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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Nutrition, Growth and Physiology » Research » Research Project #433257

Research Project: Improve Nutrient Management and Efficiency of Beef Cattle and Swine

Location: Nutrition, Growth and Physiology

2022 Annual Report

Objective 1: Determine the effects of dietary changes on efficiency of growth and nutrient utilization of beef cattle and swine. Sub-objective 1A: Prediction of dry matter intake from neutral detergent fiber concentration. Sub-objective 1B: Determine the effects of feed additives on feed efficiency. Sub-objective 1C: Evaluate the use of an antibiotic alternative in swine. Objective 2: Improve determination of dynamic changes in nutrient requirements as the animal's physiological status changes to allow for timed nutrient delivery. Objective 3: Use novel forage systems for growing and maintaining beef cattle. Objective 4: Determine metabolic and physiological mechanisms responsible for variation in feed efficiency that is under genetic control. Sub-objective 4A: Evaluate genetic relationships with feed efficiency. Sub-objective 4B: Effects of metabolites and hormones on feed efficiency. Sub-objective 4C: Relationships between mitochondrial function and feed efficiency. Objective 5: Determine the environmental factors that contribute to the variation in feeding behavior, growth, and well-being of livestock. Sub-objective 5A: Novel methods for early detection of illness. Sub-objective 5B: Relationships between swine feeding behavior with feeder size and placement. Sub-objective 5C: Effects of weather on cattle well-being and feeding behavior.

Feed costs represent the single largest input in both beef and swine production; however, less than 20% of the energy from feed is converted to edible product. Improving the efficiency that feed is converted to animal products has the potential to improve the economic efficiency of animal production while also improving the sustainability of animal agriculture. To maximize feed efficiency the correct profile of nutrients are matched to meet an animal’s needs for its current biological status (growth, pregnancy, lactation, previous nutrient history, and disease). In order to provide the correct profile of nutrients, the nutrient composition of feeds and the dynamic nutrient requirements of the animal must both be identified and then synchronized. There is genetic variation among animals in their ability to utilize feed. Multiple genes are associated with the regulation of feed intake, weight gain, and the utilization of ingested nutrients. Differential expression of these genes results in variation of feed efficiency among animals within populations, and these genetic differences potentially change the nutrient requirements of the animal. Identifying the role of nutrition in regulating gene expression and the mechanisms by which efficient animals utilize nutrients is needed to develop nutrition management strategies. In addition to variation in physiological responses, there is a need to understand genetic and environmental variation in animal feeding behavior that lead to variation in nutrient utilization.

Progress Report
This is the final report for project 3040-31000-097-000D “Improve Nutrient Management and Efficiency of Beef Cattle and Swine”. This project will be replaced with project 3040-31000-102-000D in fiscal year (FY) 2023. Studies under Objective 1 were conducted to evaluate the effects of dietary changes on efficiency of growth and nutrient utilization of beef cattle and swine. Twenty steers fit with rumen and duodenal cannulas were used to determine the impacts of rumen protected lysine and/or methionine supplementation on intake, nutrient digestibility, duodenal flow of amino acids and nitrogen balance in beef steers fed low-protein high-concentrate finishing diets. Sixteen steers fit with rumen and duodenal cannulas were utilized to evaluate supplementation frequency on intake, nutrient digestibility, duodenal lysine flow and nitrogen balance in beef steers fed a low-protein high-concentrate finishing diets. Gut histology, circulating cytokine concentrations, and pathogen shedding were measured from 352 pigs fed the commensal fungi, K. slooffiae, in the nursery. The mycobiome and bacteriome have been measured and data analysis is underway. A study was performed to determine if feeding an essential oil would decrease the presence of liver abscesses at harvest in 768 finishing cattle. This work was published in a peer-reviewed journal and showed that limonene did not reduce the incidence of liver abscesses, but there was a relationship between the rumen microbiota and rumen papillae gene expression of animals with and without liver abscesses. Three levels of ferric citrate were fed to eight steers to determine its effects on enteric methane. The study was published in a peer-reviewed journal and showed that ferric citrate may not be a viable option to decrease enteric methane production. In Objective 2, studies were focused on defining energy utilization by beef cattle on contemporary diets. There is little data available to define energy metabolism in beef cattle. A total of 167 calves born from heifers individually supplemented with 0.91 kg distillers grains or not receiving supplementation on pasture and bred to yearling bulls that were fed to gain two different rates of gain prior to the breeding season, were measured for the interactive effects of heifer supplementation and bull rate of gain on calf performance measures. A study was performed and published that demonstrated that the conversion factor used to predict metabolizable energy from digestible energy was flawed particularly on high grain diets and proposed an alternative equation. A study to evaluate the utilization of the constitutive components of the feed, beyond that of overall energy and protein, in 16 pregnant heifers was also completed. A study to determine the effects of forage and concentrate diets fed to heifers in an intensified management setting was performed on 14 bred heifers. Results indicated that strategic diet construction can be used to improve efficiency of energy conversion and therefore the sustainability of intensive cow systems. Studies to evaluate the differences of the microbiome between calves and their dams, and to examine the changes of the microbiome of calves as they transition from milk to forage were conducted on 30 cow-calf pairs. Studies were performed that demonstrated that maternal nutrient restriction in the second trimester did not have an impact on subsequent growth and fertility of offspring; however, restriction in the first trimester affected fetal development and concentrations of energetic and one-carbon metabolites such as glucose, fructose, methionine, and homocysteine without affecting uteroplacental transporters. The purpose of Objective 3 was to use novel forage systems for growing and maintaining beef cattle. Cows in two fall calving production systems were evaluated. Data collection for feed and forage intake and animal performance traits have been completed. Data from the feedlot performance of the final year of calves is being collected. Spring-born heifers were used in a 3-year study to evaluate performance in winter development systems which utilized cover crop and corn residue grazing. The results showed that the use of oat-brassica cover crops early in the winter followed by a lower rate of gain while grazing corn residue appear to be effective for developing beef heifers. Objective 4 encompassed discovery of molecular and physiological mechanisms of feed efficiency in livestock. Heifers were fed a methyl rich or methyl deficient diet from -63 to +63 days relative to insemination with sexed semen for bull calves to determine the effects on fetal development and whether the effects seen in the fetus maintain through the finishing period. We anticipate 40 heifers carrying fetuses for fetal measurements and 120 heifers carrying fetuses for calving and performance data. A feed efficiency panel for 36 genetic variants was finalized and tested on 500 pigs with feed efficiency phenotypes. Rumen tissue and white blood cell samples from 16 heifers with high and low gain phenotypes while on a forage diet were processed for RNA and sequenced. These data will be analyzed to determine which genes are involved with body weight gain. Feed efficiency phenotypes were collected from approximately 400 grow/finish pigs in the U.S. Meat Animal Research Center Feed Efficiency Barn. This data will be used for genomic analyses, correlation with reproductive traits, correlation with the microbiome and other studies. A positive genetic correlation between feed intake and body weight gain in 682 heifers and 622 female adult cows was identified. This is the first study to show that selection for decreased feed intake and average daily gain in growing animals will likely have the same directional effects on mature beef cows, which means that selection for these traits in heifers may be used by cow-calf producers to alter feed intake of mature cows. Studies were completed and published that identified genes differentially expressed in the skeletal muscle and mesenteric fat of 80 steers in animals with variation in feed efficiency from five unrelated cohorts of animals. Additional studies were performed to validate differential gene expression for feed efficiency in two unrelated and geographically distant populations of 34 animals that identified genes common to both populations. These data showed that meta-analysis is a powerful approach for defining the molecular basis of differences in performance. Microbial communities from six locations in the digestive tract of 16 beef heifers differed in animals with high and low residual gain. While numerous studies have demonstrated microbial community differences in the rumen, these studies suggest important differences in the intestine as well. Studies were also conducted that demonstrated that the muscle and adipose transcriptomes change in 24 mature cows during realimentation. Differences in the expression of genes involved in oxidative phosphorylation, mitochondrial dysfunction, and cholesterol biosynthesis pathways in adipose tissue, and lysosome and glutathione metabolism pathways in muscle tissue were identified and published in peer-reviewed journals. Studies were conducted to evaluate the transcriptome of tissues and circulating peripheral cells from animals (128 cattle, 192 swine) with variation in feed efficiency phenotypes. Genes involved in immune function and inflammatory responses were identified. In this project plan cycle, studies were performed to evaluate the metabolome of the blood and urine of cattle and differences were identified between animals with variation in feed efficiency and carcass quality. In Objective 5, experiments were designed to determine the environmental factors that contributed to the variation in feeding behavior, growth, and well-being of livestock. A lipopolysaccharide challenge pilot study was performed on four animals. Physical reaction to the lipopolysaccharide, hematology parameters, acute phase proteins, and cytokines were tested from 0 to 72 hours. A genome wide association study was performed on 1,154 grow-finish pigs with feeding behavior data. Results showed that genetic differences exist for changes in feeding behavior induced by elevated ambient temperatures. Selection for heat-tolerant pigs should improve production efficiency during warm months in commercial production. A total of 932 pigs of three breeds were monitored for feeding behavior over two years. Feeding behavior differences among breed types and sex during heat stress were identified and the data was published in a peer-reviewed journal. Hematology parameters and gene expression data were evaluated in calves with bovine respiratory disease and control animals at three time points (pre-weaning, weaning, and detection of illness). Expression of cytokine genes were increased in bovine respiratory disease positive animals compared to controls and may help to provide insight into an animal's health.

1. Urinary metabolites associated with steer growth rate. Growth rate is dictated by the regulation of many physiological processes, making their metabolites potential markers to identify animals that will have superior or inferior growth rates. ARS scientists at Clay Center, Nebraska, and a collaborator at the University of Nebraska-Lincoln, developed a non-invasive approach for sample collection, which combined with non-targeted and targeted metabolomics, was investigated as a method to predict growth. Urine samples were collected from steers when they were fed a high-forage growing diet and again when they were fed a high-grain finishing diet. Mass spectrometry was used to identify urine metabolites that correlated with differences in growth. Overall, 85 metabolites segregated between the steers classified as having the least or greatest average daily body weight gain. From the 85 metabolites, 18 bile acids and five steroids were quantified and associated with divergent growth and carcass quality. The use of metabolite markers is a novel and powerful approach for identifying differences in performance among cattle, which may lead to opportunities to improve growth rates through selection or predicting animal performance.

2. Candidate genes identified for feed efficiency in cattle across two populations. The rumen makes up a large portion of the digestive tract of beef cattle and is responsible for the absorption of nutrients and microbial by-products. Variation in an animal’s ability to take up and utilize these nutrients affects feed efficiency and can be influenced by the genes expressed in the rumen; however, current studies to identify differences in gene expression are limited by differences specific to each population (breed/genotype, environment, management). ARS scientists at Clay Center, Nebraska, in collaboration with researchers at the University of Wyoming and the University of Missouri, identified genes involved in feed efficiency that are expressed in two unrelated and physically distant populations of Angus and Hereford crossbred steers. A total of 38 genes were identified that may be useful indicators of feed efficiency in cattle. The use of multiple, diverse populations of cattle allows the identification of gene expression regulating key biological drivers of feed efficiency that will be robust for the selection of feed efficiency traits across the cattle industry.

3. Hematology measures are associated with swine feed efficiency. The cost of feed is the largest expense to producers of meat animals, and the ability to identify and select for animals that are more feed efficient is critical for profitability. However, determining feed efficiency requires measuring individual animal feed intakes using specialized and costly equipment. An indirect measurement for feed efficiency that is inexpensive and easy to sample would be of benefit to producers. ARS scientists at Clay Center, Nebraska, evaluated whether standard hematology measurements on whole blood would be predictive of an animal’s feed intake, body weight gain and gain-to-feed ratio. Whole blood samples from 178 pigs were taken at the beginning and end of a feed efficiency study. Blood samples were analyzed on a hematology instrument for white and red blood cell parameters. In the early sample, platelet and lymphocyte counts were associated with feed intake suggesting that they may have predictive value for feed intake. The strongest associations with body weight gain and feed intake were with changes that occurred over the study for red blood cell parameters, hemoglobin concentration, and packed hematocrit (red blood cell volume). This is the first report of associations between changes in red blood cell parameters and feed efficiency phenotypes in finishing pigs. This easy to obtain, inexpensive measurement may serve as a biological marker to identify pigs that differ in weight gain and feed intake.

4. Novel supplementation improves cattle embryonic cell growth through developmental programing. Prenatal vitamins consist of one-carbon metabolites (methionine, choline, folate, and vitamin B12) which are important for early embryonic development in mammals, but their requirements and roles in beef cattle are not well understood. It has been thought that one-carbon metabolites were provided to cattle in sufficient concentrations in their diets, but recent data has suggested that these may actually be limited in beef cattle diets. ARS scientists at Clay Center, Nebraska, in collaboration with scientists at North Dakota State University, investigated the supplementation of one-carbon metabolites to embryonic cells to determine the effects on cell growth rate, mitochondrial function, and DNA methylation. One-carbon metabolite supplementation of 2.5 and 5 times the basal levels improved cell growth rate and mitochondrial function, but increasing to 10 times the basal levels resulted in no improvement and even decreased growth compared with no supplementation. This data demonstrates that current one-carbon metabolite requirements in beef cattle have been underestimated. Modified embryonic growth has the potential to alter the trajectory of growth and development of calves after birth.

Review Publications
Artegoitia, V.M., Newman, J.W., Foote, A.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lewis, R.M., Freetly, H.C. 2022. Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits. Scientific Reports. 12. Article 231.
Rathert-Williams, A.R., Salisbury, C.M., Lindholm-Perry, A.K., Pezeshki, A., Lalman, D.L., Foote, A.P. 2021. Effects of increasing calcium propionate in a finishing diet on dry matter intake and glucose metabolism in steers. Journal of Animal Science. 99(12). Article skab314.
Crouse, M.S., Caton, J.S., Claycombe-Larson, K.J., Diniz, W.J., Lindholm-Perry, A.K., Reynolds, L.P., Dahlen, C.R., Borowicz, P.P., Ward, A.K. 2022. Epigenetic modifier supplementation improves mitochondrial respiration growth rates and alters DNA methylation of bovine embryonic fibroblast cells cultured in divergent energy supply. Frontiers in Genetics. 13. Article 812764.
Lindholm-Perry, A.K., Kuehn, L.A., Wells, J., Rempel, L.A., Chitko-McKown, C.G., Keel, B.N., Oliver, W.T. 2021. Hematology parameters as potential indicators of feed efficiency in pigs. Translational Animal Science. 5(4). Article txab219.
Cunningham-Hollinger, H.C., Kuehn, L.A., Cammack, K.M., Hales, K.E., Oliver, W.T., Crouse, M.S., Chen, C.T., Freetly, H.C., Lindholm-Perry, A.K. 2021. Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation. BMC Research Notes. 14. Article 361.
Cushman, R.A., Bennett, G.L., Tait, R.G., McNeel, A.K., Casas, E., Smith, T.P.L., Freetly, H.C. 2021. Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf. Theriogenology. 173:128-132.
Nonneman, D.J., Keel-Mercer, B.N., Lindholm-Perry, A.K., Rohrer, G.A., Wheeler, T.L., Shackelford, S.D., King, D.A. 2022. Transcriptomic analysis for pork color – The ham halo effect in biceps femoris. Meat and Muscle Biology. 6(1):1-8. Article 13050.
Rempel, L.A., Keel, B.N., Oliver, W.T., Wells, J.E., Lents, C.A., Nonneman, D.J., Rohrer, G.A. 2022. Dam parity structure and body condition during lactation influence piglet growth and gilt sexual maturation through pre-finishing. Journal of Animal Science. 100(4):1-9. Article skac031.
Walsh, S.C., Miles, J.R., Keel, B.N., Rempel, L.A., Wright-Johnson, E.C., Lindholm-Perry, A.K., Oliver, W.T., Pannier, A.K. 2022. Global analysis of differential gene expression within the porcine conceptus transcriptome as it transitions through spherical, ovoid, and tubular morphologies during the initiation of elongation. Molecular Reproduction and Development. Article 23553.
Pickinpaugh, W.J., Neville, B.W., Moore, R.L., Caton, J.S. 2022. Impacts of added roughage on growth performance, digestibility, ruminal fermentation, and ruminal pH of feedlot steers fed wheat-based feedlot diets containing 30% modified distillers grains with solubles. Translational Animal Science. 6(2). Article txac051.
Lindholm-Perry, A.K., Meyer, A.M., Kern-Lunbery, R.J., Cunningham-Hollinger, H.C., Funk, T.H., Keel, B.N. 2022. Genes involved in feed efficiency identified in a meta-analysis of rumen tissue from two populations of beef steers. Animals. 12(12). Article 1514.
Neville, B.W., Pickinpaugh, W.J., Mittleider, L.J., Moore, R.L., Swanson, K.C., Caton, J.S. 2022. Interaction of replacing corn silage with soyhulls as a roughage source with or without 3% added wheat straw in the diet: Impacts on intake, digestibility and ruminal fermentation in steers fed high-concentrate diets. Translational Animal Science. 6(2). Article txac061.
Keel, B.N., Lindholm-Perry, A.K., Oliver, W.T., Wells, J.E., Jones, S.A., Rempel, L.A. 2021. Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. BMC Genomic Data. 22. Article 25.
Henniger, M.T., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Schneider, L.G., McLean, K.J., Campagna, S.R., Christopher, C.J., Myer, P.R. 2022. Effects of a moderate or aggressive implant strategy on the rumen microbiome and metabolome in steers. Frontiers in Animal Science. 3. Article 889817.
Snider, A.P., Crouse, M.S., Rosasco, S.L., Epperson, K.M., Northrop-Albrecht, E.J., Rich, J.J., Chase, C.C. Jr., Miles, J.R., Perry, G.A., Summers, A.F., Cushman, R.A. 2022. Greater numbers of antral follicles in the ovary are associated with increased concentrations of glucose in uterine luminal fluid of beef heifers. Animal Reproduction Science. 239. Article 106968.