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Objective Our objective was to evaluate fasting heat production in cattle with and without the GDF8 mutation. Materials and Methods The heifers used in this study were genotyped for the myostatin(MSTN) gene mutation to determine their MSTN genotype as either homozygous normal for phenylalanine at amino acid position 94 of MSTN (0 copy; n = 5) or homozygous for F94L variant in MSTN (2 copy; n = 6). Oxygen consumption was measured using portable headbox respiration calorimeters, and heat production was calculated. Results and Discussion Body weight was not different between treatments (P = 0.33), but it did differ across days (P Implications and Applications Therefore, it is likely that cattle with 2 copies of the F94L MSTN substitution have lower maintenance energy requirements than cattle without the MSTN gene. Thus, genotype, if known, should be considered when assessing energy requirements of beef cattle.

Follicular progression during peripuberty is affected by diet. Vascular endothelial growth factor A (VEGFA) induces follicle progression in many species; however, there are limited studies to determine if diet may alter the effects of angiogenic VEGFA165-stimulated follicle progression or antiangiogenic VEGFA165b follicle arrest. We hypothesized that diet affects the magnitude of angiogenic and antiangiogenic VEGFA isoform actions on follicular development through diverse signal transduction pathways. To test this hypothesis, beef heifers in our first trial received Stair-Step (restricted and refeeding) or control diets from 8 to 13 months of age. Ovaries were collected to determine follicle stages, measure vascular gene expression and conduct ovarian cortical cultures. Ovarian cortical cultures were treated with phosphate-buffered saline (control), 50 ng/ml VEGFA165, VEGFA165b, or VEGFA165 + VEGFA165b. The Stair-Step heifers had more primordial follicles (P

A study of multiple tissues was conducted to identify potential metabolic differences in cattle differing in feed efficiency. Individual feed intake and body weight was measured on 144 steers during 105 days on a high-concentrate ration. Steers were selected according to differences in average daily gain (ADG) with those with the greatest ADG (n = 8; 1.96 ± 0.02 kg/day) and least ADG (n = 8; 1.57 ± 0.02 kg/day), whose dry matter intake was within 0.32 SD of the mean intake (10.10 ± 0.05 kg/day). Duodenum, liver, adipose, and longissimus-dorsi were collected at slaughter, and metabolomics profiles were performed by ultra performance liquid chromatography quadrupole-time of-flight mass spectrometry. Principal components analyses, t-tests, and fold changes in tissues profile were used to identify differential metabolites between ADG groups. These were primarily involved in α-linolenic metabolism, which was downregulated in the greatest ADG as compared to least-ADG group in duodenum, adipose, and longissimus-dorsi. However, taurine and glycerophospholipids metabolisms were both upregulated in the greatest ADG compared with least-ADG group in the liver. The phospholipids and cholesterol were quantified in the tissues. Lipid transport and oxidation were the main common metabolic mechanisms associated with cattle feed efficiency. Combining analyses of multiple tissues may offer a powerful approach for defining the molecular basis of differences in performance among cattle for key production attributes.

The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.

The period of heifer development is a relatively small fraction of a cow’s life; however, her pattern of growth may have permanent effects on her productivity as a cow. We hypothesized that altering the growth pattern during the peri-pubertal period would increase life-time productivity across genetic types of Bos taurus cows. The objective was to determine the stayability, calf production, and weight of calf weaned across six calf crops. Heifers (n = 685) were placed on one of two developmental programs at 256 ± 1 d of age. Control heifers received a diet that provided 228 kcal ME·(body weight [BW], kg) −0.75 daily, and stair-step heifers were allocated 157 kcal ME·(BW, kg)−0.75 daily for 84 or 85 d, and then the daily allocation was increased to 277 kcal ME·(BW, kg)−0.75. Stair-step heifers (0.33 ± 0.02 kg/d) had a lower average daily gain (ADG) than control heifers (0.78 ± 0.02 kg/d; P < 0.001) during Period 1, and stair-step heifers (0.93 ± 0.03 kg/d) had a greater ADG than controls (0.70 ± 0.03 kg/d; P < 0.001) during Period 2. There were no treatment (P = 0.28) or breed type differences (P = 0.42) for the proportion of cows weaning a calf; however, the proportion of cows weaning a calf decreased with cow age (P < 0.001). Calves from stair-step dams had heavier weaning weights (193 ± 1 kg) compared to control calves (191 ± 1 kg; P = 0.007). There was not a treatment (P = 0.25) or breed type differences in cumulative BW weaned (P = 0.59). A diverse genetic population of cattle within B. taurus was tested and responses in calf production did not differ between stair-step growth pattern and a more constant nonobese growth pattern.

Objective Realimentation can compensate for weight loss from poor-quality feedstuffs or drought. Mature cows fluctuate in body weight throughout the year due to nutrient availability. The objective of this study was to determine whether cows that differ in weight gain during realimentation also differ in the abundance of transcripts for enzymes associated with energy utilization in skeletal muscle. Mature cows were subjected to feed restriction followed by ad libitum feed. Skeletal muscle transcriptome expression differences during the two feeding periods were determined from cows with greater (n = 6) and less (n = 6) weight gain during the ad libitum feeding period. Results A total of 567 differentially expressed genes (408 up- and 159 down-regulated) were identified for the comparison of restriction and ad libitum periods (PBonferroni

One approach to reducing calving difficulty is to select heifers with higher breeding value for calving ease. Calving ease is often associated with lower birth weight and that may result in other possible effects on lifetime productivity. Females from experimental select and control calving ease lines within each of the seven populations were compared. Random samples of 720 heifers from lines selected for better calving ease breeding values and 190 heifers from control lines selected for average birth weights were followed through four parities. Select and control lines within the same population were selected to achieve similar yearling weight breeding values. Weights of sampled heifers in select lines were 2.6 kg (P < 0.01) lighter at birth but not different from control lines at weaning. Select lines had significantly shorter hip height, lighter mature weight, and greater calving success at second parity. Their calves were born significantly earlier with lighter weights and less assistance. Significant interactions with parity showed fewer calves assisted and greater calf survival to weaning as heifers but negligible differences with control lines in later parities. Steer progeny sampled from these dams in select lines (n = 204) were not different from steers in control lines (n = 91) for hot carcass weight but had significantly greater fat depth. Two production systems were compared considering the seven populations as replicates. The systems differed in selection history of females (select and control lines) and the use of bulls within their lines as young cows, but used the same bulls in both lines as older cows. Cows were culled after single unsuccessful breeding and kept for up to four parities. Select line cows tended (P ≤ 0.10) to wean more calves and stay in the herd longer. They were assisted significantly fewer times at calving and had greater calf weight gain to weaning when evaluated over their herd life. Mature weights were lighter in select lines, but marketable cow weight from the systems was nearly identical. Control lines did have more marketable young cow weight and select lines older cow weight. Weaned calf weight per heifer starting the system was significantly greater for the select heifer system due to greater survival of calves from heifers and greater calving success at second parity. No important unfavorable effects of genetic differences in calving ease were identified in this experiment.

Methane represents an energetic loss, and it has been proposed that its reduction may be associated with improved feed efficiency. Rumen methanogens produce most of the methane. Forty-nine crossbred heifers were individually fed a ration that consisted of 67.75% rolled corn, 20% wet distillers grain with solubles, 8% chopped alfalfa and 4.25% mineral/vitamin/rumensin mix for 84 d. Residual feed intake was the residual of the observed – predicted FI for the multivariate regression of FI on ADG and mid-metabolic BW for the population. Six heifers with the greatest RFI (1.75 ± 0.31 kg DM/d) and 6 with least RFI (-1.48 ± 0.31 kg DM/d) were selected. Rumen fluid was sampled from a tube passed through the mouth into the rumen. Rumen fluid was flash frozen in liquid N2 and stored at -80°C. After the first collection, heifers with greater RFI were pair fed to the less RFI heifers and rumen fluid was sampled 5 wk later. DNA was isolated from the rumen fluid and primer sets targeting total methanogens, Methanomicrobiales, Methanobacteriales, Methanosarcina, Methanobacterium, Methanobrevibacter ruminantium + Mbb. Cuticularis, and Methanobrevibacter smithii + Mbb. wolinii + Mbb. thaueri + Mbb. gottschalkii + Mbb. Woesei were amplified with real-time quantitative PCR (qPCR). Standard curves were generated to quantify copy number. There were no differences in copy number for the interaction of RFI classifications and sample period for all primer sets (P > 0.18). There were no differences in (P > 0.15) in RFI classification for all qPCR primer sets. There were fewer copies for the Methanobrevibacter ruminantium + Mbb. Cuticularis qPCR for samples collected in the first week compared to the 5 wk sample (P = 0.03); however, there were no difference for collection week for the other qPCR assays (P > 0.16). USDA is an equal opportunity provider and employer.

In 1996, the NASEM beef cattle committee developed and published an equation to estimate cow feed intake using results from studies conducted or published between 1979 and 1993 (Nutrient Requirements of Beef Cattle). The same equation was recommended for use in the most recent version of this publication (2016). The equation is sensitive to cow weight, diet digestibility and milk yield. Our objective was to validate the accuracy of this equation using more recent published and unpublished data. Criteria for inclusion in the validation data set included projects conducted or published within the last ten years, direct measurement of forage intake, adequate protein supply, and pen feeding (no tie stall or metabolism crate data). The validation data set included 29 treatment means for gestating cows and 26 treatment means for lactating cows. Means for the gestating cow data set was 11.4 ± 1.9 kg DMI, 599 ± 77 kg BW, 1.24 ± 0.14 Mcal/kg NEm per kg of feed and lactating cow data set was 14.5 ± 2.0 kg DMI, 532 ± 116.3 kg BW, and 1.26 ± 0.24 Mcal NEm per kg feed, respectively. Non intercept models were used to determine equation accuracy in predicting validation data set DMI. The slope for linear bias in the NASEM gestation equation did not differ from 1 (P = 0.07) with a 3.5% positive bias. However, when the NASEM equation was used to predict DMI in lactating cows, the slope for linear bias significantly differed from 1 (P < 0.001) with a downward bias of 13.7%. Therefore, a new multiple regression equation was developed from the validation data set: DMI= (-4.336 + (0.086427 (BW^.75) + 0.3 (Milk yield)+6.005785(NEm)), (R-squared=0.84). The NASEM equation for gestating beef cows was reasonably accurate while the lactation equation underestimated feed intake.

Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, ¼ Hereford, ¼ Red Poll, and ¼ Pinzgauer) that had been selectively bred to increase the frequency of these polymorphisms were submitted for monthly ultrasound exams beginning at 333 d of age and continuing until the start of breeding to determine pubertal status. At the last exam before breeding, all antral follicles were counted, and the length and height of each ovary was measured to determine if genomic selection for slice shear force associated with ovarian follicle number. Calving date, calf gender, and calf birth weight were recorded at parturition. Regression analysis of the molecular breeding value for slice shear force of the heifers on ordinal calving date indicated no association between genomic prediction of tenderness and calving date (P = 0.16); however, there was a tendency for age at puberty to be delayed in heifers as genetic merit for tenderness improved (P = 0.09). The results of the present study indicate that within experimental precision, selecting for tenderness using genomic predictions had minimal or no antagonistic association with reproductive performance in heifers. Further analysis of reproductive performance as cows is needed within this population but applying these genetic markers to select for tenderness in steers does not antagonize reproductive traits influencing conception or first calf birth date and birth weight in replacement beef heifers.

The cow herd consumes approximately 70% of the annual feed resources. To date, most genetic evaluations of feed intake in beef cattle have been made in growing animals and little information is available for mature cows. Genetic evaluations in mature cows have predominately been confined to lactating dairy cows and the relationship between feed intake as growing heifers and mature cows has not been addressed. It was the purpose of this study to estimate the heritability of feed intake when measured as growing heifers and mature cows and determine the genetic correlation between these measurements. Individual feed intake and BW gain were measured on 687 heifers and 622 5-yr-old cows. The heritability of average daily DMI (ADDMI) estimated in heifers was 0.84 ± 0.12 and 0.53 ± 0.12 in cows. The heritability of ADG estimated in heifers was 0.53 ± 0.12 and 0.34 ± 0.11 in cows. The genetic correlation between heifer and cow ADDMI was 0.84 ± 0.09. The genetic correlation between heifer and cow ADG was 0.73 ± 019. Heritability of residual feed intake in heifers was 0.25 ± 0.11 and 0.16 ± 0.10 in cows. Heritability for residual gain in heifers was 0.21 ± 0.11 and 0.14 ± 0.10 in cows. Feed intake and ADG are heritable and genetically correlated between heifers and cows. Selection for decreased feed intake and ADG in growing animals will probably have the same directional effects on mature cows.

The objective of this study was to determine the association of insulin, glucagon, and glucagon-like peptide (GLP-1) with production traits of growing and finishing beef heifers fed a forage- (FOR) and concentrate-based (CONC) ration. This experiment was conducted over 2 years. Shortly after weaning, heifers (n = 74 and 62, for year 1 and 2, respectively) were placed on a ration containing (DM basis) 69.8% corn silage, 30% alfalfa hay, and 0.2% salt. Feed intake was measured for 84 d using Calan gates and BW were measured at 7-time points to calculate ADG using a quadratic regression of BW on time. Cattle were then transitioned to a concentrate-based finishing ration containing (DM basis) 67.8% dry-rolled corn, 20% wet distillers grains with solubles, 8% alfalfa hay, and 4.2% vitamin/mineral supplement. Blood samples were collected on day 42 of each period. Data were analyzed as a mixed model with fixed effects of sire breed, period, and the random variable of year. Hormone concentration was included as an interaction with period to determine the association of the hormones with production traits. Dry matter intake (DMI), average daily body weight gain (ADG), gain:feed (G:F), and all three hormones were greater in the CONC period (P < 0.01). Insulin was negatively associated with DMI only during the CONC period (P = 0.04) and positively associated with G:F (P = 0.01). GLP-1 was positively associated with CONC DMI (P < 0.01), FOR ADG (P < 0.01), and positively associated with FOR G:F and negatively associated with CONC G:F (P < 0.01). Glucagon was positively associated with residual feed intake (P = 0.04). While these data do not infer causality, they do indicate that more in-depth understanding of the role of gut peptide and insulin signaling in feed efficiency needs to be evaluated.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to equalize CAPN1 haplotypes, CAST, and GHR genetic marker frequencies. The objective was to estimate the pleiotropic effects of these carcass quality oriented markers for body weight, reproduction, and first calf performance traits in 174 replacement beef females which were managed under 2 post-weaning development protocols. Heifers were weighed at 11-, 12-, and 13-mo, at first breeding season pregnancy evaluation, and prior to first calving season. Pubertal status was determined at 11-, 12-, and 13-mo of age. Antral follicles were counted, reproductive tracts were scored, and tract dimensions were measured at 13-mo. Body condition and hip height were scored and measured at pregnancy evaluation and prior to calving season. Heifer pregnancy and weaning rates and ordinal birth date were recorded. Calf body weights at birth and weaning were analyzed. Single df linear contrasts for recessive effects of the GHR heterozygous genotype showed significant decreases of 2.5–3.6% in 11-, 12-, and 13-mo heifer body weights and heifer weight prior to calving. The additive differences between GHR homozygotes were small and not significant for all body weights measured but a 1 wk difference in calf birth date was significant. For all 13-mo uterine measurements, scores, and antral follicle counts, only the CAST dominance contrast for medium antral follicle count was significant. The CAPN1 haplotype with a strong additive effect for increased beef tenderness also had a significant additive effect on calving date. Heifers homozygous for the tender haplotype calved 7.9 days later than heifers homozygous for the tough haplotype. Most heifer reproductive traits were not significantly affected by CAST and CAPN1 markers that are widely used to improve beef tenderness by selection and breeders should not be concerned with how these markers affect reproduction and other heifer traits with the possible exception of CAPN1 effects on calving date.

Drylot beef cow-calf systems are viable alternative management systems to traditional forage-based systems. In such confinement, adding ionophores such as monensin to the diets of beef cattle is common, and has been shown to improve feed efficiency and increase average daily gain. The addition of monensin is also commonly utilized as a strategy for methane mitigation, as this ionophore class antimicrobial acts to interfere with ion flux primarily within Gram-positive cells through its action as an ion carrier. It is widely accepted that suppression of these ruminal organisms results in the reduction of substrates for rumen methanogenic archaea, reducing methane production. However, several studies have indicated that cattle may adapt to monensin, and within weeks of feeding, may return to prior levels of methane production. Our hypothesis is that feeding monensin to bred beef heifers in confinement will temporarily decrease methane production from shifts in the methanogenic archaeal and bacterial communities. Sixteen fall-born bred heifers were randomly assigned to 2 treatment groups (n = 8 per treatment) and were fed a control diet or a diet containing monensin for 70 days using headgates. In vivo gas exchange of oxygen consumption, carbon dioxide and methane production were measured for 24-h periods throughout the trial using individual calorimeter head boxes. Rumen content sampling was conducted on day 0, 18 and 53 of the trial through oral lavage. Upon completion of sampling, DNA was isolated for ruminal bacteriome composition utilizing deep, next-generation sequencing of the V1-V3 hypervariable regions of the 16S bacterial rRNA gene. Level of methanogen 16S rRNA was quantified using qPCR. There was a significant reduction in phylum SR1 (P 0.05). Heifers fed monensin did not produce significantly less methane than the control (P > 0.05) on a liters per day basis, which was consistent throughout the study. These data suggest methane production is not reduced long-term when animals are fed monensin in confinement. Additionally, the data suggest that monensin supplementation does not suppress all classical Gram-positive populations, rather it influences finer shifts in bacterial species that may be key in ruminant function. Determining the stability of the ruminal microbiome over time in heifers fed monensin may provide further insights to long-term methane mitigation in cow-calf systems.

Background Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency. In each cohort, 16 steers were selected from one of four gain and feed intake phenotypes (n = 4 per phenotype) in a 2 × 2 factorial arrangement with gain and feed intake as main effect variables. Each cohort was analyzed as a single experiment using a generalized linear model and results from the 5 cohort analyses were combined in a meta-analysis to identify differentially expressed genes (DEG) across the cohorts. Results A total of 51 genes were differentially expressed for the main effect of gain, 109 genes for the intake main effect, and 11 genes for the gain x intake interaction (Pcorrected

Feed costs comprise the majority of variable expenses in beef cattle systems making feed efficiency an important economic consideration within the beef industry. Due to the expense of recording individual feed-intake phenotypes, a genomic-enabled approach could be advantageous toward improving this economically relevant trait complex. A genome-wide association study (GWAS) was performed using 748 crossbred steers and heifers representing seven sire breeds with phenotypes for ADG and ADFI. Animals were genotyped with the BovineSNP50v2 BeadChip containing approximately 54,000 SNP. Both traits were analyzed using univariate SNP-based (BayesC) and haplotype-based (BayesIM) models and jointly using BayesIM to perform a bivariate GWAS. For BayesIM, a hidden Markov model (HMM) of haplotype segments of variable length was built where haplotypes were mapped to clusters based on local similarity. The estimated HMM was then used to assign haplotype cluster genotypes, instead of SNP genotypes, as latent covariates in a Bayesian mixture model. The number of haplotype clusters at each location was assumed to be either 8 (BayesIM8) or 16 (BayesIM16). A total of three univariate analyses for each trait and two bivariate analyses were performed. Posterior SD (PSD) for ADG were 0.28 (0.08), 0.37 (0.11), 0.37 (0.11), 0.35 (0.11), and 0.35 (0.12) for BayesC, BayesIM8, BayesIM16, BayesIM8 bivariate, and BayesIM16 bivariate, respectively. ADFI PSD were 0.30 (0.07), 0.44 (0.13), 0.42 (0.12), 0.38 (0.10), and 0.38 (0.10) for the same models. The top 1% of 1-Mb windows that explained the largest fraction of genetic variation in common between univariate SNP and haplotype models ranged from 24% to 40% and from 20% to 32% for ADG and ADFI, respectively. Spearmen rank correlations between molecular breeding values from SNP and haplotype-based models in the training data were similar for both traits (>0.96) suggesting that either model would lead to similar rankings of animals, although resolution of potential QTL appeared to be greater for BayesIM.

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses.

AIMS: The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration. METHODS AND RESULTS: Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high‐quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P

Feed costs are a major economic expense in finishing and developing cattle; however, collection of feed intake data is costly. Examining relationships among measures of growth and intake, including breed differences, could facilitate selection for efficient cattle. Objectives of this study were to estimate genetic parameters for growth and intake traits and compare indices for feed efficiency to accelerate selection response. On-test ADFI and on-test ADG (TESTADG) and postweaning ADG (PWADG) records for 5,606 finishing steers and growing heifers were collected at the U.S. Meat Animal Research Center in Clay Center, NE. On-test ADFI and ADG data were recorded over testing periods that ranged from 62 to 148 d. Individual quadratic regressions were fitted for BW on time, and TESTADG was predicted from the resulting equations. We included PWADG in the model to improve estimates of growth and intake parameters; PWADG was derived by dividing gain from weaning weight to yearling weight by the number of days between the weights. Genetic parameters were estimated using multiple-trait REML animal models with TESTADG, ADFI, and PWADG for both sexes as dependent variables. Fixed contemporary groups were cohorts of calves simultaneously tested, and covariates included age on test, age of dam, direct and maternal heterosis, and breed composition. Genetic correlations (SE) between steer TESTADG and ADFI, PWADG and ADFI, and TESTADG and PWADG were 0.33 (0.10), 0.59 (0.06), and 0.50 (0.09), respectively, and corresponding estimates for heifers were 0.66 (0.073), 0.77 (0.05), and 0.88 (0.05), respectively. Indices combining EBV for ADFI with EBV for ADG were developed and evaluated. Greater improvement in feed efficiency can be expected using an unrestricted index versus a restricted index. Heterosis significantly affected each trait contributing to greater ADFI and TESTADG. Breed additive effects were estimated for ADFI, TESTADG, and the efficiency indices.

Cows selected for heifer calving ease and yearling weight might also show changes in other important traits. Cattle from select and control lines within 7 populations were selected for reduced heifer calving difficulty EPD (select) or for average birth weight EPD (control) and for identical yearling weight EPD (select and control). Heifers randomly sampled within sire and born in the 4th and 5th of 7 years of selection were retained until 6 years of age with culling for once open and health, but not for other performance. Both lines were bred to the same bulls for calves born during the 3 years post-selection. Select line heifers were 7% lighter (-2.6 ± 0.5 kg, P < 0.01) at birth and not different at weaning (0.2 ± 1.5 kg) or yearling ages (-2.1 ± 2.7 kg). Select cow mature weights estimated by Brody growth curves were 5.2% lighter (-32.9 ± 3.7 kg, P < 0.01) and heights were 2.2% shorter (-3.0 ± 0.7 cm, P < 0.01) than controls. Calf weaning weights were not different. Interactions between 1st calving select (bred to select bulls) and control heifers (bred to control bulls) vs. older cows (all bred to the same bulls) were significant for survival (P < 0.01) and calving assistance (P = 0.03). Select line heifers increased calf survival (86.8% vs. 70.9%) and had decreased calving assistance (16.4% vs. 39.3%), but differences in cows for these traits were negligible. Calves born per select cow exposed exceeded those born per control cow only for 2nd calving (7.1%, P = 0.04), possibly due to reduced calving difficulty as heifers. Selection for calving ease and yearling weight resulted in cows with smaller mature size and similar or better calving ease, calf survival, and calf weaning weight. USDA is an equal opportunity provider and employer.

We hypothesized cattle that differed in BW gain had different digestive tract microbiota. Two experiments were conducted. In both experiments, steers received a diet that consisted of 8.0% chopped alfalfa hay, 20% wet distillers grain with solubles, 67.75% dry-rolled corn, and 4.25% vitamin/mineral mix (including monensin) on a dry matter basis. Steers had ad libitum access to feed and water. In experiment 1, 144 steers (age = 310 ± 1.5 d; BW = 503 ± 37.2 kg) were individually fed for 105 d. Ruminal digesta samples were collected from eight steers with the greatest (1.96 ± 0.02 kg/d) and eight steers with the least ADG (1.57 ± 0.02 kg/d) that were within ±0.32 SD of the mean (10.1 ± 0.05 kg/d) dry matter. In experiment 2, 66 steers (age = 396 ± 1 d; BW = 456 ± 5 kg) were individually fed for 84 d. Rumen, duodenum, jejunum, ileum, cecum, and colon digesta samples were collected from eight steers with the greatest (2.39 ± 0.06 kg/d) and eight steers with the least ADG (1.85 ± 0.06 kg/d) that were within ±0.55 SD of the mean dry matter intake (11.9 ± 0.1 kg/d). In both studies, DNA was isolated and the V1 to V3 regions of the 16S rRNA gene were sequenced. Operational taxonomic units were classified using 0.03 dissimilarity and identified using the Greengenes 16S rRNA gene database. In experiment 1, there were no differences in the Chao1, Shannon, Simpson, and InvSimpson diversity indexes or the permutation multivariate analysis of variance (PERMANOVA; P = 0.57). The hierarchical test returned six clades as being differentially abundant between steer classifications (P < 0.05). In experiment 2, Chao1, Shannon, Simpson, and InvSimpson diversity indexes and PERMANOVA between steer classified as less or greater ADG did not differ (P > 0.05) for the rumen, duodenum, ileum, cecum, and colon. In the jejunum, there tended to be a difference in the Chao1 (P = 0.09) and Simpson diversity (P = 0.09) indexes between steer classifications, but there was no difference in the Shannon (P = 0.14) and InvSimpson (P = 0.14) diversity indexes. Classification groups for the jejunum differed (P = 0.006) in the PERMANOVA. The hierarchical dependence false discovery rate procedure returned 11 clades as being differentially abundant between steer classifications in the jejunum (P < 0.05). The majority of the OTU were in the Families Corynebacteriaceae and Coriobacteriaceae. This study suggests that intestinal differences in the microbiota of ruminants may be associated with animal performance.

AIMS The objective of the study was to determine levels of Escherichia coli O157:H7 colonization in the gastrointestinal tract (GIT) of naturally shedding cattle shedding the pathogen at low- or super-shedder levels. METHODS AND RESULTS Over 2 years, feedlot cattle were sampled multiple times for faecal shedding of E. coli O157:H7. Just prior to harvest (1-2 days), animals that were super-shedders (≥104 CFU per gram of faeces) were specifically identified, and based on the longer term screening data, pen cohorts that were low-shedders (years 1 and 2) or chronic-shedders (year 1) were also identified. At harvest, samples were collected from throughout the GIT, including the rectoanal junction (RAJ) for enumeration and enrichment of E. coli O157:H7. The mouth samples exhibited the greatest prevalence for the pathogen, and the abomasum and rumen exhibited the lowest prevalence (P

Ghrelin is a peptide hormone produced in the gut that is implicated in signaling appetite and regulating dry matter intake (DMI). The objective of this experiment was to determine the change in acyl ghrelin, total ghrelin, and the ghrelin ratio (acyl ghrelin/total ghrelin) over an 84-d DMI and average daily BW gain (ADG) measurement period and to determine the association of those ghrelin measurements with DMI, ADG, ADG:DMI ratio (G:F), and residual feed intake in finishing beef steers and heifers. Blood samples were collected on day 0 and day 83 before feeding and between 0730 h and 1130 h. Samples were analyzed for acyl and total ghrelin using commercially available RIA. DMI in steers was greater during the last 35-d period of the experiment compared with the first 35 d (P < 0.01) and was greater than heifers regardless of period (P < 0.01). Steers had greater acyl ghrelin concentrations on day 0 than heifers, but concentrations decreased by day 83 to equal concentrations in heifers (P < 0.01). Total ghrelin concentrations were lower on day 0 in heifers but increased by day 83 and did not differ from steers on day 83 (P < 0.01). A mixed model analysis was used to determine the association of ghrelin concentrations and ratio with production traits, independent of breed and sire effects. There was an interaction of day 0 acyl ghrelin concentrations with time of sample collection for 84-d DMI (P < 0.01), ADG (P < 0.01), and G:F (P = 0.09), indicating a general positive association of acyl ghrelin with production traits, but the association weakened as time of sample collection increased. The mean ghrelin ratio tended (P = 0.08) to be positively associated with DMI in the last 35-d period. The ghrelin ratio on day 0 interacted with time of sample collection for ADG and G:F (P < 0.05), indicating an overall positive association of the ghrelin ratio with ADG and G:F. Results indicate that ghrelin is associated with DMI, ADG, and feed efficiency of finishing beef cattle, and data lend more evidence that ghrelin is involved in appetite regulation of ad libitum fed cattle.

Diets high in protein are associated with lower reproductive performance and changes in the uterine environment. The objective of this study was to determine the effect of elevated systemic concentrations of urea nitrogen on the uterine environment and pregnancy success in beef heifers. Heifers (n=150) were matched by breed, age, and body weight then randomly assigned to one of two dietary treatments: 1) Control (10% CP) or 2) High protein (14% CP) over three replicates (n=40/replicate). Estrus was synchronized with an injection of PGF2α. Uterine pH, plasma urea nitrogen (PUN), ammonia, and glucose concentrations were determined on d 7 of the estrous cycle. Pregnancy status was determined by ultrasonography 30 d following the breeding season. In vitro fertilization was performed on heifers precluded from uterine analysis (n=15/diet) to determine the effect of a High Protein diet on oocyte quality. Plasma urea concentrations were greater in the High Protein diet compared to Control (P0.001). There was no effect of diet on plasma ammonia (P=0.12), plasma glucose (P=0.40), uterine pH (P=0.67), interval to estrus (P=0.54), duration of estrus (P=0.38), or pregnancy rate (P=0.83). There was no effect of diet (P0.40) on the number of oocytes collected, number of oocytes cleaved, amount of blastocysts, percentage of oocytes cleaved and percentage of blastocysts present. In summary, high nitrogen diets increased PUN concentrations in heifers; however, there were no deleterious effects on reproduction.

Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq platform were used to generate V1-V3 sequence, while long "circular consensus" reads from the Pacific Biosciences RSII instrument were used to generate V1-V8 data. The two platforms revealed similar microbial operational taxonomic units (OTUs), as well as similar species richness, Good's coverage, and Shannon diversity metrics. However, the V1-V8 amplified ruminal community resulted in significant increases in several orders of taxa, such as phyla Proteobacteria and Verrucomicrobia (P < 0.05). Taxonomic classification accuracy was also greater in the near full-length read. UniFrac distance matrices using jackknifed UPGMA clustering also noted differences between the communities. These data support the consensus that longer reads result in a finer phylogenetic resolution that may not be achieved by shorter 16S rRNA gene fragments. Our work on the cattle rumen bacterial community demonstrates that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to use in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing.

Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. For more information, see “Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers” P.R. Myer, M. Kim, H.C. Freetly, T.P.L. Smith (2016) [1]. Keywords: 16S rRNA gene, MiSeq, Pacific Biosciences, Rumen microbiome

Small intestine mass and cellularity were previously associated with cattle feed efficiency. The small intestine is responsible for the digestion of nutrients and absorption of fatty acids, amino acids and carbohydrates, and it contributes to the overall feed efficiency of cattle. The objective of this study was to evaluate transcriptome differences among the small intestine from cattle with divergent gain and feed intake. Animals most divergent from the bivariate mean in each of the four phenotypic Cartesian quadrants for gain × intake were selected, and the transcriptomes of duodenum, jejunum and ileum were evaluated. Gene expression analyses were performed comparing high gain vs. low gain animals, high intake vs. low intake animals and each of the phenotypic quadrants to all other groups. Genes differentially expressed within the high gain-low intake and low gain-high intake groups of animals included those involved in immune function and inflammation in all small intestine sections. The high gain-high intake group differed from the high gain-low intake group by immune response genes in all sections of the small intestine. In all sections of small intestine, animals with low gain-low intake displayed greater abundance of heat-shock genes compared to other groups. Several over-represented pathways were identified. These include the antigen-processing/presentation pathway in high gain animals and PPAR signaling, starch/sucrose metabolism, retinol metabolism and melatonin degradation pathways in the high intake animals. Genes with functions in immune response, inflammation, stress response, influenza pathogenesis and melatonin degradation pathways may have a relationship with gain and intake in beef steers.

Feed costs are the most expensive input in beef production. Improvement in the ability of beef cattle to convert feed into meat would lower feed inputs and reduce the cost of production. The rumen epithelium is responsible for absorption and metabolism of nutrients and microbial by-products, and may play a significant role in gain or feed intake. Our objective was to determine the relationships among rumen papillae morphology, gene expression, volatile fatty acid concentrations, and gain and feed intake. Average daily gain (ADG) and average daily feed intake (ADFI) were collected on a crossbred population of beef steers over three feeding trials. Based on feed intake and weight gain differences, 48 steers were selected for the project (16 from each feeding study). At harvest, rumen epithelial samples were taken from three locations in the rumen of each animal. The number of papillae on 1 cm 2 of epithelium was counted to determine density. Papillae ( n =30) from each sample were measured for length and width. The density, length, and width were combined to determine surface enlargement factor (SEF). None of the morphological characteristics of the papillae (length, width, density or SEF) were associated with feed intake or gain ( P ≥0.10). Ruminal fluid was collected from steers ( n =15) in the third trial for volatile fatty acid (VFA) analysis to determine if a relationship between VFA and ADG or ADFI existed. No differences in volatile fatty acid (VFA) concentrations were associated ( P ≥0.17) with ADFI or ADG. VFA variation was also evaluated for a relationship with kallikrein ( KLK ) genes since ruminal butyrate concentrations have previously been associated with the transcript abundance KLK genes. Additionally, qRT-PCR data showed that variation in the transcript abundance of KLK6,8-10, and 13 associated with feed intake in our first trial of steers. Thus, we evaluated the transcript abundance of eight KLK genes in rumen papillae from steers in the third trial ( n =16). Expression levels of KLK5 correlated with valerate concentrations in the rumen ( P , KLK10 correlated with acetate concentrations in the rumen ( P KLK12 correlated with acetate and butyrate concentrations in the rumen ( P KLK9 and KLK10 were associated with gain. While rumen papillae morphology was not associated with beef steer gain or intake, our data suggests members of the kallikrein gene family have a relationship with the VFA environment in the rumen, and also appear to play a role in the highly correlated traits of ADG and ADFI.

Ractopamine hydrochloride (RAC) is used in the feedlot industry to increase daily gain, improve feed efficiency, and increase HCW. However, little work has been done to determine whether additional protein is needed in the diet to maximize the benefit of RAC in beef cattle. Objectives of our experiment were to determine if feeding additional CP in conjunction with RAC would improve animal performance and carcass characteristics. Therefore, an experiment was conducted using finishing diets containing 13.5 or 17.5% CP with 0 or 300 mg of RAC for 30 to 33 d at the end of the finishing period. Beef steers ( = 438; 387.8 ± 1.9 kg initial BW) were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial arrangement (16 pens total, 4 pens/treatment). No interactions between feeding RAC and CP level were detected ( > 0.19) for animal performance or carcass traits. Final BW did not differ among treatment ( = 0.37); however, final BW had a tendency to be 2% greater ( = 0.07) when the 13.5% CP diet was fed. Dry matter intake was not different between steers fed 0 or 300 mg/d of RAC ( = 0.20), yet DMI was 12% greater for cattle fed the 13.5% CP compared with steers fed the 17.5% CP diet ( 0.16). The G:F was 3.6% greater for cattle fed 300 vs. 0 mg/d of RAC ( = 0.04). The G:F was 8.7% greater for cattle fed the 17.5% diet vs. the 13.5% CP diet ( 0.26). Additionally, no differences in USDA yield grade or percentage of cattle grading USDA Choice were detected for RAC or CP treatments ( > 0.26), which also supports the idea that quality grade of cattle fed RAC at the same level of fatness is not impacted. Our data indicate excess protein did not enhance the response to RAC, and furthermore, the improved performance from RAC reported by others was not observed other than a small increase in G:F.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation.

Research regarding the association between the microbial community and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when determining the interplay between host and nonhost factors affecting feed efficiency. The objective of this study was to characterize the microbial communities of the jejunum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual ADFI and ADG were determined from animals fed the same diet. At the end of each feeding period, steers were ranked based on their standardized distance from the bivariate mean (ADG and ADFI). Four steers with the greatest deviation within each Cartesian quadrant were sampled ( = 16/group; 2 groups). Bacterial 16S rRNA gene amplicons were sequenced from the jejunum content using next-generation sequencing technology. The phylum Firmicutes accounted for up to 90% of the populations within all samples and was dominated by the families Clostridiaceae and Ruminococcaceae. UniFrac principal coordinate analyses did not indicate any separation of microbial communities within the jejunum based on feed efficiency phenotype, and no significant changes were indicated by bacterial diversity or richness metrics. The relative abundances of microbial populations and operational taxonomic units did reveal significant differences between feed efficiency groups ( < 0.05), including the phylum Proteobacteria ( = 0.030); the families Lachnospiraceae ( = 0.035), Coriobacteriaceae ( = 0.012), and Sphingomonadaceae ( = 0.035); and the genera ( = 0.019), ( = 0.018), and ( = 0.022). The study identified jejunal microbial associations with feed efficiency, ADG, and ADFI. This study suggests the association of the jejunum microbial community as a factor influencing feed efficiency at the 16S level.

The objective of this experiment was to determine the association of glucocorticoids and markers for immune status in finishing beef steers and heifers with DMI, growth, and efficiency. Steers ( = 127) and heifers ( = 109) were individually fed a finishing ration for 84 d with BW measured every 21 d. Blood samples were collected via jugular venipuncture for metabolite (glucose and lactate) and cortisol analysis and rectal grab samples of feces were collected for corticosterone analysis on d 83 of the experiment. Plasma cortisol was not correlated to DMI ( = -0.08, > 0.05) or fractional DMI (g DMI/kg BW; = -0.03, > 0.05) but was negatively correlated with ADG ( = -0.17, 0.05) but fecal corticosterone was positively associated with fractional DMI only in heifers ( = 0.04). Plasma lactate ( < 0.01) was and plasma cortisol ( < 0.10) tended to be negatively associated with ADG. Plasma cortisol ( < 0.05) and fecal corticosterone tended ( < 0.10) to be negatively associated with G:F. Fecal corticosterone was positively associated with RFI in heifers ( < 0.04). In a mixed model analysis, total leukocyte count was positively associated with ADG ( < 0.04) and tended to be positively associated with G:F ( < 0.06). Among leukocyte subtypes, neutrophil count was positively associated with ADG in steers ( < 0.02) and monocytes were positively associated with ADG in heifers ( < 0.03). Lymphocyte counts (LY) in steers were negatively associated with DMI ( = 0.03) and fractional DMI ( < 0.03). In heifers, LY tended to be positively associated with DMI ( < 0.09) and fractional DMI ( < 0.06). Lymphocyte count was also positively associated with ADG ( < 0.01) and G:F ( = 0.05) in heifers. The association of production traits with immune status seems to be different between steers and heifers. There was a stronger relationship of cortisol than fecal corticosterone to feed efficiency measures, suggesting that cortisol concentrations could be a better marker for feed efficiency traits than fecal corticosterone concentrations.

The bovine rumen papillae are in contact with a wide array of microorganisms and the metabolites they produce, which may activate an inflammatory and/or immune response. Cytokines, chemokines and their receptor genes were tested for differential expression in the rumen and jejunum of beef steers with greater and lesser average daily body weight gain (ADG) near the average daily dry matter intake (DMI) for the population. Angus-sired steers (n = 16) were used to represent the greater (ADG = 2.2 ± 0.07 kg/day; DMI = 10.1 ± 0.05 kg/day) and lesser (ADG = 1.7 ± 0.05 kg/day; DMI = 10.1 ± 0.05 kg/day) ADG groups with eight steers each. Rumen epithelium and jejunum mucosal samples were collected at slaughter, and gene expression was evaluated using a commercially available qRT-PCR array containing 84 genes representing chemokines, cytokines and their receptors. None of the genes on the array were differentially expressed in the jejunum of the steers with greater vs. lesser ADG. However, in the rumen, two chemokine genes (CCL11, CXCL5) and one receptor gene (IL10RA) were detected as differentially expressed (P < 0.05). The genes IL1A, BMP2, CXCL12 and TNFSF13 also displayed trends for differential expression (P < 0.10). All of the genes identified were lower in transcript abundance in the greater ADG animals. Thus, greater ADG steers have a lesser inflammatory response in the rumen papillae, which may lead to a more efficient use of nutrients.

Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake. RNA-Seq was used to evaluate the transcript abundance of genes in the mesenteric fat from a total of 78 steers collected over 5 different cohorts. A meta-analysis was used to identify genes involved with gain, feed intake or the interaction of both phenotypes. The interaction analysis identified 11 genes as differentially expressed. For the main effect of gain, a total of 87 differentially expressed genes (DEG) were identified (PADJ

Feed costs account for over 70% of the annual expenditures in cow/calf production. During the production year the cow uses nutrients to support conceptus growth, milk production, work (grazing and locomotion), and maintenance requirements. The majority of the nutrients are used to support maintenance. Substrate cycling has been identified as one of the major contributors toward energy expenditure associated with maintenance in mature cows. The objective of this study was to determine whether beef cows that differ in the efficiency of weight gain differ in the relative abundance of transcripts for metabolic regulation in adipose tissue. Mature beef cows were subjected to feed restriction followed by ad libitum feed. Adipose tissue from twelve cows with high (n = 6) and low (n = 6) gain based on growth performance during the ad libitum feeding period was evaluated for transcriptome expression differences. A total of 496 genes were differentially expressed and passed Bonferroni correction for the animals with greater gain between restriction and realimentation and 491 genes were differentially expressed among animals with lesser gains between feed restriction and realimentation. Of these two differentially expressed gene lists, 144 genes were common between animals with greater and those with lesser gain. Enriched biological processes included the TCA cycle, oxidative phosphorylation, respiratory electron transport chain and fatty acid metabolic processes. Specific to adipose tissue of low gaining animals was glycolysis and to high gain animals was coenzyme, steroid, cellular amino acid, nitrogen compound metabolic processes, and sensory perception. The oxidative phosphorylation, mitochondrial dysfunction and cholesterol biosynthesis pathways were commonly associated with the high gain animals between feed restriction and realimentation, as well as with the low gaining animals between the two time points. Unique to the high gaining animals were valine degradation and LPS/IL-1 mediated inhibition of RXR function pathways. In this discovery study, genes involved in lipid metabolism, mitochondrial respiration and oxidative phosphorylation pathways appear to be critical to mature cows during times of abundant feed after feed restriction.

The objective of this 2-yr study was to evaluate growing and finishing performance as well as carcass characteristics of spring-born steers backgrounded on 3 different systems, using feedstuffs readily available in the Midwest: 1) grazing corn residue and being supplemented with dried distillers plus solubles at 2.68 kg DM/steer 6 d/wk (RESIDUE), 2) grazing a late summer–planted oat–brassica forage mix (CCROP), or 3) being fed a corn silage–based diet in a drylot (DRYLOT). Steers (n = 715) were stratified by BW (278 kg ± 23 in yr 1 and 291 kg ± 91 in yr 2) and assigned to treatment and replicate (4 replications per treatment per yr). Steers assigned to DRYLOT were fed a corn silage–based diet for 54 d in yr 1 and 52 d in yr 2 before being transitioned to the finishing diet. Steers assigned to RESIDUE and those assigned to CCROP grazed 65 d in yr 1 and 66 d in yr 2 and then were fed a corn silage–based diet for 21 d in yr 1 and 33 d in yr 2 before being transitioned to the finishing diet. During backgrounding, the ADG (SEM 0.022) of steers assigned to DRYLOT (1.48 kg/d) was greater (P < 0.01) than that of steers assigned to both CCROP (1.05 kg/d) and RESIDUE (0.87 kg/d) and ADG of steers assigned to CCROP was greater (P < 0.01) than that of steers assigned to RESIDUE. At the start of the finishing period, BW of steers assigned to CCROP (381 kg) was greater (P < 0.01, SEM 2.5) than that of steers assigned to DRYLOT (361 kg) and RESIDUE (366 kg). The finishing period lasted 160 d for all treatments. Both 12th-rib fat (P = 0.89) and calculated yield grade (P = 0.39) did not differ among treatments. Finishing G:F of steers assigned to DRYLOT (0.162 kg/kg) was greater (P < 0.01, SEM 0.0015) than that of steers assigned to RESIDUE (0.153 kg/kg) and CCROP (0.153 kg/kg), which did not differ (P = 0.79). In yr 1, HCW of steers assigned to CCROP (402 kg) was greater (P < 0.01, SEM 2.1) than that of steers assigned to both RESIDUE (389 kg) and DRYLOT (391 kg), which did not differ (P = 0.40). This difference in HCW is most likely a result of differences in BW at the start of the finishing phase in yr 1. However in yr 2, HCW of steers assigned to CCROP (400 kg) and RESIDUE (397 kg) did not differ (P = 0.26, SEM 2.1) but were greater (P < 0.01) than that of steers assigned to DRYLOT (367 kg), despite the fact that steers assigned to RESIDUE entered the finishing phase at a lighter BW than steers assigned to CCROP. Marbling was greater (P = 0.01, SEM 3.9) for steers assigned to DRYLOT (429) than for steers assigned to RESIDUE (414), although steers assigned to CCROP (424) were not different (P ≥ 0.10) from steers assigned to DRYLOT or RESIDUE. When cost and price scenarios from the last 5 yr were conducted, no treatment appeared to be consistently superior in terms of cost of gain or net return. Therefore, all 3 systems appear to be viable options for producers.

The purpose of this study was to identify differentially expressed genes (DEG) in the mesenteric fat associated with body weight gain that will be robust across a large segment of the cattle industry. Crossbred steers with high and low body weight gain and feed intake (2x2 factorial design) were selected from five different cohorts over three years. RNA sequencing was performed on mesenteric fat from the 80 selected steers (5 cohorts, each with 16 animals). A meta-analysis procedure was used to identify DEG across the five cohorts. Analyses for DEG were performed separately on each cohort using a generalized linear model with body weight gain and feed intake as main effects, and the resulting P-values were combined into a meta-P-value. A total of 41 DEG were associated with the main effect of gain in the meta-analysis (meta-PFDR< 0.05). These DEG were enriched for functions related to fatty acid metabolism due to the expression of ACLY, ACSM3, ACSL3. Genes that did not cluster into biological processes or pathways have functions in cell signaling, cell proliferation, oxidative stress, molecular chaperone, as well as immune and inflammatory responses were also identified. In this study, there were considerable differences between the DEG identified in each of the individual cohort analyses; however, the use of a meta-analysis allowed the identification of genes across these cohorts that were associated with weight gain in beef steers. These genes will be important for further evaluation to elucidate and validate their functional roles in body weight gain in cattle. USDA is an equal opportunity provider and employer.

The objective of this 2-yr study was to evaluate the performance of steers grazing a late summer planted oat monoculture (OAT) compared to a mixture (MIX) of oats (Avena sativa) and rapeseed (Brassica napus). The three 52 ha fields (one in yr 1 and two in yr 2) were divided into four quarters and two quarters being planted in late August with 112 kg/ha of oats and two with 56 kg/ha of oats plus 3.4 kg/ha of rapeseed at a seed cost of $62/ha for OAT and $38/ha for MIX. Crossbred beef steers, 120 in yr 1 and 240 in yr 2, were stratified by BW (280 ± 32 kg) and assigned to treatment and replicate (30 steers/13 ha quarter). Forage biomass and quality samples were taken before turning out to graze in early November. Initial forage yield did not differ (P = 0.80; SEM±635) among treatments (3,610 and 3,779 kg DM/ha for MIX and OAT, respectively). The MIX contained 73% oats and 27% rape (on DM basis). The CP (SEM±1.6) and IVOMD (SEM±0.82) content of the forage was greater (P ≤ 0.04 for the MIX (20.5%; 78.4%) than OAT (16.1%; 75.7%), respectively. Steers grazed until forage appeared to be limiting for one of the quarters, resulting in 99 d of grazing in yr 1 and 71 d in yr 2. Ending forage biomass tended (P = 0.09; SEM±119) to be greater for OAT compared to MIX at 1,741 and 1,476 kg DM/ha, respectively. There was a tendency (P = 0.07; SEM±0.03) for ADG to be greater for the MIX (0.96 kg/d) than OAT (0.88 kg/d). The lower seed costs coupled with increased gain suggests that adding rapeseed to oats may be beneficial for producers grazing growing calves in fall.

Using results from a previous GWAS, we chose to evaluate seven genes located within a 229Kb region on BTA15 for variation in RNA transcript abundance in a library of tissue samples that included adipose, liver, rumen papillae, spleen, muscle, and small intestine epithelial layers from the duodenum, ileum and jejunum collected from steers (n = 14) with positive and negative residual GN near mean dry matter intake (DMI). The genes evaluated were two olfactory receptor-like genes (LOC525033 and LOC618173), RRM1, STIM1, RHOG, PGAP2, and NUP98. The rumen papillae transcript abundance of RHOG was positively correlated with residual GN (P = 0.02) and ruminal STIM1 exhibited a trend towards an association with residual GN (P = 0.08). The transcript abundance of one olfactory receptor (LOC618173) in the ileum was also positively associated with residual GN (P = 0.02) and PGAP2 and LOC525033 in the ileum displayed trends for association with GN (P ≤ 0.1). To further evaluate the differential expression detected in the ileum and rumen of these animals, the transcript abundance of STIM1 and RHOG in the rumen and of PGAP2 and the olfactory receptors in the ileum were assessed in an additional group of 32 animals with divergent average daily gain (ADG) and average daily feed intake (ADFI) collected over two groups. The olfactory receptor, LOC525033, was not expressed in the ileum for the majority of these animals. Only RHOG showed a slight, but non-significant trend towards greater expression in animals with greater gain. We have detected differences in the transcript abundance of genes within this region in the rumen and ileum of animals selected for greater and less residual gain; however, we were unable to validate the expression of these genes in the larger group of cattle possibly due to the differences in phenotype or contemporary group.

Apart from the rumen, limited knowledge exists regarding the structure and function of bacterial communities within the gastrointestinal tract and their association with beef cattle feed efficiency. The objective of this study was to characterize the microbial communities of the cecum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual feed intake and BW gain were determined from animals fed the same diet. Within both of 2 contemporary groups, BW was regressed on feed intake and 4 steers within each Cartesian quadrant were sampled ( = 16/group). Bacterial 16S rRNA gene amplicons were sequenced from the cecal content using next-generation sequencing technology. No significant changes in diversity or richness were detected among quadrants, and UniFrac principal coordinate analysis did not show any differences among quadrants for microbial communities within the cecum. The relative abundances of microbial populations and operational taxonomic units revealed significant differences among feed efficiency groups ( < 0.05). Firmicutes was the dominant cecal phylum in all groups and accounted for up to 81% of the populations among samples. Populations were also dominated by families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae, with significant shifts in the relative abundance of taxa among feed efficiency groups, including families Ruminococcaceae ( = 0.040), Lachnospiraceae ( = 0.020), Erysipelotrichaceae ( = 0.046), and Clostridiaceae ( = 0.043) and genera ( = 0.049), ( = 0.044), ( = 0.042), ( = 0.040), ( = 0.042), and ( = 0.042). The study identified cecal microbial associations with feed efficiency, ADG, and ADFI. This study suggests an association of the cecum microbial community with bovine feed efficiency at the 16S level.

Peripubertal caloric restriction increases primordial follicle numbers at breeding, which may improve reproductive potential. Our hypothesis was that feed restriction was changing primordial follicle number through stimulation of follicle formation via leptin, roundabout axon guidance receptor, homolog 4 (), or or through inhibition of follicle activation via anti-Mullerian hormone (). Heifers ( = 30) were fed a ration consisting of 30% alfalfa hay, 69.8% corn silage, and 0.2% salt as DM. Heifers received the control diet for 42 d before an initial 6 heifers were ovariectomized at 8 mo of age. The remaining 24 heifers were divided into 2 treatment groups. Controls were offered 97.9 g DM/kg BW over the entire feeding period. Stair-step heifers received 67.4 g DM/kg BW for 84 d. Following the 84-d restriction, heifers were stepped up to receive 118.9 g DM/kg BW over a 15-d period and were held at this feeding level 68 d. At the end of the feed restriction (11 mo of age), ovaries were collected from 6 heifers per treatment, and at the end of the refeeding period (13 mo of age), ovaries were collected from 6 heifers per treatment. Plasma leptin concentrations were greater in control heifers than in stair-step heifers at 11 mo of age ( 0.10). In conclusion, developing heifers on a stair-step compensatory growth scheme resulted in larger ovarian reserve before the onset of breeding, which may have beneficial effects on increasing reproductive lifespan.

The objective of this experiment was to determine the association of serum leptin concentrations with production measures including DMI, ADG, and G:F as well as carcass characteristics in genetically diverse finishing beef steers. Three cohorts of steers ( = 473 total) were individually fed a finishing ration for 92, 64, and 84 d for cohort 1, 2, and 3, respectively. Serum was collected on d 42, 22, and 19 of the experiment for cohort 1, 2, and 3, respectively. Leptin concentrations were positively correlated to DMI ( = 0.21, < 0.01) but negatively correlated to grams DMI per kilogram initial BW ( = -0.21, < 0.01). Leptin concentrations were also negatively correlated to ADG and G:F ( < 0.01). Leptin concentrations were positively correlated to 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and negatively correlated to LM area ( < 0.01). Using a mixed model analysis (SAS 9.3; SAS Inst. Inc., Cary, NC) to account for breed effects, leptin concentrations were positively associated with DMI ( = 0.01) and accounted for 1.10% of the variance. However, if initial BW and yield grade were included as covariates to account for body size and fatness, leptin was negatively associated with DMI ( = 0.02) and accounted for 0.54% of the variance. Regardless of covariates included in the model, leptin was negatively associated with ADG ( < 0.01) and G:F ( < 0.01) and accounted for 2.62 and 7.87% of the variance for ADG and G:F, respectively. Leptin concentrations were also positively associated with 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and accounted for 14.74, 12.74, and 6.99% of the variance for 12th-rib fat, yield grade, and marbling score, respectively. Leptin concentrations could be a useful physiological marker for growth and feed efficiency of finishing beef cattle. Genetic influences on the biology of leptin also need to be considered when using leptin as physiological marker for production measures.

Methane (CH4) gas released by cattle isa product of fermentation in the digestive tract. The 2 primary sites of CH4 production in ruminants are the reticulum-rumen complex and the cecum. Methane release from cattle represents a 2% to 12% loss of the energy intake. Reducing the proportion of feed energy lost as CH4 has the potential of improving feed efficiency as well as decreasing the contribution of cattle to greenhouse gas production. Feed intake and growth were measured on 132 fall-born steers for 70 d. Seven steers with extreme positive residual gain (RG) and 7 steers with extreme negative RG whose DMI was within 0.32 SD of the mean intake were selected for subsequent measurements. Enteric CH4 production was measured via indirect calorimetry. Rumen, cecum, and rectal contents were obtained from steers at slaughter for measurement of in vitro CH4 production and methanogen 16S rRNA levels. Enteric CH4 production did not differ (P = 0.11) between the positive RG (112 ± 13 L/d)and the negative RG (74 ± 13 L/d) steers. In vitro rumen methane production did not differ between positive RG(64.26 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (61.49 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1)DM∙min(-1); P = 0.86). In vitro cecum methane production did not differ between positive RG (4.24 ×10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (4.35 × 10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1); P = 0.97). Methanogen 16S rRNA as a percentage of the total bacteria16S rRNA did not differ between RG groups (P = 0.18). The methanogen 16S rRNA as a percentage of rumen fluid total bacteria 16S rRNA (5.3% ±3.1%) did not differ from the methanogen 16S rRNA asa percentage of cecum content total bacteria 16S rRNA(11.8% ± 3.1%; P = 0.14). The methanogen 16S rRNA as a percentage of the rectum content total bacteria 16SrRNA (0.7% ± 3.1%) was not different from the rumen content (P = 0.29) but was less than the cecum content(P = 0.01). Methanomicrobiales 16S rRNA as a percentage of total methanogen 16S rRNA did not differ across sample sites (P = 0.81); however, steers with positive RG (10.5% ± 1.6%) were more numerous than steers with negative RG (5.1% ± 1.6%; P = 0.02). Cattle that differ in RG at the same DMI do not differ in characteristics associated with CH4 production.

Expansion of the biodiesel industry has increased the glycerin (GLY) supply. Glycerin is an energy-dense feed that can be used in ruminant species; however, the energy value of GLY is not known. Therefore, the effects of GLY inclusion at 0, 5, 10, and 15% on energy balance in finishing cattle diets were evaluated in 8 steers (BW = 503 kg) using a replicated Latin square design. Data were analyzed with the fixed effects of dietary treatment and period, and the random effects of square and steer within square were included in the model. Contrast statements were used to separate linear and quadratic effects of GLY inclusion. Glycerin replaced dry-rolled corn (DRC) at 0, 5, 10, and 15% of dietary DM. Dry matter intake decreased linearly (P = 0.02) as GLY increased in the diet. As a proportion of GE intake, fecal energy loss tended to decrease linearly (P 0.31) as a proportion of GE as GLY increased in the diet. Methane energy loss as a proportion of GE intake tended to respond quadratically (P = 0.10), decreasing from 0 to 10% GLY inclusion and increasing thereafter. As a proportion of GE intake, ME tended to respond quadratically (P = 0.10), increasing from 0 to 10% GLY and then decreasing. As a proportion of GE intake, heat production increased linearly (P = 0.02) as GLY increased in the diet. Additionally, as a proportion of GE intake, retained energy (RE) tended to respond quadratically (P = 0.07), increasing from 0 to 10% GLY inclusion and decreasing thereafter. As a proportion of N intake, urinary and fecal N excretion increased linearly (P < 0.04) as GLY increased in the diet. Furthermore, grams of N retained and N retained as a percent of N intake both decreased linearly (P < 0.02) as GLY increased in the diet. Total DM digestibility tended (P < 0.10) to respond quadratically, increasing at a decreasing rate from 0 to 5% GLY inclusion. Overall, RE tended to decrease as GLY increased in the diet in conjunction with a decrease in N retention, which could indicate an increased metabolic cost to the animal associated with feeding GLY. Based on RE, the feeding value of GLY in high-concentrate diets is greater than DRC at 5 and 10% of DM but less at 15% of DM.

The use of genetic markers to aid in selection decisions to improve carcass and growth characteristics is of great interest to the beef industry. However, it is important to examine potential antagonistic interactions with fertility in cows before widespread application of marker-assisted selection. The objective of the current experiment was to examine the influence of 2 commercially available markers currently in use for improving carcass traits, the myostatin (MSTN) F94L and μ-calpain (CAPN1) 316 and 4751 polymorphisms, on heifer development and reproductive performance. In Exp. 1, beef heifers (n = 146) were evaluated for growth and reproductive traits over a 3-yr period to determine if these polymorphisms influenced reproductive performance. In Exp. 2, heifers representing the 2 homozygous genotypes for the MSTN F94L polymorphism were slaughtered on d 4 of the estrous cycle and reproductive tracts were collected for morphological examination. In Exp. 1, there was a tendency (P = 0.06) for birth BW to be affected by MSTN with the Leu allele increasing birth BW in an additive fashion. Additionally, MSTN significantly affected the proportion of pubertal heifers by the start of the breeding season (P 0.15). The GT haplotype of CAPN1, which was previously associated with decreased meat tenderness, was associated with an additive decrease in birth BW of the first calf born to these heifers (P 0.05). From these results, we concluded that the MSTN F94L and CAPN1 polymorphisms can be used to improve carcass traits without compromising fertility in beef heifers. The influence of these markers on cow performance and herd life remains to be determined. While the delay in puberty associated with the MSTN F94L polymorphism did not negatively impact reproductive performance in heifers, caution should be used when combining this marker with other markers for growth or carcass traits until the potential interactions are more clearly understood.

Replacing cows in the herd is second only to nutrition as the single greatest input cost in cow/calf beef production. The increased availability of cereal grains for feeding livestock has allowed replacement heifers to enter the production system at younger ages. Many heifer development programs feed to ensure heifers reach puberty before the time that they are mated to calve at 2 yr of age. Nutrition level during development has been associated with altered milk production and stayability. We hypothesized that heifers exposed to a lower nutrition level during the peripubertal period would have less methylation of the DNA in the mammary gland and ovarian cortex. We also hypothesized that the ovarian reserve would decrease in heifers fed for rapid growth compared to heifers fed for slow growth during puberty. At 257±1 d of age, heifers in the Stair-Step treatment (n=6) received 157 kcal ME/BW kg0.75 for 84 d and heifers in the Conventional treatment (n=6) were offered 228 kcal ME/BW kg0.75. At d 84, heifers were fed for an additional 83 d. Stair-Step heifers were offered 277 kcal ME/BW kg0.75, and heifers on the Conventional treatment received 228 kcal ME/BW kg0.75. Mammary weights (P=0.43), capillary area density (P=0.74), and capillary surface density (P=0.18) did not differ between treatments and neither did alveolar number (P=0.55) and alveolar density (P=0.49). Reproductive tract weights (P=0.69) and ovarian weight (P=0.68) and ovarian size (P>0.75) did not differ between treatments. In histological sections, Stair-Step heifers had more primordial follicles than Conventional heifers (P=0.02), but primary (P=0.59) and secondary (P=0.15) follicles did not differ. Global methylation of parenchymal tissue (P=0.82), mammary fat pad (P=0.45), and ovarian cortex (P=0.14) did not differ between treatments. Anterior pituitary weight did not differ between treatments (P=0.16). Our hypothesis that modifying peripubertal nutrition modifies global methylation of the mammary and ovary is not supported; however, our hypothesis that it modifies the ovarian reserve is supported.

Ruminal genes differentially expressed in crossbred beef steers from USMARC with variation in gain and feed intake were identified in a previous study. Several of the genes identified with expression patterns differing between animals with high gain-low feed intake and low gain-high feed intake were evaluated in a separate, unrelated population of Angus × Hereford beef steers from the University of Wyoming that was classified to differ in residual feed intake (RFI). Of the 17 genes tested, two were differentially expressed by RFI class in the Angus × Hereford animals. These genes included NAD(P)H dehydrogenase, quinone 1 (NQO1; P = 0.0009) and regulator of G-protein signaling 5 (RGS5; P = 0.01). A third gene, acetyl-CoA acetyltransferase 1 (ACAT1; P = 0.06), displayed a trend toward association with RFI. These data suggest that some of the genes identified in a previous rumen transcriptome discovery study may have utility for identifying or selecting for animals with superior feed efficiency phenotypes across cattle breeds and populations.