US Meat Animal Research Center Research Articles

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.

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 > 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.

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.

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.

A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.

Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.

A life cycle assessment of the environmental impacts of a beef system in the USA

PurposeThe need to assess the sustainability attributes of the United States beef industry is underscored by its importance to food security locally and globally. A life cycle assessment (LCA) of the US beef value chain was conducted to develop baseline information on the environmental impacts of the industry includ`ing metrics of the cradle-to-farm gate (feed production, cow-calf, and feedlot operations) and post-farm gate (packing, case-ready, retail, restaurant, and consumer) segments.MethodsCattle production (cradle-to-farm gate) data were obtained using the integrated farm system model (IFSM) supported with production data from the Roman L. Hruska US Meat Animal Research Center (USMARC). Primary data for the packing and case-ready phases were obtained from packers that jointly processed nearly 60% of US beef while retail and restaurant primary data represented 8 and 6%, respectively, of each sector. Consumer data were obtained from public databases and literature. The functional unit or consumer benefit (CB) was 1 kg of consumed, boneless, edible beef. The relative environmental impacts of processes along the full beef value chain were assessed using a third party validated BASF Corporation Eco-Efficiency Analysis methodology.Results and discussionValue chain LCA results indicated that the feed and cattle production phases were the largest contributors to most environmental impact categories. Impact metrics included water emissions (7005 L diluted water eq/CB), cumulative energy demand (1110 MJ/CB), and land use (47.4 m2a eq/CB). Air emissions were acidification potential (726 g SO2 eq/CB), photochemical ozone creation potential (146.5 g C2H4 eq/CB), global warming potential (48.4 kg CO2 eq/CB), and ozone depletion potential (1686 μg CFC11 eq/CB). The remaining metrics calculated were abiotic depletion potential (10.3 mg Ag eq/CB), consumptive water use (2558 L eq/CB), and solid waste (369 g municipal waste eq/CB). Of the relative points adding up to 1 for each impact category, the feed phase contributed 0.93 to the human toxicity potential.ConclusionsThis LCA is the first of its kind for beef and has been third party verified in accordance with ISO 14040:2006a and 14044:2006b and 14045:2012 standards. An expanded nationwide study of beef cattle production is now being performed with region-specific cattle production data aimed at identifying region-level benchmarks and opportunities for further improvement in US beef sustainability.

Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase

ObjectiveO-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) catalyzes the addition of O-GlcNAc and GlcNAcylation has extensive crosstalk with phosphorylation to regulate signaling and transcription. Pig OGT is located near the region of chromosome X that affects follicle stimulating hormone level and testes size. The objective of this study was to find the variations of OGT between European and Chinese pigs.MethodsPigs were tested initially for polymorphism in OGT among European and Chinese pigs by polymerase chain reaction and sequencing at the U.S. Meat Animal Research Center (USMARC). The polymorphism was also determined in an independent population of pigs including European and Chinese Meishan (ME) breeds at the National Institute of Animal Science (NIAS, RDA, Korea).ResultsThe intron 20 of OGT from European and Chinese pigs was 514 and 233 bp, respectively, in the pigs tested initially. They included 1 White composite (WC) boar and 7 sows (2 Minzu×WC, 2 Duroc [DU]×WC, 2 ME×WC, 1 Fengzing×WC) at USMARC. The 281-bp difference was due to an inserted 276-bp element and GACTT in European pigs. When additional WC and ME boars, the grandparents that were used to generate the 1/2ME×1/2WC parents, and the 84 boars of 16 litters from mating of 1/2ME×1/2WC parents were analyzed, the breeds of origin of X chromosome quantitative trait locus (QTL) were confirmed. The polymorphism was determined in an independent population of pigs including DU, Landrace, Yorkshire, and ME breeds at NIAS. OGT was placed at position 67 cM on the chromosome X of the USMARC swine linkage map.ConclusionThere was complete concordance with the insertion in European pigs at USMARC and NIAS. This polymorphism could be a useful marker to identify the breed of origin of X chromosome QTL in pigs produced by crossbreeding Chinese and European pigs.

A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome.

Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits. Whole-genome sequence was obtained from 72 of the founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace) and 48 Yorkshire-Landrace composite sows. Sequence reads were mapped to the Sscrofa10.2 genome build, resulting in a mean of 6.1 fold (×) coverage per genome. A total of 22342915 high confidence SNPs were identified from the sequenced genomes. These included 21million previously reported SNPs and 79% of the 62163 SNPs on the PorcineSNP60 BeadChip assay. Variation was detected in the coding sequence or untranslated regions (UTRs) of 87.8% of the genes in the porcine genome: loss-of-function variants were predicted in 504 genes, 10202 genes contained nonsynonymous variants, 10773 had variation in UTRs and 13010 genes contained synonymous variants. Approximately 139000 SNPs were classified as loss-of-function, nonsynonymous or regulatory, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of functional SNPs during future analyses.

Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multibreed population.

Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was transformed from the USMARC scores to corresponding -scores from the standard normal distribution based on the incidence rate of the USMARC scores. Breed fraction covariates were included to estimate breed differences. Heritability estimates (SE) for BWT direct, CD direct, BWT maternal, and CD maternal were 0.34 (0.10), 0.29 (0.10), 0.15 (0.08), and 0.13 (0.08), respectively. Calving difficulty direct breed effects deviated from Angus ranged from -0.13 to 0.77 and maternal breed effects deviated from Angus ranged from -0.27 to 0.36. Hereford-, Angus-, Gelbvieh-, and Brangus-sired calves would be the least likely to require assistance at birth, whereas Chiangus-, Charolais-, and Limousin-sired calves would be the most likely to require assistance at birth. Maternal breed effects for CD were least for Simmental and Charolais and greatest for Red Angus and Chiangus. Results showed that the diverse biological types of cattle have different effects on both BWT and CD. Furthermore, results provide a mechanism whereby beef cattle producers can compare EBV for CD direct and maternal arising from disjoined and breed-specific genetic evaluations.

Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle.

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII and advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Angus, Charolais, Gelbvieh, Simmental, Limousin and Composite MARC III. Heterosis was further estimated by proportions of British × British (B × B), British × Continental (B × C) and Continental × Continental (C × C) crosses and by breed-specific combinations. Model 1 fitted fixed covariates for heterosis within biological types while Model 2 fitted random breed-specific combinations nested within the fixed biological type covariates. Direct heritability estimates (SE) for birth, weaning ,and yearling weight for Model 1 were 0.42 (0.04), 0.22 (0.03), and 0.39 (0.05), respectively. The direct heritability estimates (SE) of birth, weaning, and yearling weight for Model 2 were the same as Model 1, except yearling weight heritability was 0.38 (0.05). The B × B, B × C, and C × C heterosis estimates for birth weight were 0.47 (0.37), 0.75 (0.32), and 0.73 (0.54) kg, respectively. The B × B, B × C, and C × C heterosis estimates for weaning weight were 6.43 (1.80), 8.65 (1.54), and 5.86 (2.57) kg, respectively. Yearling weight estimates for B × B, B × C, and C × C heterosis were 17.59(3.06), 13.88 (2.63), and 9.12 (4.34) kg, respectively. Differences did exist among estimates of breed-specific heterosis for weaning and yearling weight, although the variance component associated with breed-specific heterosis was not significant. These results illustrate that there are differences in breed-specific heterosis and exploiting these differences can lead to varying levels of heterosis among mating plans.

Evaluation of Columbia, USMARC-Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: VIII. Quality measures of lamb longissimus dorsi.

Quality measures of lamb longissimus dorsi were evaluated in 514 crossbred wether lambs to assess sire breed differences. Wethers were produced over 3 yr from single-sire matings of 22 Columbia, 22 U.S. Meat Animal Research Center (USMARC)-Composite (Composite), 21 Suffolk, and 17 Texel rams to adult Rambouillet ewes. Lambs were reared to weaning in an extensive western rangeland production system and finished in a feedlot on a high-energy finishing diet. One of three harvest groups were randomly assigned to each lamb, and lambs were transported to The Ohio State University abattoir when the mean BW of wethers remaining in the feedlot reached 54.4, 61.2, or 68.0 kg. After harvest, subjective lean quality scores were assigned and LM pH (immediately after and 24 h after harvest), color (quantified as Minolta L*, a*, and b*), intramuscular fat (IMF), cooking loss percentage, and Warner-Bratzler shear force (WBSF) were determined. Statistical models included fixed effects of sire breed, year of birth, and harvest group and random effects of sire (nested within sire breed and year) and maternal grandsire. Year and harvest group were significant (P < 0.04) for all traits, except harvest group was not for WBSF and lean quality (P > 0.28). At comparable numbers of days on feed, Texel-sired wethers had the greatest (more desirable; P < 0.01) subjective lean quality scores while Composite- and Suffolk-sired lambs were intermediate and Columbia-sired lambs had the lowest (less desirable). Minolta L* values were greater (P < 0.02) for Texel- than Columbia-sired lambs, although this difference is not visually discernible by humans. No significant (P > 0.05) sire breed effects were detected for LM pH at or 24 h after harvest, Minolta a* and b*, IMF, percentage of cooking loss, and WBSF at comparable numbers of days on feed. At comparable chilled carcass weight, significant (P < 0.01) sire breed effects were detected for subjective lean quality score. Texel-sired lambs had greater scores than Columbia- and Suffolk-sired lambs, but Composite-sired lambs did not differ from lambs sired by the other sire breeds. Sire breed effects were not detected (P > 0.15) for LM pH at or 24 h after harvest, Minolta L*, a*, and b*, cooking loss percentage, IMF, and WBSF at comparable chilled carcass weight. Therefore, results of the present study indicated that the 4 sire breeds produced crossbred lamb carcasses that had similar and desirable LM quality measurements, meeting consumer expectations.

Evaluation of Columbia, U.S. Meat Animal Research Center Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: VI. Measurements of live-lamb and carcass shape and their relationship to carcass yield and value1,2

Linear measurements on live lambs and carcasses can be used to characterize sheep breeds and may have value for prediction of carcass yield and value. This study used 512 crossbred lambs produced over 3 yr by mating Columbia, U.S. Meat Animal Research Center (USMARC) Composite, Suffolk, and Texel rams to adult Rambouillet ewes to assess sire-breed differences in live-animal and carcass shape and to evaluate the value of shape measurements as predictors of chilled carcass weight (CCW), weight of high-value cuts (rack, loin, leg, and sirloin; HVW), weight of trimmed high-value cuts (trimmed rack and loin and trimmed, boneless leg and sirloin; TrHVW), and estimated carcass value before (CVal) and after trimming of high-value cuts (TrCVal). Lambs were produced under extensive rangeland conditions, weaned at an average age of 132 d, fed a concentrate diet in a drylot, and harvested in each year in 3 groups at target mean BW of 54, 61, and 68 kg. Canonical discriminant analysis indicated that over 93% of variation among sire breeds was accounted for by the contrast between tall, long, less-thickly muscled breeds with greater BW and CCW (i.e., the Columbia and Suffolk) compared with shorter, more thickly muscled breeds with smaller BW and CCW. After correcting for effects of year, harvest group, sire breed, and shipping BW, linear measurements on live lambs contributed little to prediction of CCW. Similarly, after accounting for effects of CCW, linear measurements on live animals further reduced residual SD (RSD) of dependent variables by 0.2 to 5.7%, with generally positive effects of increasing live leg width and generally negative effects of increasing heart girth. Carcass measurements were somewhat more valuable as predictors of carcass merit. After fitting effects of CCW, additional consideration of carcass shape reduced RSD by 2.1, 3.6, 9.5, and 2.2% for HVW, TrHVW, CVal, and TrCVal, respectively. Effects of increasing carcass leg width were positive for HVW, TrHVW, and TrCVal. We also observed positive effects of increasing carcass length on TrCVal and negative effects of increasing cannon bone length on HVW and CVal. Increasing shoulder width had positive effects on CVal but negative effects on TrHVW. Differences in lamb and carcass shape were significantly associated with carcass yield and value, but the additional accuracy associated with use of these measurements was modest relative to that achieved from use of only shipping BW or CCW.

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle1,2,3,4

Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome. Our lab previously reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency. To further evaluate this region for genomic variations such as CNV, we initially applied a genomewide association approach based on the >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in central Florida. A genomic segment located on chromosome 5, spanning the region of approximately 58.37 to 58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency. To verify this deletion, a quantitative real-time PCR test was developed to evaluate additional females in the central Florida and U.S. Meat Animal Research Center (USMARC) populations. The frequency of the homozygous deletion was 7% (23/319) in the central Florida population (Bos indicus cross) for females with 2 consecutive failed breeding seasons and 0% in the USMARC population (predominantly Bos taurus) of low reproductive females. To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle. From these data, we have identified a deletion on chromosome 5 associated with reproductive efficiency in Bos indicus-influenced cattle.

Heifer calving date positively influences calf weaning weights through six parturitions1

Longevity and lifetime productivity are important factors influencing profitability for the cow-calf producer. Heifers that conceive earlier in the breeding season will calve earlier in the calving season and have a longer interval to rebreeding. Calves born earlier in the calving season will also be older and heavier at weaning. Longevity data were collected on 2,195 heifers from producers in South Dakota Integrated Resource Management groups. Longevity and weaning weight data were collected on 16,549 individual heifers at the U.S. Meat Animal Research Center (USMARC). Data were limited to heifers that conceived during their first breeding season. Heifers were grouped into 21-d calving periods. Heifers were determined to have left the herd when they were diagnosed not pregnant at the end of the breeding season. Heifers that left the herd for reasons other than reproductive failure were censored from the data. Heifers that calved with their first calf during the first 21-d period of the calving season had increased (P < 0.01) longevity compared with heifers that calved in the second 21-d period, or later. Average longevity for South Dakota heifers that calved in the first or later period was 5.1 ± 0.1 and 3.9 ± 0.1 yr, respectively. Average longevity for USMARC heifers that calved in the first, second, or third period was 8.2 ± 0.3, 7.6 ± 0.5, and 7.2 ± 0.1 yr, respectively. Calving period as a heifer influenced (P < 0.01) unadjusted weaning BW of the first 6 calves. Estimated postpartum interval to conception as a 2-yr-old cow was greater for females that calved in the first period as heifers but did not differ between heifer calving periods in subsequent calving seasons. In summary, heifers that calved early in the calving season with their first calf had increased longevity and kilograms weaned, compared with heifers that calved later in the calving season.

Development of a system for classification of pork loins for tenderness using visible and near-infrared reflectance spectroscopy1,2

Boneless pork loins (n = 901) were evaluated either on the loin boning and trimming line of large-scale commercial plants (n = 465) or at the US Meat Animal Research Center abattoir (n = 436). Exposed LM on the ventral side of boneless loins was evaluated with visible and near-infrared spectroscopy (VISNIR; 450 to 1,000 nm) using a commercial system that was developed for on-line evaluation of beef tenderness. Boneless loin sections were aged (2°C) until 14 d postmortem, and two 2.54-cm-thick chops were obtained from the 11th-rib region. Fresh (never frozen) chops were cooked (71°C) and LM slice shear force (SSF) was measured on each of the 2 chops. Those 2 values were averaged, and that value was used for all analyses. Loins were blocked by plant (n = 3), production day (n = 24), and observed SSF (mean = 13.9 kg; SD = 3.7 kg; CV = 26.8%; range 6.4 to 32.4 kg). One-half of the loins were assigned to a calibration data set, which was used to develop regression equations, and one-half of the loins were assigned to a prediction data set, which was used to validate the regression equations. A partial least-squares regression model was developed, and loins were classified as predicted tender or not predicted tender if their VISNIR-predicted SSF was <14.0 kg or ≥14.0 kg, respectively. Analysis of variance was used to determine the effect of VISNIR classification on SSF. The calibration data set and prediction data set had 61.9 and 60.9% of the loins classified as predicted tender, respectively. For both the calibration data set and the prediction data set, mean SSF was less for loins predicted tender than loins not predicted tender (P < 0.001). Relative to loins that were not predicted tender, the percentage of loins with SSF ≥20 kg was less for loins predicted tender in the calibration data set (3.6 vs. 8.1%) and prediction data set (1.8 vs. 13.6%). These results clearly indicate that the VISNIR technology could be used to noninvasively classify pork loins on-line for tenderness.

Factors affecting pregnancy rate to estrous synchronization and fixed-time artificial insemination in beef cattle1,2

Application of AI in extensive beef cattle production would be facilitated by protocols that effectively synchronize ovarian follicular development and ovulation to enable fixed-time AI (TAI). The objectives were to determine whether use of a controlled internal drug release (CIDR) device to administer progesterone in a GnRH-based estrous synchronization protocol would optimize blood progesterone concentrations, improve synchronization of follicular development and estrus, and increase pregnancy rates to TAI in beef cows. Beef cows (n = 1,240) in 6 locations within the US Meat Animal Research Center received 1 of 2 treatments: 1)an injection of GnRH [100 µg intramuscularly (i.m.)] followed by PGF(2α) (PGF; 25 mg i.m.) 7 d later (CO-Synch), or 2) CO-Synch plus a CIDR during the 7 d between GnRH and PGF injections (CO-Synch + CIDR). Cows received TAI and GnRH (100 µg i.m.) at 60 h after PGF. Progesterone was measured by RIA in blood samples collected 2 wk before and at initiation of treatment (d 0) and at PGF injection (d 7). Estrous behavior was monitored by Estrotect Heat Detectors. Pregnancy was diagnosed by ultrasonography 72 to 77 d after TAI. Plasma progesterone concentrations did not differ (P > 0.10) between synchronization protocols at first GnRH injection (d 0), but progesterone was greater (P < 0.01) at PGF injection (d 7) in cows receiving CO-Synch + CIDR vs. CO-Synch as a result of fewer CIDR-treated cows having progesterone ≤1 ng/mL at PGF (10.7 vs. 29.6%, respectively). A greater (P < 0.01) proportion of CO-Synch + CIDR vs. CO-Synch cows were detected in estrus within 60 h after PGF (66.7 vs. 57.8 ± 2.6%, respectively) and a greater (P < 0.01) proportion were pregnant to TAI (54.6 vs. 44.3 ± 2.6%, respectively). For both synchronization protocols, cows expressing estrus within 60 h before TAI had a greater pregnancy rate than cows without estrus. For cows with plasma progesterone ≤1 ng/mL at PGF injection, CO-Synch + CIDR increased pregnancy rate (65.2 ± 5.9 vs. 30.8 ± 3.4% with vs. without CIDR), whereas pregnancy rates did not differ (P > 0.10) between protocols (52.1 ± 2.1 vs. 50.0 ± 2.4%, respectively) when progesterone was >1 ng/mL (treatment × progesterone; P < 0.01). Inclusion of a CIDR in the synchronization protocol increased plasma progesterone concentration, proportion of cows detected in estrus, and pregnancy rate; however, the increase in pregnancy rate from inclusion of the CIDR was primarily in cows with decreasing or low endogenous progesterone secretion during treatment.

Partial-genome evaluation of postweaning feed intake and efficiency of crossbred beef cattle1,2

The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F(1) × F(1) (F(1)(2)) steers were AI-sired F(1) progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies >0.05 in the F(1)(2) generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a polygenic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P < 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations.