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

Location: Nutrition, Growth and Physiology

2020 Annual Report

Objectives
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.

Approach
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
Bovine embryonic fibroblasts were cultured to determine if supplementing one-carbon metabolites (methionine, choline, folate, and vitamin B12) to cells cultured in either a low or high glucose media improved cell growth and proliferation. Proliferation analysis, mitochondrial respiration assays, and reduced representation bisulfite sequencing were performed on treated cells to elucidate effects on growth rate and mitochondrial efficiency of bovine cells as well as the epigenetic mechanisms that regulate cell growth and development. (Objective 1) Heifers (n = 36) were used for a dose analysis study to determine the correct dose of one-carbon metabolites (methionine, choline, folate, and vitamin B12) to be included in the diet to maintain increased plasma and uterine laminal fluid levels of one-carbon metabolites. Heifer treatments have been conducted and all plasma, uterine fluid, and liver samples have been collected. (Objective 2) Cows in a fall production system (n = 240) are being evaluated in a drylot or pasture production system. Feed and forage intake are being measured and reproductive efficiency and calf growth rates are being measured. (Objective 3) Production data is being collected on 1,156 cows that were developed on corn stalks with distillers grains or wheat middles, or were developed on a combination of cover crops and corn stalks. (Objective 3) Completed the sequencing of 400 transcriptome libraries from pigs with feed efficiency phenotypes. (Objective 4) Created whole genome libraries from the 48 pigs and 24 cattle for low pass next generation genotyping. (Objective 4) Heifers (n = 136) were individually fed a forage-based diet and eight heifers with the greatest and eight with the least body weight gain at the average feed intake were selected to determine if there were differences in digestive tract microbiota, transcriptomics and enzyme expression. In addition, rumen fluid and cecum samples were collected to determine if they differed in in vitro neutral detergent fiber digestion. Muscle samples were collected to determine if there were differences in mitochondrial function. (Objective 4) Feed efficiency phenotypes were collected from approximately 1,000 grow/finish pigs. These data will be used for genomic analyses, correlation with reproductive traits, correlation with the microbiome, as well as other studies. (Objective 4) Reproductive tracts and small intestinal samples were collected from 40 ten-day-old pigs to determine the effect of colostrum intake on the development of the reproductive and gastrointestinal systems. Blood was collected from one-day-old pigs to determine the immunocrit (a measure of colostrum intake). Paired piglets with low and high immunocrits from the same sow were selected for sampling. Histological analysis of the reproductive and intestinal samples is underway. (Objective 4) Plasma samples from 82 steers and cows were analyzed for circulating cytokine profiles. (Objectives 4 and 5) Created libraries from 20 cattle from a population of cattle designated for disease resistance studies. These libraries were from whole blood samples collected at preconditioning and weaning stages, and again at time of illness diagnosis, along with case controls. (Objective 5)

Accomplishments
1. The microbiome of beef cattle is associated with economically important traits. Bacteria are found throughout the length of the digestive tract. Bacteria can modify consumed nutrients before the animal has an opportunity to use them. This is especially true in ruminant animals with an anatomic feature, the rumen, that results in the fermentation of their feed before it reaches their true stomach. ARS scientists at Clay Center, Nebraska, proposed that differences in feed utilization may be associated with differences in the bacterial communities in the digestive tract and studied the microbial populations in the digestive tracts of 16 steers with variation in average daily weight gain. Differences in bacterial communities were found by region of the digestive tract and were also detected in the small intestine of cattle that differed in their ability to convert feed to weight gain. This study showed a relationship between specific intestinal bacterial populations and beef cattle performance suggesting that solely studying the microbiota of the rumen may not be adequate.

2. Molecular markers for gain and feed intake identified in mesenteric fat of feedlot steers. Mesenteric fat is a visceral fat depot that increases as an animal ages and can also be influenced by diet. The purpose of this study was to determine whether there is a relationship between the mesenteric fat and feed efficiency in beef cattle by identifying genes that may be differentially expressed in steers with high and low body weight gain and feed intake. Because studies of global gene expression have been notoriously difficult to validate in other populations of animals due to breed, environment and management differences, this study included mesenteric fat from 78 crossbred steers collected over 3 years during spring and fall seasons. ARS scientists at Clay Center, Nebraska, used an analysis method that allows for the inclusion of multiple groups of animals to determine which genes were differentially expressed for gain and intake. The 111 genes identified were involved in lipid metabolism, stress responses, cell growth, inflammation and immunity. The use of several cohorts of animals with meta-analyses provides a novel approach to identify robust, key biological markers that can be used to improve feed efficiency in feedlot steers.

3. Feed intake and average daily gain are correlated between heifers and cows. 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. To determine whether measures of feed intake and gain obtained in young animals could be extrapolated to mature animals, individual feed intake and body weight gain was measured on 687 heifers and 622 5-yr-old cows. ARS scientists at Clay Center, Nebraska, determined that there was a positive genetic correlation between feed intake in young females and adult females. The results also illustrated a positive genetic correlation between body weight gain in young females and adult females. 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.

4. Molecular marker for feed efficiency identified across two populations of beef cattle. A better understanding of the cellular mechanisms of the rumen to process feed will help to identify and predict animals with superior feed efficiency. Studies to determine which genes are expressed differently in the rumen tissue from the most and least feed efficient beef steers have been performed. Validating this research is critical to determine whether these same genes are associated with feed efficiency in other populations of beef cattle to ensure they are robust across populations and environments. A previous study of the genes expressed in the rumen of Canadian Hereford x Angus steers identified 122 differentially expressed genes associated with residual feed intake, a measure of feed efficiency. ARS scientists at Clay Center, Nebraska, in collaboration with the University of Missouri and the University of Wyoming, tested the 13 most up- and down-regulated genes from the Canadian study in the rumen tissue of an unrelated population of U.S. Angus x Hereford steers. One gene, centromere protein E (CENPE), was identified with less expression in inefficient steers in both populations. Identified in two separate populations of beef cattle, the CENPE gene is a compelling molecular marker for feed efficiency. Genetic variants in CENPE that are involved in its expression may prove to be effective markers for feed efficiency across populations of beef cattle.

5. Pregnant heifers utilize the energy from forage- and corn-based diets differently. Feeding cattle in intensified settings (drylot) allows cow-calf producers to decrease their reliance on grazed forage and utilize alternative feedstuffs. During times of intense management, diet type may alter energy utilization. ARS scientists at Clay Center, Nebraska, in collaboration with Texas A&M University, studied pregnant heifers to determine effects of diet type on nutrient and energy utilization. Heifers were assigned to either a forage diet or a concentrate (corn-based) diet, and individually fed to meet energy requirements for maintenance and conceptus growth. Feeding concentrate-based rather than forage-based diets increased energy retained by the cattle, without changing body condition score. Although, heifers fed concentrate-based diets retained more energy, in part because they had larger calves. Pregnant heifers utilize forage and concentrate diets, fed at the same energy levels, differently. This study demonstrates the need to understand the utilization of the constitutive components of the feed beyond that of energy and protein.

6. Development of a more accurate method to predict methane greenhouse gas emissions by cattle. Greenhouse gas emissions are thought to be a contributor to increasing global temperatures and shifts in climate worldwide. Beef cattle enteric methane production is thought to contribute to global greenhouse gas emissions. Robust models are needed to reliably estimate beef cattle methane emissions. However, reliable models require data from cattle under different management systems worldwide. ARS scientists at Clay Center, Nebraska, and Bushland, Texas, joined with numerous scientists worldwide to develop a global database of methane production by beef cattle and predict methane production under different management schemes. A relatively simple model was better than more complex and Europe-specific models. Evaluation of current Inter-governmental Panel Climate Change models indicated revised methane emission conversion factors for feedlot and non-feedlot cattle will improve methane production estimates globally. This method improves the accuracy of livestock methane production measurements, which is important for estimating its contribution to greenhouse gas emissions.

7. Development of depth imaging to predict the weight of pigs. Continuously monitoring animal weight would be beneficial to producers to ensure all animals are gaining weight as expected and would assist in the precision of marketing pigs. Electronically monitoring weight without moving the pigs to the scale would also make real time tracking of the weight on all pigs possible. The development of methods for monitoring the physical conditions of animals without the need for animal handling would improve animal well-being and maximize the profitability of production. ARS scientists at Clay Center, Nebraska, conducted research to validate the use of depth images to predict live animal weight in grow-finish pigs. Nine hundred twenty depth images and weights were collected from a population of grow-to-finishing pigs that were equally divided between sex and three commercial lines. Depth images were used to calculate pigs’ volumes. An equation was developed to predict pig weight from the calculated volumes. It was determined that this equation could be used to predict the weight regardless of sire lines or sex. This method of precision monitoring of live animal weights reduces animal stress related to animal handling and provides an effective technology to monitor pig weight gains for animal marketability.

8. Heat stress alters pig feeding behavior. Heat stress is a major economic and animal well-being factor affecting pork production. The use of a feed monitoring system to evaluate the feeding behavior of pigs under various temperature conditions will lead to a greater understanding of impacts of heat on animals. ARS scientists at Clay Center, Nebraska, in collaboration with South Dakota State University, conducted a study utilizing a feed monitoring system that is representative of commercial conditions to determine feeding behavior patterns of grow-finish pigs throughout the year and to identify changes that occurred during heat stress events. Feeding behavior was compared between temperature-humidity index categories including normal (less than 23.33°C), alert (23.33 - 28.88°C), danger (26.11 - 28.88°C) and emergency (greater than 28.8°C). Feeding behavior differences among breeds and sex were observed across all temperature humidity index categories. These differences demonstrated that heat stress affects sire breeds and sexes differently. This study describes the novel use of abnormal feeding behavior to allow producers to identify animals suffering from heat stress quickly and easily, while also eliminating the stress associated with animal handling.

9. New method to improve the identification of genetic markers for feed efficiency. Typical studies designed to identify genetic markers for livestock traits include several thousand animals and thousands of genetic markers being tested. Statistically, this is challenging and makes analysis and interpretation of the study difficult. The ability to select the most appropriate markers to test for association with specific traits would reduce the complexity of the study. ARS scientists at Clay Center, Nebraska, developed a methodology that uses gene expression data from four tissues from high and low feed efficient pigs to rank genomic regions. Less than 1,000 markers were then selected from these regions to evaluate for association with feed efficiency. A total of 36 of these markers were associated with swine feed efficiency and 29 of them were in genomic regions previously identified for swine feed efficiency. A comparative analysis without using the gene expression data for selection of markers identified only two markers associated with feed efficiency and neither were in genomic regions related to swine feed efficiency. This novel method using gene expression information with genetic variants is a powerful, new approach to identify markers responsible for economically important livestock traits. The 36 markers identified in this study are available to commercial genotyping companies for producers to improve feed efficiency in pigs.

Review Publications
Freetly, H.C., Kuehn, L.A., Thallman, R.M., Snelling, W.M. 2020. Heritability and genetic correlations of feed intake, body weight gain, residual gain, and residual feed intake of beef cattle as heifers and cows. Journal of Animal Science. 98(1):1-6. https://doi.org/10.1093/jas/skz394.
Lindholm-Perry, A.K., Freetly, H.C., Oliver, W.T., Rempel, L.A., Keel, B.N. 2020. Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. PLoS One. 15(1):e0227154. https://doi.org/10.1371/journal.pone.0227154.
Baber, J.R., Wickersham, T.A., Sawyer, J.E., Freetly, H.C., Brown-Brandl, T.M., Hales, K.E. 2020. Effects of diet type on nutrient utilization and energy balance in drylot heifers. Journal of Animal Science. 98(1):1-8. https://doi.org/10.1093/jas/skaa006.
Cole, N.A., Parker, D.B., Todd, R.W., Leytem, A.B., Dungan, R.S., Hales Paxton, K.E., Ivey, S., Jennings, J. 2018. Use of new techniques to evaluate the environmental footprint of feedlot systems. Translational Animal Science. 2:89-100. https://doi.org/10.1093/tas/txx001.
Condotta, I.C.F.S., Brown-Brandl, T.M., Silva-Miranda, K.O., Stinn, J.P. 2018. Evaluation of a depth sensor for mass estimation of growing and finishing pigs. Biosystems Engineering. 173:11-18. https://doi.org/10.1016/j.biosystemseng.2018.03.002.
Thorson, J.F., Prezotto, L.D., Adams, H., Petersen, S.L., Clapper, J.A., Wright, E.C., Oliver, W.T., Freking, B.A., Foote, A.P., Berry, E.D., Nonneman, D.J., Lents, C.A. 2018. Energy balance affects pulsatile secretion of luteinizing hormone from the adenohypophesis and expression of neurokinin B in the hypothalamus of ovariectomized gilts. Biology of Reproduction. 99(2):433-445. https://doi.org/10.1093/biolre/ioy069.
Lenz, M.E., Cox-O'Neill, J.L., Hales, K.E., Drewnoski, M.E. 2019. Nutritive value change during the fall of late-summer planted oats, radishes, and turnips. Crop, Forage & Turfgrass Management. 5(1):180097. https://doi.org/10.2134/cftm2018.12.0097.
Van Lingen, H.J., Niu, M., Kebreab, E., Valadares Filho, S.C., Rooke, J.A., Duthie, C., Schwarm, A., Kreuzer, M., Hynd, P.I., Caetano, M., Eugene, M., Martin, C., McGee, M., O'Kiely, P., Hunerburg, M., McAllister, T.A., Berchielli, T.T., Messana, J.D., Peiren, N., Chaves, A.V., Charmley, E., Cole, N.A., Hales Paxton, K.E., Lee, S., Berndt, A., Reynolds, C.K., Crompton, L.A., Bayat, A., Yanez-Ruiz, D.R., Yu, Z., Bannink, A., Dijkstra, J., Casper, D.P., Hristov, A.N. 2019. Prediction of enteric methane production, yield and intensity of beef cattle using an intercontinental database. Agriculture, Ecosystems and Environment. 283:106575. https://doi.org/10.1016/j.agee.2019.106575.
Keel, B.N., Snelling, W.M., Lindholm-Perry, A.K., Oliver, W.T., Kuehn, L.A., Rohrer, G.A. 2020. Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs. Frontiers in Genetics. 10:1339. https://doi.org/10.3389/fgene.2019.01339.
Cross, A.J., Brown-Brandl, T.M., Keel, B.N., Cassady, J.P., Rohrer, G.A. 2020. Feeding behavior of grow-finish swine and the impacts of heat stress. Translational Animal Science. 4(2):986-992. https://doi.org/10.1093/tas/txaa023.
Rathert, A.R., Meyer, A.M., Foote, A.P., Kern, R.J., Cunningham-Hollinger, H.C., Kuehn, L.A., Lindholm-Perry, A.K. 2020. Ruminal transcript abundance of the centromere-associated protein E gene may influence residual feed intake in beef steers. Animal Genetics. 51(3):453-456. https://doi.org/10.1111/age.12926.
Leonard, S.M., Xin, H., Brown-Brandl, T.M., Ramirez, B.C., Dutta, S., Rohrer, G.A. 2020. Effects of farrowing stall layout and number of heat lamps on sow and piglet production performance. Animals. 10(2).Article 348. https://doi.org/doi:10.3390/ani10020348.
Freetly, H.C., Dickey, A., Lindholm-Perry, A.K., Thallman, R.M., Keele, J.W., Foote, A.P., Wells, J.E. 2020. Digestive tract microbiota of beef cattle that differed in feed efficiency. Journal of Animal Science. 98(2):1-16. https://doi.org/10.1093/jas/skaa008.
Brown-Brandl, T.M., Adrion, F., Maselyne, J., Kapun, A., Hessel, E.F., Saeys, W., Van Nuffel, A., Gallmann, E. 2019. A review of passive radio frequency identification systems for animal monitoring in livestock facilities. Applied Engineering in Agriculture. 35(4):579-591. https://doi.org/10.13031/aea.12928.