (Figure 1). For scenarios with 5% pedigree errors, prediction accuracy ranged from 0.33 ± 0.02 for 5% of males and females genotyped to 0.71 ± 0.02 for 100% of animals genotyped. For the scenario with 20% pedigree errors, prediction accuracy ranged from 0.26 ± 0.06 for 5% of males and females genotyped to 0.67 ± 0.03 for 100% of animals genotyped. Across pedigree error scenarios, trends were similar. Importantly, genotyping 5% of one sex and 100% of the other resulted in similar accuracies to genotyping 100% of animals. In scenarios with few animals genotyped, accuracies were higher when errors in pedigree were avoided. These preliminary results reinforce the importance of genomics in correcting pedigree errors, with high levels of prediction accuracy when at least most animals of one sex are genotyped.

147 Determining Status of Five Genetic Conditions in U.S. Sheep with a Medium-Density Ovine Bead Array

Abstract Using molecular information in genetic evaluation has become routine in most livestock species. Small ruminants, however, are lagging in use of this technology, partly due to the higher cost of genotyping versus the value of the individual animal. Using a single genotyping platform to simultaneously obtain information for making genomic predictions, identifying genetic condition status, and verifying parentage avoids costs of running multiple DNA tests. Our objective was to develop and validate a process to obtain accurate genotypes for genetic conditions using a medium-density array, and to estimate their frequencies in U.S. sheep breeds. Samples (DNA) from 10,569 sheep from 9 breeds in the National Sheep Improvement Program, primarily Katahdin (8,657), Rambouillet (886), and Polypay (584), were genotyped with a commercial 50k single nucleotide polymorphism (SNP) bead chip. Genotypes for 5 genetic conditions, ovine progressive pneumonia (OPP) susceptibility (TMEM154), scrapie susceptibility (PRNP), double muscle (MSTN), callipyge (CLPG), and booroola FecB (BMPR1B), were determined using 66 SNP genotypes extracted from the bead chip. Targeted SNP markers were replicated 2 to 8 times on the array. The TMEM154 diplotypes were obtained by combining genotypes at 10 SNP markers. Variants for PRNP codon 136 and 171 were determined using 6 markers. The accuracy of assigning genetic status was validated using 15 reference DNA with known genotypes submitted blindly to the commercial laboratory. Consistency of replicated calls for an SNP was also evaluated. Following in-house laboratory-based quality control of the assay, acceptance of a genotype involved two steps. First, at least 60% of the replicated SNP on an animal needed to be assigned a genotype. Second, amongst those SNP genotyped, at least 60% needed to detect the same nucleotide. This strategy resulted in 98.4% and 90.9% of the animals having genetic status scored for PRNP and TMEM154, respectively. Where genotypes were accepted, OPP and scrapie susceptibility was assigned based on TMEM154 diplotypes and PRNP codons 136 and 171 genotypes, respectively. As shown in Table 1, genetic condition status differed appreciably among Katahdin, Polypay, and Rambouillet. Nearly 60% of Katahdins were characterized as highly susceptible to OPP while such was so in less than 15% Polypay and Rambouillet. Most (93.3%) Polypay were deemed scrapie resistant, with a majority of Katahdin (93.1%) and Rambouillet (80.6%) either resistant or rarely susceptible to this disease. However, 18.6% of Rambouillet were characterized as highly susceptible to scrapie. No animals carried the callipyge or FecB mutation. The double muscle mutation also was rare; in Katahdins, 2.7 and 0.2% of animals carried one or two copies, respectively. The approach developed accounted for genotyping inaccuracies, with full validation of genetic status. Furthermore, considerable variation in susceptibilities to OPP and scrapie was detected among breeds, which can be used in defining breeding objectives.

PSV-23 Characterization of Katahdin Lamb Carcasses in a Traditional Lamb Marketing Context

Abstract The Katahdin breed has grown in popularity in the US, but it is relatively unknown if their carcasses conform to expectations of the traditional commodity lamb industry. Purebred Katahdin wethers (n = 223) were sourced from the genetic reference flock at the U.S. Meat Animal Research Center over two consecutive years. The flock is enrolled in the National Sheep Improvement Program (NSIP) and estimated breeding values (EBV) were available on standard production traits. Lambs were assigned to one of three groups per year based on body weight (BW) and fed a common finishing diet through harvest at similar end BW (51.3 ± 5.6 kg) but varying age (223.8 ± 32.2 d). Lambs were harvested at a commercial processor, hot carcass weight (HCW) was recorded, dressing percentage (DP) was calculated, and carcasses were chilled for 24 h. Carcasses were then ribbed and 12th rib backfat thickness (BFT), and loin muscle area (LMA) were measured. Traits were analyzed in mixed models with fixed class effects of finishing group (6 levels) and rearing type (single or multiple), a linear covariate of harvest age, and a random effect of sire (n = 16). There were no differences in BW, HCW, BFT, and LMA between rearing types but lambs reared as multiples had greater DP than those reared as singles (P = 0.02; Table). End BW increased while DP decreased with lamb harvest age (P ≤ 0.03). Pearson correlation coefficients were estimated between traits including post-weaning weight (PWWT) NSIP EBV. There was a strong, positive correlation between HCW and BFT (0.52) and HCW and BWT (0.54; P < 0.001). In contrast, HCW was only moderately correlated to LMA (0.35; P < 0.001). The PWWT EBV is the best genetic predictor of post-weaning lamb growth and was moderately correlated with end BW (0.38), HCW (0.35), and LMA (0.35; P < 0.001). Traditional markets prefer carcasses to be 29.5 – 36.3 kg HCW and < 6.4 mm BFT; 91% and 51% of Katahdin carcasses were below the HCW and BFT thresholds, respectively. Katahdins are capable of producing lean carcasses that conform to packer ideals for BF when fed to harvest BW of the present study, which may reduce excess fat trimming during fabrication. However, HCW observed in the present study may suggest greater suitability for non-traditional (i.e., ethnic) markets. Lower correlations between carcass traits in Katahdin compared with past research in Western white-faced lambs may highlight important biological differences in growth and fat deposition among divergent breed types. Crossbreeding Katahdin ewes with terminal sire breeds and within breed selection will improve growth and carcass traits without exceeding HCW thresholds commonly reached in wool sheep but should be considered in tandem with other breeding objectives.

100 Pedigree Effective Population Size Affects Genomic Prediction Accuracy in Katahdin Sheep

Abstract Katahdin sheep are a composite hair breed of medium-size, relatively prolific, with potential to exhibit resistance to gastrointestinal parasites. Recently, genomic predictions of breeding values were introduced in Katahdins. Prediction accuracy depends on the genetic variation present, and selection using genomically-enhanced breeding values may reduce diversity. We aimed to characterize the current genetic variability in Katahdins utilizing their extensive pedigree. The National Sheep Improvement Program provided the pedigree of 92,030 sheep born from 1984-2019. Two reference populations were defined for animals born between 2017-2019: all Katahdins (n = 23,494), and Katahdins with at least three generations of known Katahdin ancestry (n = 9,327). Using ENDOG and PopReport, effective population sizes (Ne) were estimated. We then considered the effect of Ne on the size of the genomic reference population needed to achieve certain levels of prediction accuracy. Weaning weight, a lowly heritable trait for this breed (h2 = 0.13), was evaluated. Based on individual increase in inbreeding, inbreeding coefficient of animal adjusted for equivalent complete generations, the estimated Ne for the full pedigree, reference 1, and reference 2 were 92, 104, and 87, respectively. When inbreeding coefficients were regressed or log-regressed on birth date and adjusted for generation interval, the Ne estimates were 53 and 49 for reference 1, and 76 and 67 for reference 2, respectively. For our average Ne = 75 with 3,960 effective chromosomal segments, the accuracy of prediction for weaning weight was estimated for genomic reference population sizes (N) of 10k, 15k, 20k, and 25k. Starting at N = 10k, the prediction accuracy was 0.58, and as N increased by 5k increments the accuracy increased to 0.65, 0.70, and 0.74. Conversely, with our smallest Ne = 49 with 2,548 effective chromosomal segments, the prediction accuracy was 0.64, 0.71, 0.75, and 0.78 for N = 10k, 15k, 20k, and 25k, respectively. Estimated Ne varied depending on the method utilized, and tended to be larger for reference 1 than 2. However, this was not the case for Ne based on regression. Inbreeding coefficients were greater in reference 2 than 1, and the generation interval was shorter in reference 2 (2.84 years) than in 1 (2.97 years). These combined differences led to larger Ne estimates for reference 2 than 1, reflecting the impact of different criteria used to obtain this statistic. The generally small, estimated Ne benefitted genomic prediction due to a greater shared number of effective chromosomal segments. Investing in larger genomic reference populations will only marginally increase prediction accuracy even for lowly heritable traits. Selection using genomically-enhanced breeding values will accelerate genetic gains, potentially reducing the Ne of Katahdins and thereby increasing prediction accuracy. Yet, long-term gains may be at risk due to the loss of genetic diversity.

155 Rams Enrolled in the National Sheep Improvement Program have Improved Performance and Value in Ram Test Program

Abstract Genetic evaluation programs can provide valuable selection tools for sheep breeders. However, industry acceptance and utilization of these tools is still limited. The objective here was to evaluate the performance and value of rams enrolled in the National Sheep Improvement Program (NSIP) compared with those not enrolled during a ram test program. Rams (Katahdin = 16, Texel = 3) were delivered to the Southwest Virginia Agricultural Research and Extension Center Ram Test on May 31. Rams were dewormed and rested for two weeks. On June 21, rams were given Haemonchus contortus L3 larvae adjusted for body weight (average = 5000 L3). FAMACHA scores and fecal egg counts (FEC) were monitored every two weeks until August 30. Rams were dewormed based on FAMACHA ≥ 3. The top 50% of rams, excluding any dewormed rams, based on the sale index [Sale Index = 0.50*(0.33*average daily gain ratio + 0.67*weight per day of age ratio) + 0.50*logFEC ratio] were sold at auction as breeding stock. Rams were classified as NSIP if enrolled. Statistical analyses were performed using SAS (SAS Institute, Cary, NC). Of the19 rams on test, 52% were NSIP. Thirteen rams required deworming during the test (38% of these were NSIP rams). Average sale index of NSIP rams tended to be greater than that of non-NSIP rams (101.4 vs. 98.3, P = 0.06). Of rams with sale index ≥ 100 (top 50%), a greater percentage of these rams were NSIP vs. non-NSIP (61% vs. 39%, respectively; P < 0.05). When NSIP status was evaluated for the top 20% of rams (sale index ≥07), a greater percentage of these rams were also NSIP vs. non-NSIP (78% vs. 22%, respectively; P < 0.01). Rams (n = 57) were sold on September 23 with an average sale price of $1,482. Rams enrolled in NSIP commanded greater prices than those not enrolled ($1,659 vs. $1,222, P < 0.05). When sale price was regressed on sale index for NSIP and non-NSIP rams, R2 for NSIP rams was 0.19 compared with the R2 for non-NSIP rams of 0.76. Given the weaker relationship between price and sale index for NSIP rams, estimated breeding values (EBVs) were evaluated. NSIP rams with EBVs reported for post-weaning weight, post-weaning FEC, and Maternal Hair Index sold for greater prices than those rams missing one or all of these EBVs ($1,837 vs. $971, respectively; P < 0.05). In summary, NSIP rams had greater performance (as indicated by sale index) and value compared with non-NSIP rams. For rams enrolled in NSIP, sale index was a poor predictor of value indicating buyers may be considering other factors besides sale index, such as EBVs, when purchasing NSIP rams.

156 The Impact of Sire Parasite Resistance on Offspring Gastrointestinal Nematode Indicators, and Relative Impact of Lamb Breeding Values on sale Value of Ram Lambs

Abstract Genetic selection of sheep for resistance to gastrointestinal nematodes (GIN) has become a priority for pasture-based production of lambs to minimize the need for deworming. The first objective of this experiment was to determine the impact of sire weaning or post-weaning fecal egg count (FEC) estimated breeding value (EBV; WFEC and PFEC, respectively) from the National Sheep Improvement Program (NSIP) on GIN infection in Katahdin lambs born in fall (Oct – Nov; n = 459) or winter (Jan – Feb; n = 378) of 2018 through 2021 at the USDA Agricultural Research Service (ARS). FAMACHA scores were determined, and blood samples and feces were collected from the lambs to determine packed cell volume (PCV), and FEC at 60, 90, 120, and 150 days of age, and lambs were selectively dewormed if anemic. Data were analyzed using mixed models. The offspring FEC was positively (P < 0.001) and the PCV negatively (P < 0.001) related to the sire WFEC and PFEC. This implies that offspring parasitism would be less and survival greater from highly resistant sires. A second objective was to examine effects on sale prices of breeding-quality ram lambs from four farms, including ARS, of lamb EBV for WFEC and ewe productivity trait (EPT) designed to identify ewes with superior maternal ability. Sale price effects were dominated by sale type with a premium of $1,086/animal relative to direct sales from the farm for animals in NSIP or specialty sales. EPT EBV was impactful yielding a-SD increase of 2.3 units or an extra $39/animal. WFEC had no effect on sale value. Thus, while more parasite-resistant sires produced offspring with decreased FEC, the sale value of these ram lambs appeared to have been more strongly associated with EPT, or with a desire to obtain ram lambs with balanced EBV rather than elite EBV for parasite resistance.

The impact of sire fecal egg count estimated breeding values on indicators of offspring gastrointestinal nematode infection, and relative impact of lamb estimated breeding values on sale value of ram lambs

Genetic selection of sheep for resistance to gastrointestinal nematodes (GIN) has become a priority for pasture-based production of lambs to minimize the need for deworming. The objective of this experiment was to determine the impact of sire weaning or post-weaning fecal egg count (FEC) estimated breeding value (EBV; WFEC and PFEC, respectively) from the National Sheep Improvement Program (NSIP) on GIN infection in Katahdin lambs born in fall (Oct – Nov; n = 459) or winter (Jan – Feb; n = 378) of 2018 through 2021 at the USDA Agricultural Research Service (ARS). FAMACHA scores were determined, and blood samples and feces were collected from the lambs to determine packed cell volume (PCV), and FEC at 60, 90, 120, and 150 days of age, and lambs were selectively dewormed if anemic. Data were analyzed using mixed models containing fixed effects of year, sex, age at sampling (fitted as a repeated measure), and their interactions, and continuous effects of sire FEC EBV. The FEC and PCV of offspring was positively (P < 0.001) and negatively (P < 0.001), respectively, related to the sire WFEC and PFEC. A second objective was to examine effects on sale prices of breeding-quality ram lambs from four farms, including ARS, of lamb EBV for WFEC and a ewe productivity trait (EPT) designed to identify ewes with superior maternal ability. Sale price effects were dominated by sale type with a premium of $1086/head relative to direct sales from the farm for animals in NSIP or Katahdin Hair Sheep International Expo sales. Producers likewise assigned a premium of $107/head to animals retained for use in their own breeding herds. The next most impactful variable was the EPT EBV. A 1-SD increase of 2.3 units in EPT yielded an extra $39/head whereas a similar 1-SD decrease in EPT resulted in a $32/head discount. Lambs born in fall were discounted by $6/head relative to those born in winter. Lambs that were not dewormed received a $29/head premium over lambs that were dewormed and was presumably taken as a phenotypic signal that the lamb was resistant. A ± 1-SD change in WFEC had no effect on sale value, which changed by less than $0.01/head. This result may have been confounded with whether or not the lamb had been dewormed. Thus, while more parasite-resistant sires produced offspring with lower FEC, the sale value of these ram lambs appeared to have been more strongly associated with other EBV such as EPT or with a desire to obtain ram lambs with balanced EBV rather than elite EBV for parasite resistance.

376 Genetic Approaches to Improve Reproductive Performance in the U.S. Sheep Industry

Abstract The U.S. sheep industry has experienced many changes over the last 50 years, the most prominent being a 75% reduction in the national breeding ewe inventory. Wool now accounts for ~10% of enterprise returns compared to ~80% from the sale of market lambs. Most breeding objective work indicates greatest emphasis should be placed on traits associated with ewe reproductive efficiency [e.g., number of lambs born/weaned (NLB/NLW), lamb survival]. Still, average NLB across the U.S. (1.07 lambs/ewe) and within geographic regions (East = 1.13, Midwest = 1.25, West = 1.09, Southwest = 0.79 lambs/ewe) remains low. Several genetic technologies are available to improve reproductive performance. Introgression of large effect gene variants, such as those within BMPR-1B, have increased NLB by ~1.0 and ~1.5 lambs in heterozygous and homozygous ewes, respectively. However, without joint improvement in maternal ability and/or husbandry, advantages in NLW are less pronounced and few U.S. producers utilize such variants in practice. Reproductive efficiency traits present challenges in selection programs as they are lowly heritable (&amp;lt; 0.15) and sex-limited. Previous single-trait selection experiments had modest improvement in NLB (0.01 – 0.02 lambs/yr). Selection accuracy is greatly improved by including pedigree and/or genomic relationships when deriving estimated breeding values (EBV). Since 2000, NLW EBV have increased by 0.01 lambs/yr with concurrent improvement in direct (0.02 kg/yr) and maternal (0.04 kg/yr) weaning weight for Polypay flocks enrolled in the National Sheep Improvement Program (NSIP). Still, NSIP flocks represent &amp;lt; 1% of production-oriented U.S. flocks so considerable expansion is needed to realize within-breed genetic improvement at a national level. Perhaps most importantly, large differences in reproductive efficiency traits exist across breeds and should be utilized to a greater extent in strategic crossbreeding systems. Optimizing reproductive performance for specific production environments is essential for the sustainability of the U.S. sheep industry.

Assessing Population Structure and Genetic Diversity in US Suffolk Sheep to Define a Framework for Genomic Selection.

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the United States was evaluated in four ways: 1) using genetic relationships from pedigree data [(n = 64 310 animals recorded in the US National Sheep Improvement Program (NSIP)]; 2) using molecular data (n = 304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n = 109) and Irish (n = 55) Suffolk sheep to those in the United States using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n = 18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the US population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in US Suffolk sheep engaged in NSIP was proposed.