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.

Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes.

Introduction: Improving ewe longevity is an important breeding and management goal, as death loss and early culling of mature ewes are economic burdens in the sheep industry. Ewe longevity can be improved by selecting for positive reproductive outcomes. However, the breeding approaches for accomplishing this come with the challenge of recording a lifetime trait. Characterizing genetic factors underpinning ewe longevity and related traits could result in the development of genomic selection strategies to improve the stayability of sheep through early, informed selection of replacement ewes. Methods: Towards this aim, a genome-wide association study (GWAS) was performed to identify genetic markers associated with ewe longevity, reproductive, and production traits. Traits evaluated included longevity (i.e., length of time in the flock), parity and the lifetime number of lambs born, lambs born alive, lambs weaned, and weight of lambs weaned. Ewe records from previous studies were used. Specifically, Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182), and Columbia (n = 64) breed ewes (N = 1,130) were analyzed against 503,617 SNPs in across-breed and within-breed GWAS conducted with the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model in R. Results: The across-breed GWAS identified 25 significant SNPs and the within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 19 significant SNPs. The most significant markers were rs411309094 (13:22,467,143) associated with longevity in across-breed GWAS (p-value = 8.3E-13) and rs429525276 (2:148,398,336) associated with both longevity (p-value = 6.4E-15) and parity (p-value = 4.8E-15) in Rambouillet GWAS. Significant SNPs were identified within or in proximity (±50 kb) of genes with known or proposed roles in reproduction, dentition, and the immune system. These genes include ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, and ZNF804B. Discussion: This study proposes multiple SNPs as candidates for use in selection indices and suggests genes for further research towards improving understanding of the genetic factors contributing to longevity, reproductive, and production traits of ewes.

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.

Do plant-soil feedbacks promote coexistence in a sagebrush steppe?

Recent studies have shown the potential for negative plant-soil feedbacks (PSFs) to promote stable coexistence, but have not quantified the stabilizing effect relative to other coexistence mechanisms. We conducted a field experiment to test the role of PSFs in stabilizing coexistence among four dominant sagebrush steppe species that appear to coexist stably, based on previous work with observational data and models. We then integrated the effects of PSF treatments on focal species across germination, survival, and first-year growth. To contribute to stable coexistence, soil microbes should have host-specific effects that result in negative feedbacks. Over two replicated growing seasons, our experiments consistently showed that soil microbes have negative effects on plant growth, but these effects were rarely host-specific. The uncommon host-specific effects were mostly positive at the germination stage, and negative for growth. Integrated effects of PSF across early life-stage vital rates showed that PSF-mediated self-limitation occasionally had large effects on projected plant biomass, but occurred inconsistently between years. Our results suggest that while microbially-mediated PSF may not be a common mechanism of coexistence in this community, it may still affect the relative abundance of dominant plant species via changes in host fitness. Our work also serves as a blueprint for future investigations that aim to identify underlying processes and test alternative mechanisms to explain important patterns in community ecology.

Using whole genome sequence to compare variant callers and breed differences of US sheep.

As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.

A high-density genome-wide association with absolute blood monocyte count in domestic sheep identifies novel loci.

Monocytes are a core component of the immune system that arise from bone marrow and differentiate into cells responsible for phagocytosis and antigen presentation. Their derivatives are often responsible for the initiation of the adaptive immune response. Monocytes and macrophages are central in both controlling and propagating infectious diseases such as infection by Coxiella burnetii and small ruminant lentivirus in sheep. Genotypes from 513 Rambouillet, Polypay, and Columbia sheep (Ovis aries) were generated using the Ovine SNP50 BeadChip. Of these sheep, 222 animals were subsequently genotyped with the Ovine Infinium® HD SNP BeadChip to increase SNP coverage. Data from the 222 HD genotyped sheep were combined with the data from an additional 258 unique sheep to form a 480-sheep reference panel; this panel was used to impute the low-density genotypes to the HD genotyping density. Then, a genome-wide association analysis was conducted to identify loci associated with absolute monocyte counts from blood. The analysis used a single-locus mixed linear model implementing EMMAX with age and ten principal components as fixed effects. Two genome-wide significant peaks (p < 5x10-7) were identified on chromosomes 9 and 1, and ten genome-wide suggestive peaks (p < 1x10-5) were identified on chromosomes 1, 2, 3, 4, 9, 10, 15, and 16. The identified loci were within or near genes including KCNK9, involved into cytokine production, LY6D, a member of a superfamily of genes, some of which subset monocyte lineages, and HMGN1, which encodes a chromatin regulator associated with myeloid cell differentiation. Further investigation of these loci is being conducted to understand their contributions to monocyte counts. Investigating the genetic basis of monocyte lineages and numbers may in turn provide information about pathogens of veterinary importance and elucidate fundamental immunology.

Validation of fetal microchimerism after pregnancy in the ovine using qPCR.

Fetal microchimerism has been detected in maternal tissues of humans and rodents during and after pregnancy. Studies focusing on fetal DNA transfer to maternal tissues in domestic animals are limited, especially in sheep. Fetal ram DNA was observed in the maternal circulation during pregnancy, but it is not known if this chimerism persists in soft tissues after parturition. The objectives of this exploratory study were to: 1) determine if male fetal DNA is detectable in soft tissues of mature ewes after parturition and if so, determine if detection repeatability differed with lifetime offspring sex ratio and 2) determine if male fetal DNA was present in soft tissues of yearling (primiparous) ewes shortly after parturition. Eight mature (open, non-lactating) and 8 yearling (primiparous, periparturient) Rambouillet ewes were used. Mature ewes (5- to 7-yr old) had given birth to primarily 82% males (n = 4) or 71% female (n = 4) over a lifetime. Yearling ewes had birthed either a singleton male (n = 4) or female (n = 4) lambs. DNA was extracted from 10 and 11 different soft tissues from the mature and yearling ewes, respectively. Real-time PCR (qPCR) was used to identify the presence of the SRY gene in each tissue sample. Male DNA was detected in the brain and liver from one mature open ewe that had given birth to two males and six females during her lifetime. In younger ewes that gave birth to a ram lamb, male DNA was observed in the thyroid of one ewe and the pancreas and brain of a second ewe. Male DNA was detected in the ovary of one ewe that had given birth to a female lamb. Based on these data, we suggest fetal microchimerism in soft maternal tissues is possible in sheep and may remain after pregnancy has ended. The detection repeatability of male fetal DNA was not associated with sex ratio of lifetime offspring. Male DNA was observed in maternal soft tissues collected shortly after parturition. The greater detection of fetal male DNA found in younger ewes shortly after parturition may be due to not having enough time for fetal DNA clearance to occur. Future studies are warranted to further study XY chimerism in maternal tissues of the ewe and its potential role in ovine physiology.

Genes involved in immune, gene translation and chromatin organization pathways associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep.

Mycoplasma ovipneumoniae contributes to polymicrobial pneumonia in domestic sheep. Elucidation of host genetic influences of M. ovipneumoniae nasal detection has the potential to reduce the incidence of polymicrobial pneumonia in sheep through implementation of selective breeding strategies. Nasal mucosal secretions were collected from 647 sheep from a large US sheep flock. Ewes of three breeds (Polypay n = 222, Rambouillet n = 321, and Suffolk n = 104) ranging in age from one to seven years, were sampled at three different times in the production cycle (February, April, and September/October) over four years (2015 to 2018). The presence and DNA copy number of M. ovipneumoniae was determined using a newly developed species-specific qPCR. Breed (P<0.001), age (P<0.024), sampling time (P<0.001), and year (P<0.001) of collection affected log10 transformed M. ovipneumoniae DNA copy number, where Rambouillet had the lowest (P<0.0001) compared with both Polypay and Suffolk demonstrating a possible genetic component to detection. Samples from yearlings, April, and 2018 had the highest (P<0.046) detected DNA copy number mean. Sheep genomic DNA was genotyped with the Illumina OvineHD BeadChip. Principal component analysis identified most of the variation in the dataset was associated with breed. Therefore, genome wide association analysis was conducted with a mixed model (EMMAX), with principal components 1 to 6 as fixed and a kinship matrix as random effects. Genome-wide significant (P<9x10-8) SNPs were identified on chromosomes 6 and 7 in the all-breed analysis. Individual breed analysis had genome-wide significant (P<9x10-8) SNPs on chromosomes 3, 4, 7, 9, 10, 15, 17, and 22. Annotated genes near these SNPs are part of immune (ANAPC7, CUL5, TMEM229B, PTPN13), gene translation (PIWIL4), and chromatin organization (KDM2B) pathways. Immune genes are expected to have increased expression when leukocytes encounter M. ovipneumoniae which would lead to chromatin reorganization. Work is underway to narrow the range of these associated regions to identify the underlying causal mutations.

Variation in type two taste receptor genes is associated with bitter tasting phenylthiocarbamide consumption in mature Targhee and Rambouillet rams.

Bitter taste perception in sheep can lead to avoidance of specific types of forage, such as sagebrush, which is present on many rangeland grazing systems in the Intermountain West. In humans, bitter taste perception is influenced by variation in several TAS2R genes, including more extensively studied TAS2R38 and TAS2R16. We hypothesize that variation in taste receptor genes in sheep is associated with bitter taste. Therefore, the objective of this study was to examine variation in TAS2R genes in relation to consumption of a bitter tasting compound phenylthiocarbamide (PTC) which determines bitter "taster" and "non-taster" status in humans. Rambouillet and Targhee rams (n = 26) were offered various concentrations of PTC solution (0.2-12.29 mM) and water in a side-by-side presentation during two experiments. Blood was collected for DNA isolation and sequencing. Nineteen TAS2R genes were amplified and sequenced with long read Oxford Nanopore MinION technology. A total of 1,049 single nucleotide polymorphisms (SNPs) and 26 haplotypes were identified in these genes. Of these, 24 SNPs and 11 haplotypes were significantly (P < 0.05) associated with PTC consumption in TAS2R3, TAS2R5, TAS2R8, TAS2R9, TAS2R16, TAS2R31-like, TAS2R38, TAS2R39, and TAS2R42-like. Over 50% of the SNPs resulted in a change in amino acid sequence and several resided in potential regulatory regions, which could have downstream functional consequences and influence bitter taste perception in sheep. Further research is needed to validate these associations and elucidate the mechanisms that link variation in TAS2R genes to bitter taste perception in sheep. This may enable producers to select sheep more likely to consume bitter forage such as sagebrush as a flock and rangeland management strategy.

A DNA Regulatory Element Haplotype at Zinc Finger Genes Is Associated with Host Resilience to Small Ruminant Lentivirus in Two Sheep Populations.

Small ruminant lentivirus (SRLV) causes Maedi-Visna or Ovine Progressive Pneumonia in sheep and creates insidious livestock production losses. This retrovirus is closely related to human immunodeficiency virus and currently has no vaccines or cure. Genetic marker assisted selection for sheep disease resiliency presents an attractive management solution. Previously, we identified a region containing a cluster of zinc finger genes that had association with ovine SRLV proviral concentration. Trait-association analysis validated a small insertion/deletion variant near ZNF389 (rs397514112) in multiple sheep breeds. In the current study, 543 sheep from two distinct populations were genotyped at 34 additional variants for fine mapping of the regulatory elements within this locus. Variants were selected based on ChIP-seq annotation data from sheep alveolar macrophages that defined active cis-regulatory elements predicted to influence zinc finger gene expression. We present a haplotype block of variants within regulatory elements that have improved associations and larger effect sizes (up to 4.7-fold genotypic difference in proviral concentration) than the previously validated ZNF389 deletion marker. Hypotheses for the underlying causal mutation or mutations are presented based on changes to in silico transcription factor binding sites. These variants offer alternative markers for selective breeding and are targets for future functional mutation assays.

Grazing behavior and production characteristics among cows differing in residual feed intake while grazing late season Idaho rangeland.

The objectives were to determine whether cows previously classified during a postweaning test as either low or high residual feed intake (LRFI or HRFI) differed in BW, BCS, and winter grazing activity while consuming poor-quality forage. Thirty Hereford × Angus (LRFI = 16; HRFI = 14) 2-yr-old mid- to late-gestation cows (pregnant with second calf) grazed sagebrush steppe for 78 d beginning 29 September 2015. BW and BCS were collected before and after grazing. Five cows of each RFI classification were fitted with global positioning system (GPS) collars on 16 November 2015 with data collection commencing 3 d later and continuing for 25 d in a 323-ha pasture. The GPS units collected location coordinates every 2 min from which total daily travel distance (DTD) was calculated. Visual counts for bite rate were obtained from collared cows over 8 d. Coordinate data, daily bite rate, BW, and BCS were analyzed as repeated measures using a mixed model, which included RFI group, day, and RFI group × day as fixed effects and cow within RFI group as the random effect. Change in BW and BCS was analyzed by ANOVA with RFI group as the main effect. Cow BCS and BW differed for both day (P < 0.0001) and day × RFI (P < 0.05). Body condition was less (P < 0.05) in LRFI cows at the beginning (5.8 ±â€…0.13 vs. 6.2 ±â€…0.14 BCS), but similar (P = 0.67) to HRFI at the end of the study (4.6 ±â€…0.13 vs. 4.6 ±â€…0.14). BW among the RFI groups did not differ (P = 0.20) prior to going to range. However, BW-change and BCS-change differed (P < 0.05) between RFI groups. Not only did the LRFI cows lose less BW (-50.0 ±â€…5.41 kg vs. -66.6 ±â€…5.78 kg) over the trial, they also were less variable with respect to BW loss. Cows did not differ (P > 0.21) by RFI for DTD or bite rate, but day was significant (P < 0.0001) with cows increasing bite rate as the season of year progressed (55.2 ±â€…5.63 bites/min for day 4 vs. 84.8 ±â€…5.32 bites/min for day 21) and increasing DTD as snow storms occurred. Although LRFI cows were leaner than HRFI cows at the commencement of the project, they lost less BW in a late season rangeland environment.

Association of TMEM8B and SPAG8 with Mature Weight in Sheep.

Signature of selection studies have identified many genomic regions with known functional importance and some without verified functional roles. Multiple studies have identified Transmembrane protein 8B (TMEM8B)rs426272889 as having been recently under extreme selection pressure in domesticated sheep, but no study has provided sheep phenotypic data clarifying a reason for extreme selection. We tested rs426272889 for production trait association in 770 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. TMEM8Brs426272889 was associated with mature weight at 3 and 4 years (p < 0.05). This suggested selection for sheep growth and body size might explain the historical extreme selection pressure in this genomic region. We also tested Sperm-associated antigen 8 (SPAG8) rs160159557 encoding a G493C substitution. While this variant was associated with mature weights at ages 3 and 4, it was not as strongly associated as TMEM8Brs426272889. Transmembrane protein 8B has little functional information except as an inhibitor of cancer cell proliferation. To our knowledge, this is the first study linking TMEM8B to whole organism growth and body size under standard conditions. Additional work will be necessary to identify the underlying functional variant(s). Once identified, such variants could be used to improve sheep production through selective breeding.

Avoidance of phenylthiocarbamide in mature Targhee and Rambouillet rams.

Shrub encroachment on grasslands is a worldwide issue and sheep are a potential tool for mitigating shrub encroachment. Many shrubs, however, contain bitter-tasting compounds that may deter grazers. Cattle and sheep commonly graze rangelands, but of the two, sheep have a greater tolerance for bitter compounds and would be expected to consume more bitter-tasting vegetation. We hypothesized that sheep could detect (i.e., taste) bitter-tasting compounds and the sensitivity to these compounds would vary from animal to animal. The objective of this study was to determine whether sheep could detect the bitter-tasting compound phenylthiocarbamide (PTC), and if so, what PTC concentration would elicit an avoidance response. Using a crossover study design, mature Rambouillet and Targhee rams (n = 30) were subjected in randomized order to various PTC concentrations mixed in the drinking water (PTC solution). In trials 1 and 2 (n = 15/trial), 0.20, 0.56, 1.57, 4.39, and 12.29 mM and 0.20, 0.43, 0.94, 2.03, and 4.39 mM of PTC were tested, respectively. On test days, PTC solution (trial 1: 1.5 kg; trial 2: 3.0 kg) and water (same amounts) were offered for ad libitum intake in a side-by-side presentation for 1 h in trial 1 and 2 h in trial 2. Each test day was followed by a rest day where PTC solution was replaced with water to limit potential carry over effects into the next test day. Consumption of PTC solution for each PTC concentration was expressed as the percentage of PTC solution intake of total morning fluid intake. There was no effect (P > 0.74) of sequence that rams received PTC solutions on PTC consumption during either trial. As PTC concentration increased, percentage of PTC solution intake decreased (P ≤ 0.01) for both trials. The greatest decrease in percentage of PTC solution intake occurred between 1.57 and 4.39 mM (58%) for trial 1 and 2.03 and 4.39 mM (72%) for trial 2. In trial 2, the least percentage of PTC solution intake was the 4.39 mM PTC concentration, which was different (P ≤ 0.05) from lesser PTC concentrations. All other PTC concentrations did not differ (P > 0.05) from each other in percentage intake. This research suggests rams could taste the PTC, and the concentration at which PTC solution was avoided varied across rams. It may be possible to select sheep, based on demonstrated avoidance of PTC, for targeted grazing applications to manipulate vegetation toward range management goals.

Evaluation of Rambouillet, Polypay, and Romanov-White Dorper × Rambouillet ewes mated to terminal sires in an extensive rangeland production system: body weight and wool characteristics1,2.

Though lamb sales account for the majority of annual receipts on U.S. sheep operations, wool is an important income source for many Western flocks. Crossing fine-wool sheep with prolific or composite hair sheep breeds can increase lamb production, but fleece quality and marketability may be reduced by a greater content of nonwool fibers (e.g., med and kemp). The objectives of this study were to compare BW and wool characteristics of Rambouillet, Polypay, and Romanov-White Dorper × Rambouillet (RW-RA) ewes under extensive rangeland management conditions. Ewe BW was collected before mating (fall) and 30 d postlambing (spring) each year from 1 yr up to 4 yr of age. In spring and fall, Rambouillet and Polypay ewes were similar in BW (P ≥ 0.94). Spring BW did not differ (P = 0.13) between RW-RA and Polypay, but Rambouillet ewes were heavier than RW-RA in the spring (P = 0.02). Both Rambouillet and Polypay ewes were heavier (P < 0.07) than RW-RA in the fall. Greasy fleece weight and mid-side wool samples were collected from ewes at 1 and 4 yr of age. Clean fleece weights (CFW) were estimated from average laboratory scoured yield of mid-side wool samples composited within-breed. Average fiber diameter (AFD), SD of fiber diameter (SD-FD), and percentage med (%M), kemp (%K), and total medullated fibers (%T) were quantified on individual mid-side wool samples. There was no difference in 1-yr-old CFW among breed types (P ≥ 0.96). Four-yr-old Rambouillet ewes had heavier CFW (2.29 kg; P < 0.001) than 4-yr-old Polypay (1.83 kg) and RW-RA ewes (1.86 kg), which were not different (P > 0.99). Within 1- and 4-yr-olds, AFD differed among breed type (P < 0.001) and was the finest for Rambouillet (20.1 and 21.9 µm, respectively), intermediate for RW-RA (22.8 and 24.8 µm), and coarsest for Polypay (24.2 and 26.7 µm). Also within 1- and 4-yr olds, SD-FD was lowest in Rambouillet, intermediate in Polypay, and greatest in RW-RA (P < 0.01). Wool from RW-RA ewes had greater %M, %K, and %T (P < 0.001) than wool from Rambouillet and Polypay ewes, which were not different (P > 0.99). Results indicated superior wool production for Rambouillet compared with the coarser, more variable wool produced by Polypay and RW-RA. Still, past research reported greater lamb production in Polypay and RW-RA ewes which, under recent market conditions, would be associated with greater annual gross revenue for these breed types than for Rambouillet.

Ecosystem functional response across precipitation extremes in a sagebrush steppe.

BACKGROUND: Precipitation is predicted to become more variable in the western United States, meaning years of above and below average precipitation will become more common. Periods of extreme precipitation are major drivers of interannual variability in ecosystem functioning in water limited communities, but how ecosystems respond to these extremes over the long-term may shift with precipitation means and variances. Long-term changes in ecosystem functional response could reflect compensatory changes in species composition or species reaching physiological thresholds at extreme precipitation levels. METHODS: We conducted a five year precipitation manipulation experiment in a sagebrush steppe ecosystem in Idaho, United States. We used drought and irrigation treatments (approximately 50% decrease/increase) to investigate whether ecosystem functional response remains consistent under sustained high or low precipitation. We recorded data on aboveground net primary productivity (ANPP), species abundance, and soil moisture. We fit a generalized linear mixed effects model to determine if the relationship between ANPP and soil moisture differed among treatments. We used nonmetric multidimensional scaling to quantify community composition over the five years. RESULTS: Ecosystem functional response, defined as the relationship between soil moisture and ANPP, was similar among irrigation and control treatments, but the drought treatment had a greater slope than the control treatment. However, all estimates for the effect of soil moisture on ANPP overlapped zero, indicating the relationship is weak and uncertain regardless of treatment. There was also large spatial variation in ANPP within-years, which contributes to the uncertainty of the soil moisture effect. Plant community composition was remarkably stable over the course of the experiment and did not differ among treatments. DISCUSSION: Despite some evidence that ecosystem functional response became more sensitive under sustained drought conditions, the response of ANPP to soil moisture was consistently weak and community composition was stable. The similarity of ecosystem functional responses across treatments was not related to compensatory shifts at the plant community level, but instead may reflect the insensitivity of the dominant species to soil moisture. These species may be successful precisely because they have evolved life history strategies that buffer them against precipitation variability.

Effects of rearing triplet lambs on ewe productivity, lamb survival and performance, and future ewe performance.

Increasing prolificacy has been proposed to be the most effective way to increase the biological efficiency and profitability of sheep production. However, use of prolific breeds and genes with major effects on ovulation rate can increase prolificacy to levels that may not be desirable or sustainable in extensive rangeland production systems. This study thus evaluated effects of triplet births on ewe productivity and ewe and lamb performance. An initial study used 666 purebred Polypay litters to compare ewes with triplet litters that were required to raise all the lambs (Treatment A) with those whose triplet litters were reduced to 2 lambs (Treatment R). Adult Polypay ewes had an average litter size of 2.35 lambs per litter. The frequency of litters of 3 or more lambs was 43.2%; 56.0% of lambs were born in litters of 3 or more lambs. Ewes that had singles weaned fewer lambs and less body weight (BW) of lambs (P < 0.001; 0.94 lambs and 40.4 kg, respectively) than ewes that had twins or triplets. Ewes with triplet litters in Treatment A weaned more lambs (P < 0.01) and more BW of lambs (P < 0.05) than ewes that had triplets in Treatment R (2.13 lambs and 62.9 kg, respectively, vs. 1.79 lambs and 55.0 kg, respectively), and weaned more lambs than ewes that had twins (1.77 lambs; P < 0.01). However, neither group of triplet-bearing ewes weaned more BW of lambs than ewes that had twins (58.9 kg; P ≥ 0.34). In 2 sets of data involving 442 purebred Polypay litters and 987 litters from Polypay or Romanov‒White Dorper × Rambouillet ewes mated to terminal sires, ewes were required to raise all triplet-born lambs. Death losses for triplets in these studies (39.6 and 31.6%, respectively) were higher than those in Treatment A of the initial study (26.2%), resulting in greater numbers of lambs weaned for triplet, compared to twin, litters (1.79 vs. 1.68, respectively; P = 0.02) but no greater weight of lambs weaned (54.3 vs. 55.4 kg, respectively; P = 0.17). Based on these 3 sets of data, ewes that were required to rear triplet lambs weaned 0.20 more lambs per litter than ewes that had twins but also had 0.75 additional dead lambs per litter, and thus a lamb mortality overhead of 3.75 additional dead lambs for each additional weaned lamb. We conclude that there is an intermediate optimum prolificacy level for extensive rangeland production systems. If optimum prolificacy is exceeded, removal and artificial rearing of surplus lambs are necessary to avoid increased lamb death losses.

Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes.

Coxiella burnetii is a globally distributed zoonotic bacterial pathogen that causes abortions in ruminant livestock. In humans, an influenza-like illness results with the potential for hospitalization, chronic infection, abortion, and fatal endocarditis. Ruminant livestock, particularly small ruminants, are hypothesized to be the primary transmission source to humans. A recent Netherlands outbreak from 2007-2010 traced to dairy goats resulted in over 4,100 human cases with estimated costs of more than 300 million euros. Smaller human Q fever outbreaks of small ruminant origin have occurred in the United States, and characterizing shedding is important to understand the risk of future outbreaks. In this study, we assessed bacterial shedding and seroprevalence in 100 sheep from an Idaho location associated with a 1984 human Q fever outbreak. We observed 5% seropositivity, which was not significantly different from the national average of 2.7% for the U.S. (P>0.05). Furthermore, C. burnetii was not detected by quantitative PCR from placentas, vaginal swabs, or fecal samples. Specifically, a three-target quantitative PCR of placenta identified 0.0% shedding (exact 95% confidence interval: 0.0%-2.9%). While presence of seropositive individuals demonstrates some historical C. burnetii exposure, the placental sample confidence interval suggests 2016 shedding events were rare or absent. The location maintained the flock with little or no depopulation in 1984 and without C. burnetii vaccination during or since 1984. It is not clear how a zero-shedding rate was achieved in these sheep beyond natural immunity, and more work is required to discover and assess possible factors that may contribute towards achieving zero-shedding status. We provide the first U.S. sheep placental C. burnetii shedding update in over 60 years and demonstrate potential for C. burnetii shedding to reach undetectable levels after an outbreak event even in the absence of targeted interventions, such as vaccination.

Ovar-DRB1 haplotypes *2001 and *0301 are associated with sheep growth and ewe lifetime prolificacy.

BACKGROUND: The major histocompatibility complex (MHC) is an organized cluster of tightly linked vertebrate genes with immunological and non-immunological functions. While the important MHC gene DRB1 has been examined in regard to many sheep infectious disease traits, only one study, based on microsatellite markers, has previously examined DRB1 and sheep production traits. Furthermore, to our knowledge no studies have examined DRB1 relationship with lifetime ewe prolificacy traits. Therefore, we analyzed association between the presence of DRB1 SNP haplotypes with internationally recognized standard names and production traits including growth and lifetime prolificacy in 370 Rambouillet, Columbia, and Polypay sheep. RESULTS: The DRB1 *2001 haplotype was associated with increased weaning and mature weights, as well as average daily gain (Sidák P<0.05; corrected for the number of haplotypes tested). Interestingly, the *2001 haplotype also showed a trend toward association with increased total number of lifetime lambs born (Sidák P=0.084) and number of lambs born alive (Sidák P=0.084). In contrast, the DRB1 *0301 haplotype was associated with decreased mature weight (Sidák P=0.01). CONCLUSIONS: Since the *2001 haplotype was present in all three breeds, these results suggest there is at least one functional mutation in the region that influences growth and prolificacy traits that may be broadly present across several breeds. Furthermore, combined use of the similar *2001 and *0301 multi-marker haplotypes that nonetheless have opposing directions of production trait associations will enhance mutation discovery in this region. If undesirable alleles for underlying mutations can be identified, selective pressure against one or a small number of undesirable alleles may improve production with limited impact on MHC genetic diversity and infectious disease susceptibility.