Meat Animal Research Center Research Articles

Tissue expression of porcine transient receptor potential mucolipin protein channels and their differential responses to porcine reproductive and respiratory syndrome virus infection in vitro

Abstract Introduction Porcine reproductive and respiratory syndrome virus (PRRSV) infection results in a serious disease, posing a huge economic threat to the global swine industry. The transient receptor potential mucolipin proteins (TRPMLs) have been shown to be strongly associated with virus infection and other physiological processes in humans, but their tissue distribution and responses to PRRSV in pigs remain unknown. Material and Methods Quantitative reverse-transcription PCR analysis was undertaken to determine the optimal primer for TRPML expression detection and for quantifying that expression individually in different pig tissue samples. Meat Animal Research Center 145 (MARC-145) monkey kidney cells and the TRPML-specific activator mucolipin synthetic agonist 1 (ML-SA1) were used to reveal the relationship between TRPML and PRRSV-2 infection. Results The best primers for each TRPML gene used in a fluorescence-based quantitative method were identified and TRPML1 was found to be highly expressed in the kidneys and liver of pigs, while TRPML2 and TRPML3 were observed to be primarily expressed in the kidney and spleen tissues. The expression of TRPML2 was upregulated with the rise in PRRSV-2 infection titre but not the expression of TRPML1 or TRPML3, and ML-SA1 inhibited PRRSV-2 in a dose-dependent manner. Conclusion Our research revealed the gene expression of TRPMLs in pigs and identified that TRPML channels may act as key host factors against PRRSV infection, which could lead to new targets for the prevention and treatment of pig infectious diseases.

Impacts of Farrowing Pen Design, Season, and Sow Parity on Litter Performance and Piglet Mortality.

Piglet mortality during lactation is a significant concern in swine production, influenced by complex interactions involving sow, piglet, environmental, and management factors. While crushing by the sow may be the ultimate cause of piglet mortality, there are many factors influencing the outcome, including parity, thermal stress, and animal housing systems. New farrowing systems are continuously being developed; however, it is difficult for producers to make decisions without any scientific basis. This study aimed to assess the impact of different farrowing pen layouts on piglet performance, considering parity and season. A total of 546 sows and 9123 piglets were monitored across 36 lactation cycles. Sows were randomly assigned to three farrowing pen layouts (standard, diagonal, and offset) in three rooms (20 sows by room). All farrowing pens had the same space allocations (2.7 m by 1.8 m and 2.1 m by 0.6 m for the sow area). The three types of farrowing pens were blocked by position within the room. Piglet performance traits (percent of stillborns, percent of mortality, percent of overlays, and average daily weight gain: ADG) and sows traits (health and parity) were monitored following US Meat Animal Research Center (USMARC) procedures. Results indicated that treatment, parity, and season influenced some piglet performance traits. The offset farrowing pen had a lower percent of stillborns compared to the standard. No significant differences were observed between the diagonal crate and the other treatments. When evaluating high mortality sow (>two piglets), the offset and standard treatments had a lower percent of overlays. Piglets from first-parity sows had lower ADG than those from higher-parity sows. A higher percent of overlays were observed in Autumn and Summer compared to Spring and Winter, and Summer had lower average daily weight gain than other seasons. The results suggest that modifying the layout (offset), with sows placed further away from the heating source, can reduce the percent of overlays in sows with high mortality (>2 piglets). In addition, the influence of season on the piglet production traits demonstrated the importance of proper management of the environment, even in systems with a certain level of climatic control.

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.

Statistical and machine learning approaches to describe factors affecting preweaning mortality of piglets.

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the U.S. Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, litter, environment, and piglet parameters on PWM. Then, different models (beta-regression and machine learning model: a random forest [RF]) were evaluated. Finally, the RF model was used to predict PWM and overlays for all listed contributing factors. On average, the mean birth weight was 1.44 kg, and the mean mortality was 16.1% where 5.55% was for stillbirths and 6.20% was contributed by overlays. No significant effect was found for seasonal and location variations on PWM. Significant differences were observed in the effects of litter lines on PWM (P < 0.05). Landrace-sired litters had a PWM of 16.26% (±0.13), whereas Yorkshire-sired litters had 15.91% (±0.13). PWM increased with higher parity orders (P < 0.05) due to larger litter sizes. The RF model provided the best fit for PWM prediction with a root mean squared errors of 2.28 and a correlation coefficient (r) of 0.89 between observed and predicted values. Features' importance from the RF model indicated that, PWM increased with the increase of litter size (mean decrease accuracy (MDA) = 93.17), decrease in mean birth weight (MDA = 22.72), increase in health diagnosis (MDA = 15.34), longer gestation length (MDA = 11.77), and at older parity (MDA = 10.86). However, in this study, the location of the farrowing crate, seasonal differences, and litter line turned out to be the least important predictors for PWM. For overlays, parity order was the highest importance predictor (MDA = 7.68) followed by litter size and mean birth weight. Considering the challenges to reducing the PWM in the larger litters produced in modern swine industry and the limited studies exploring multiple major contributing factors, this study provides valuable insights for breeding and production management, as well as further investigations on postural transitions and behavior analysis of sows during the lactation period.

Comparison of three maternal composite sheep breeds managed under pasture lambing and purebred or terminal mating systems: ewe body weight, reproductive efficiency, and longevity.

Extensive sheep systems have lower inputs (e.g., feed, labor, infrastructure) but, generally, lower outputs per ewe than intensively managed flocks. Average ewe prolificacy is low (< 1.1 lambs per ewe) across the United States and traditional expectation is that costs required to support larger litters will not be recovered due to greater lamb mortality. The Composite-IV (C-IV) is a 50% Romanov, 25% Katahdin, and 25% White Dorper hair sheep developed and selected for enhanced reproductive efficiency at the U.S. Meat Animal Research Center. Objectives of the current study were to compare productivity of C-IV ewes (N = 404) to Katahdin (N = 342) and Polypay (N = 390), two popular maternal composite breeds, in a lower-input system. Experimental ewes were exposed to either rams of their own breed or Texel rams for the first time at 7 mo of age and remained in the same mating system for up to 4 yr. Ewes lambed on pasture from May to June and were expected to rear their lambs in the absence of supplemental feed and with minimal intervention. The ewe age × breed interaction effect impacted all annually recorded traits (P < 0.01) including number and total weight of lamb marketed at 25 wk per ewe exposed to mating (LS25 and LW25, respectively). Within all ages, LS25 of C-IV was greater (1.2 to 1.63 lambs; P < 0.01) than Katahdin (0.71 to 1.17 lambs) and Polypay (0.68 to 1.26 lambs) which were similar. At 1, 2, and 3-yr of age, C-IV ewes had, on average, 12 to 17 kg greater LW25 (P ≤ 0.01) than other breeds. Polypay LW25 was similar to Katahdin at 1 yr of age, but 8 to 13 kg greater (P < 0.01) at older ages. At 4 yr of age, LW25 was similar for C-IV and Polypay (63 and 62 kg, respectively). Overall, Texel mating improved LW25 by 3 kg compared to purebred mating (P < 0.01). Twin litters were most common within mature ewes (> 1 yr) of all breeds (52% to 65%); however, the proportion of triplet litters was numerically greater for C-IV (13%) than Katahdin (1%) or Polypay (4%). The frequency of mature ewes that gave birth to and reared twins (75% to 82%) was high for all breeds. Most triplet-bearing mature C-IV ewes reared twins (43%) though many reared triplets (39%). Ewe reproductive efficiency can be enhanced in lower-input systems by utilizing additive breed effects and heterosis in a complimentary crossbreeding program. More research is needed to identify indicator traits associated with lamb survival and to derive appropriate levels of prolificacy to fit specific management constraints.

PSXII-18 Genome-Wide Association for Behavioral Anestrus in Swine

Abstract Gilts represent a significant portion of breeding females, and producer success largely depends on lifetime prolificacy and number of lifetime litters produced. Expression and precise detection of first estrus are key components for successful breeding. Failure to express behavioral signs of estrus, also known as prebreeding anestrus, affects 10-30% of gilts resulting in premature culling. Behavioral anestrus (BA), that is ovulatory cycles of the ovary without signs of estrus, is a major type of prebreeding anestrus that affects up to 5% of the gilt population at the U.S. Meat Animal Research Center. Examination of ovaries revealed that 38% of BA gilts had exhibited more than one ovulatory cycle. Identification of genomic predictors of BA could minimize prebreeding anestrus in gilts. Data collected from normal cyclic (n=2,421) and BA gilts (n=515) from a multigeneration Yorkshire-Landrace-Duroc composite population were used for a case-control genome-wide association to identify candidate genes and cell signaling pathways associated with BA in gilts. The genomic heritability for BA in the population was 0.35. Fifty-six genome-wide significant SNP were identified with proportion of phenotypic variance explained by each SNP ranging from 0.009 to 0.06. Quantitative trait loci identified for BA harbor candidate genes involved in olfaction (OR13H1) and behavioral disorders (PLCB4). Biologically this is expected because, activation of olfactory pathways by boar pheromones is important to stimulate female lordosis behavior and sexual receptivity to boar. Several candidate genes identified for BA (IGSF1, MSTN, RXRG) were previously reported for age at puberty in humans and cattle suggesting the pleiotropic nature of these genes influencing multiple estrus related traits in different species. To our knowledge this is the first large scale association analysis performed for BA in pigs and these data are an important first step to facilitate future studies to identify functional polymorphisms regulating estrus behavior in gilts.The USDA is an equal opportunity provider and employer.

Naturally occurring androgen excess cows are present in dairy and beef herds and have similar characteristics to women with PCOS.

Beef cows with excess androstenedione (A4; High A4) in follicular fluid (FF) and secreted by the ovarian cortex have been reported from the University of Nebraska-Lincoln physiology herd displaying characteristics reminiscent of polycystic ovary syndrome (PCOS). Thus, we hypothesized that naturally occurring High A4 cows were present in other dairy and beef herds. Fourteen Jordan (Amman, Jordon) dairy heifers and 16 U.S. Meat Animal Research Center beef heifers were classified by FF (High A4: A4 > 40 ng/mL and Control: A4 < 20 ng/mL) and/or cortex culture media (High A4 > 1 ng/mL/d or Control < 1 ng/mL/d). High A4 dairy heifers (n = 6) had greater A4 concentrations (7.6-fold) in FF and (98-fold) greater in ovarian cortex culture media with greater numbers of primordial and fewer later-stage follicles than Controls (n = 8) even after 7 d of culture. Also, the ovarian cortex had greater staining for Picro Sirius red in High A4 dairy heifers compared with Controls indicating increased fibrosis. Thecal cells from High A4 dairy heifers had greater STAR, LHCGR, CYP17A, CD68, and PECAM mRNA expression with increased mRNA abundance of CYP17A1 and CD68 in the ovarian cortex cultures compared with Control dairy heifers. Similarly, cortex culture media from High A4 beef heifers (n = 10) had increased A4 (290-fold; P ≤ 0.001), testosterone (1,427-fold; P ≤ 0.001), and progesterone (9-fold; P ≤ 0.01) compared with Control heifers with increased primordial follicles and decreased later-stage follicles even after 7 d of culture, indicating abnormal follicular development. High A4 ovarian cortex cultures from beef heifers also had increased fibrosis markers and greater expression of PECAM (P = 0.01) with a tendency for increased vascular endothelial cadherin compared with Controls (n = 6). These two trials support our hypothesis that naturally occurring androgen excess cows are present in other dairy and beef herds. The ability to identify these females that have excess A4 ovarian microenvironments may allow for their use in understanding factors causing abnormal follicle development linked to androgen excess and inflammation.

Effects of a Moderate or Aggressive Implant Strategy on the Rumen Microbiome and Metabolome in Steers

The effects of growth-promoting implants have been well-defined for their ability to impact growth performance in beef cattle. Production-relevant microbes and microbiomes in the rumen have also been associated with growth traits. However, the role of implants on the rumen microbiome has not been determined. The objective of this study was to determine if different doses of implant hormones cause gain-associated ruminal microbial community changes. To assess this, a completely randomized design was used and 336 fall-born steers 450 to 470 days of age from the germplasm evaluation population at the US Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy (n = 167) of Revalor-IS (80 mg trenbolone acetate and 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate and 24 mg estradiol) or 2) an aggressive implant strategy (n = 169) of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate and 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% vitamin and mineral supplement, and 0.75% urea, on a DM basis). On d 85 after implants administration, rumen contents were collected via orogastric tubing. Samples were sequenced to target and identify bacteria, archaea, and protozoa. Untargeted metabolomics was performed on rumen content using ultra high performance liquid chromatography high resolution mass spectrometry. Production data between implant strategies was analyzed using a mixed model ANOVA (SASv9.4, Cary, NC) followed by separation of least squares means. Microbial diversity between strategies did not differ for archaea or protozoa (P &amp;gt; 0.05). Average daily gain was different (P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated with implant strategy. Two metabolites, N-acetyllysine and N-acetylornithine, were found in greater abundance in the moderate implant strategy (P ≤ 0.04). Understanding associations between the rumen microbiome and implant strategies may allow improvement of growth efficiency in beef cattle.

Influence of environmental factors and genetic variation on mitochondrial DNA copy number.

Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.

Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle.

Understanding the genetic relationship between mature cow weight (MWT) and body condition score (BCS) is useful to implement selection programs focused on cow efficiency. The objectives of this study were to estimate genetic parameters, heterosis, and breed effects for MWT and BCS. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS on 6,138 and 6,131 cows, respectively, from the Germplasm Evaluation program, a crossbred beef population at the U.S. Meat Animal Research Center. Pedigree was available for 48,013 individuals. Univariate animal models were used to estimate heritabilities for each trait by parity. Bivariate animal models were used to estimate genetic correlations between parities within a trait and between traits within parities. Bivariate repeatability animal models were used to estimate genetic correlations between traits across parities. Estimates of heritability for different parities ranged from 0.43 ± 0.05 to 0.55 ± 0.07 for MWT and from 0.12 ± 0.03 to 0.25 ± 0.04 for BCS and were lower with the repeatability model at 0.40 ± 0.02 and 0.11 ± 0.01 for MWT and BCS, respectively. Estimates of repeatability were high for MWT (0.67 ± 0.005) and low for BCS (0.22 ± 0.006). Estimates of genetic correlation for MWT and BCS between parities were, in general, high, especially between consecutive parities. Estimates of genetic correlation between MWT and BCS were positive and moderate, ranging from 0.32 ± 0.09 to 0.68 ± 0.14. The direct heterosis estimates were 21.56 ± 3.53kg (P ≤ 0.001) for MWT and 0.095 ± 0.034 (P ≤ 0.001) for BCS. Ordered by decreasing MWT, the breeds ranked Brahman, Charolais, Angus, Simmental, Salers, Hereford, Santa Gertrudis, Chiangus, Brangus, Red Angus, Shorthorn, Maine-Anjou, Gelbvieh, Beefmaster, Limousin, and Braunvieh. Ordered by decreasing BCS, the breeds ranked Brahman, Red Angus, Charolais, Angus, Hereford, Brangus, Beefmaster, Chiangus, Salers, Simmental, Maine-Anjou, Limousin, Santa Gertrudis, Shorthorn, Gelbvieh, and Braunvieh. Estimates of breed differences for MWT were also adjusted for BCS (AMWT), and in general, AMWT depicted smaller differences between breeds with some degree of re-ranking (r = 0.59). These results suggest that MWT and BCS are at least moderately genetically correlated and that they would respond favorably to selection. Estimates of breed differences and heterotic effects could be used to parameterize multibreed genetic evaluations for indicators of cow maintenance energy requirements.

Breed and heterotic effects for mature weight in beef cattle.

Cow mature weight (MWT) is heritable and affects the costs and efficiency of a breeding operation. Cow weight is also influenced by the environment, and the relationship between the size and profitability of a cow varies depending on production system. Producers, therefore, need tools to incorporate MWT in their selection of cattle breeds and herd replacements. The objective of this study was to estimate breed and heterotic effects for MWT using weight-age data on crossbred cows. Cow's MWT at 6 yr was predicted from the estimated parameter values-asymptotic weight and maturation constant (k)-from the fit of the Brody function to their individual data. Values were obtained for 5,156 crossbred cows from the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation Program using 108,957 weight records collected from approximately weaning up to 6 yr of age. The cows were produced from crosses among 18 beef breeds. A bivariate animal model was fitted to the MWT and k obtained for each cow. The fixed effects were birth year-season contemporary group and covariates of direct and maternal breed fractions, direct and maternal heterosis, and age at final weighing. The random effects were direct additive and residual. A maternal additive random effect was also fitted for k. In a separate analysis from that used to estimate breed effects and (co)variances, cow MWT was regressed on sire yearling weight (YWT) Expected Progeny Differences by its addition as a covariate to the animal model fitted for MWT. That regression coefficient was then used to adjust breed solutions for sire selection in the USMARC herd. Direct heterosis was 15.3 ± 2.6 kg for MWT and 0.000118 ± 0.000029 d-1 for k. Maternal heterosis was -5.7 ± 3.0 kg for MWT and 0.000130 ± 0.000035 d-1 for k. Direct additive heritabilities were 0.56 ± 0.03 for MWT and 0.23 ± 0.03 for k. The maternal additive heritability for k was 0.11 ± 0.02. The direct additive correlation between MWT and k was negligible (0.08 ± 0.09). Adjusted for sire sampling, Angus was heaviest at maturity of the breeds compared. Deviations from Angus ranged from -8.9 kg (Charolais) to -136.7 kg (Braunvieh). Ordered by decreasing MWT, the breeds ranked Angus, Charolais, Hereford, Brahman, Salers, Santa Gertrudis, Simmental, Maine Anjou, Limousin, Red Angus, Brangus, Chiangus, Shorthorn, Gelbvieh, Beefmaster, and Braunvieh. These breed effects for MWT can inform breeding programs where cow size is considered a key component of the overall profitability.

Cytokine and Haptoglobin Profiles From Shipping Through Sickness and Recovery in Metaphylaxis- or Un-Treated Cattle.

Fifty-six head of cattle, 28 animals with bovine respiratory disease complex (BRDC), and 28 healthy animals that were matched by treatment, sale barn of origin, day, and interactions among these variables, were identified from a population of 180 animals (60 each purchased at three sale barns located in Missouri, Tennessee, and Kentucky) enrolled in a study comparing animals receiving metaphylaxis to saline-treated controls. Cattle were transported to a feedlot in KS and assigned to treatment group. Blood samples were collected at Day 0 (at sale barn), Day 1, Day 9, and Day 28 (at KS feedlot), and transported to the US Meat Animal Research Center in Clay Center, NE where plasma was harvested and stored at −80°C until assayed for the cytokines IFN-γ, IL-1β, IL-6, and TNF-α, and the acute stress protein haptoglobin (HPT). Our objectives were to determine if cytokine and haptoglobin profiles differed between control and metaphylaxis treatment groups over time, and if profiles differed between animals presenting with BRDC and those that remained healthy. There was no difference between the treated animals and their non-treated counterparts for any of the analytes measured. Sale barn of origin tended to affect TNF-α concentration. Differences for all analytes changed over days, and on specific days was associated with state of origin and treatment. The Treatment by Day by Case interaction was significant for HPT. The analyte most associated with BRDC was HPT on D9, possibly indicating that many of the cattle were not exposed to respiratory pathogens prior to entering the feedlot.

Potential functional variants in AHR signaling pathways are associated with age at puberty in swine.

Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P<0.005) with estimated additive SNP effects ranging from 1.6 to 5.3days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.

279 Development, selection criteria, and performance of Composite IV sheep at the U.S. Meat Animal Research Center

Abstract Average ewe prolificacy is low across the U.S., while fixed and variable costs of production can be substantial, especially in traditional shed-lambing systems. Pasture-lambing can reduce input costs but can present greater risk of inclement weather, predation, and internal parasitism. The Composite IV is a ½ Romanov, ¼ Katahdin, and ¼ White Dorper hair sheep developed at the U.S. Meat Animal Research Center. Objectives were to summarize Composite IV ewe and lamb performance under a pasture-lambing system with minimal disruption through weaning. Lamb survival to and body weight at weaning were greatest for singles (0.90 and 19.9 kg, respectively), intermediate for twins (0.82 and 15.9 kg), and lowest for triplets (0.65 and 14.6 kg; P &amp;lt; 0.01). Number of lambs born and weaned per ewe lambing were lower at 1-yr of age (1.55 and 1.24, respectively) than at 3- to 5-yr of age (2.20 to 2.23 and 1.75 to 1.82; P &amp;lt; 0.01). Within mature ewes (2- to 5-yr-old), twin litters were most frequent (58.7%), triplets intermediate (24.7%), and singles least (16.6%). While number of lambs weaned and total litter weaning weight were greater for triplet- than twin-bearing ewes (2.06 vs 1.70 and 28.9 vs 26.0 kg, respectively; P &amp;lt; 0.01), triplet-bearing ewes lost 1.78 lambs per additional lamb weaned. Results suggest productivity in pasture-lambing systems can be enhanced by identifying complementary breed combinations, maintaining heterosis, and selecting for characteristics associated with reduced labor and enhanced well-being.

PSI-10 Effects of a Moderate and Aggressive Implant Strategy on the Rumen Microbial Community in Steers

Abstract The effects of growth-promoting implant strategies have been well-defined in research for their ability to impact growth performance in beef cattle. Production-relevant microbiomes in the rumen have also been associated with growth traits. However, the role of implant strategies on the rumen microbiome is not understood. The objective was to determine if varying doses of implant hormones cause gain-associated ruminal microbial community shifts. To assess this, a completely randomized design was used and 336 fall-born steers from the germplasm evaluation population between 450–470 days of age at the U.S. Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy of Revalor-IS (80 mg trenbolone acetate, 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate, 24 mg estradiol) and 2) an aggressive implant strategy of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate, 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% supplement, and 0.75% urea, DM basis). Body weights were collected once per month with initial weights of 439.8 ± 43.1 kg. After implants were administered for 84 days, rumen content was collected via orogastric tubing. Samples were sequenced targeting bacterial V1-V3 16S rRNA gene regions, V3-V4 for archaea, and partial 18S rRNA gene of protozoa. Sequences were processed in R utilizing Phyloseq and analyzed with DESeq2 to test differential abundances. Production data between implant strategies were analyzed using a mixed model ANOVA (SASv9.4, Cary, NC). Alpha- and beta-diversity between strategies did not differ for bacteria, archaea, or protozoa (P &amp;gt; 0.05). Average daily gain was different (P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated implant strategy. USDA is an equal opportunity provider and employer.

37 Genetic parameter estimates for days on feed, age at slaughter, and carcass traits in a multi-breed beef cattle population

Abstract The objective of this study was to estimate genetic parameters for days on feed (DOF), age at slaughter (AAS), and their relationships with carcass traits, including: marbling score (MARB), adjusted fat thickness (AFT), hot carcass weight (HCW), ribeye area (REA), and final live weight (FW). Data were from steers and heifers (n = 7,747) from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center. All traits were analyzed with univariate and bivariate animal models using ASReml. Fixed effects fitted for all models included contemporary group (concatenation of birth year and season, sex, and experimental treatment group), breed fractions, and direct heterosis. Different endpoints were also investigated by fitting fixed linear covariates of AFT, HCW, REA, MARB, FW, and age (except AAS and DOF). For a given bivariate analyses, both traits were adjusted to the same endpoint. Univariate heritability estimates for AFT, AAS, DOF, FW, HCW, MARB, and REA ranged from 0.45–0.52, 0.52–0.59, 0.33–0.39, 0.34–0.55, 0.34–0.55, 0.54–0.55, and 0.50–0.56, respectively. Covariates of MARB and AFT led to the highest and lowest, respectively, heritability estimates for AAS and DOF. Depending on the endpoint, genetic correlations between AAS and AFT, FW, HCW, MARB, and REA ranged from 0.16 to 0.32, -0.08 to 0.33, 0.19 to 0.36, 0.14 to 0.20, and -0.06 to 0.13 (Table 1). Genetic correlations between DOF and AFT, MARB, and REA were negligible. Genetic correlations between DOF, FW, and HCW ranged from -0.10 to 0.29 and -0.37 to -0.17. Standard errors were less than 0.07 for all estimates. Phenotypic variability in DOF was low, and increased variability in AAS was due to differences in date of birth and thus weaning age. Results indicate DOF and AAS are moderately to highly heritable and generally lowly correlated with routine carcass traits. The USDA is an equal opportunity employer.

23 Current progress in the Agricultural Research Service Beef Grand Challenge: A large-scale genetics by environment by management evaluation project

Abstract The Agricultural Research Service (ARS) Beef Grand Challenge is a cooperative, multidisciplinary effort evaluating differences in performance of genetic lines across production environments representative of different geographical regions. Weaned spring-born calves (n = 120 per location), representing natural service matings to Angus, Hereford, Simmental, Charolais, or indicus-composite (Beefmaster or Brangus) bulls from the U.S. Meat Animal Research Center Germplasm Evaluation program in south central Nebraska, are sent to wheat pasture (central Oklahoma) and winter range (eastern Montana), and weaned fall-born calves (n=40 per location) are sent to summer grazing on shortgrass prairie (northeastern Colorado) and southern mixed-grass rangeland (western Oklahoma). All cattle are fed a finishing ration representative of the region that approximately matches energy content across locations. Each calving season has a matching counterpart of calves that remain in Nebraska on a calf-fed drylot program (receiving ration followed by longer finishing ration). Breeds and sires are represented equally, to the extent possible, at each location. To detect differences in breed effects at each location and average over yearly variation, the study is being replicated for 4 years. Weights, stress measures, carcass composition (marbling, yield grade, quality grade, etc.), steak tenderness and steak fatty acid composition are collected from each location. Additionally, rumen metagenomic composition, metagenomic samples, preharvest food safety samples, and feed intake measures are collected at some locations. Grazing impacts and supplemental range feeding are also being evaluated. One year of sampling has been completed, with numeric differences observed for marbling and tenderness as well as growth performance among locations. Statistical differences will be evaluated when replicate years are collected. The USDA is an equal opportunity provider and employer.

Genetic and nongenetic factors influencing ewe prolificacy and lamb body weight in a closed Romanov flock.

The U.S. Meat Animal Research Center was the first entity in the United States to import the Romanov breed and it has been maintained as a closed flock for over 30 yr. Incorporating this super-prolific breed into crossbred and composite populations has resulted in large improvements in ewe productivity. However, few have quantified factors contributing to genetic and nongenetic variation in ewe reproduction and lamb growth within purebred Romanov populations, which were the objectives of this study. The pedigree contained a total of 8,683 lambs born to 218 and 1,600 unique sires and dams, respectively. Number of lambs born on a per ewe exposed (NLBE) and lambing (NLBL) basis were analyzed in univariate repeatability animal models. As expected, the proportion of phenotypic variance (σP2) in litter size attributable to additive genetic (0.06 to 0.08) and permanent environmental (0.05 to 0.07) effects of the ewe was low. The service sire permanent environmental effect contributed to a small but significant amount of σP2 in NLBE (0.03) but not NLBL. However, the service sire additive genetic effect did not influence σP2 in NLBE or NLBL. Lamb body weight was recorded at birth (BWB) and upon weaning from either milk replacer (~30 d; BWW-N) or their dam (~60 d; BWW-D) and were analyzed in a three-trait model with random additive direct and maternal effects. Estimated direct heritabilities were low for all body weight (BW) traits (0.07 to 0.10). Maternal heritability was moderate for BWB (0.34) but low for weaning BW (0.11 to 0.18). This was the first to report direct and maternal genetic correlations between BW of nursery- and dam-reared lambs, and both were estimated to be moderate (0.43 to 0.47). Additionally, the direct and maternal effects of BWB were more strongly correlated with BWW-N (0.74 to 0.82) than BWW-D (0.17 to 0.33). Despite inbreeding coefficients having increased at a rate of 0.33% per birth year (1986 to 2019) in this flock, they were not consistently associated with reductions in ewe or lamb performance. Parameter estimates generally agreed with those from less-prolific breeds, and results indicate that selection can be an effective means of improving subcomponents of ewe productivity.

Using electromagnetic induction technology to identify atrazine leaching potential at field scale

Atrazine is an herbicide commonly used to control weeds in corn crop. Atrazine becomes an environmental concern when it moves off-site to surface and ground waters. Understanding how atrazine moves in the field is important for developing management controls. Electromagnetic induction (EMI) has been used to map certain contaminant transport at the field scale. This study was developed to evaluate the efficacy of EMI technology for identifying surface soil atrazine concentration in a corn crop field. The research was conducted in a corn silage field with silt, clay and loam soils at the U.S. Meat Animal Research Center (USMARC), Clay Center, NE – USA, and it was divided in three stages; i) EMI data collection and a response surface sampling design for collection of bulk soils and soil core samples, ii) atrazine transport parameters were obtained by Breakthrough Curves using the bulk soil and numerical adjustments using STANMOD (HYDRUS package), and iii) Modeling atrazine parameters through EMI signal data with posterior atrazine’s movement simulations through the soil using HYDRUS 2D. Atrazine’s retardation factor, partition coefficient, and transfer coefficient were strongly correlated with EMI signal exhibiting a strong correlation with apparent electrical conductivity (ECa). The low values for RMSE and RRMSE and the high values for Willmott and Pearson coefficients indicate EMI technology can be used to predict atrazine movement parameters. HYDRUS 2D quantitatively simulates the atrazine concentration leaching and how the temporal scale of this contamination would be. Combining EMI technology with HYDRUS 2D modeling provides researcher with additional information for developing better management practices for controlling atrazine movement to surface water; however, further studies are needed determine the effectiveness of this approach for other soil types.

Predicting Escherichia coli loads in cascading dams with machine learning: An integration of hydrometeorology, animal density and grazing pattern

Accurate prediction of Escherichia coli contamination in surface waters is challenging due to considerable uncertainty in the physical, chemical and biological variables that control E. coli occurrence and sources in surface waters. This study proposes a novel approach by integrating hydro-climatic variables as well as animal density and grazing pattern in the feature selection modeling phase to increase E. coli prediction accuracy for two cascading dams at the US Meat Animal Research Center (USMARC), Nebraska. Predictive models were developed using regression techniques and an artificial neural network (ANN). Two adaptive neuro-fuzzy inference system (ANFIS) structures including subtractive clustering and fuzzy c-means (FCM) clustering were also used to develop models for predicting E. coli. The performances of the predictive models were evaluated and compared using root mean squared log error (RMSLE). Cross-validation and model performance results indicated that although the majority of models predicted E. coli accurately, ANFIS models resulted in fewer errors compared to the other models. The ANFIS models have the potential to be used to predict E. coli concentration for intervention plans and monitoring programs for cascading dams, and to implement effective best management practices for grazing and irrigation during the growing season.