Source: IOWA STATE UNIVERSITY submitted to
IMPROVING NUTRIENT UTILIZATION AND FEED EFFICIENCY THROUGH RESEARCH AND EXTENSION TO ENHANCE PIG INDUSTRY SUSTAINABILITY AND COMPETITIVENESS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0224741
Grant No.
2011-68004-30336
Project No.
IOW05291
Proposal No.
2015-03335
Multistate No.
(N/A)
Program Code
A5101
Project Start Date
Apr 1, 2011
Project End Date
Mar 31, 2017
Grant Year
2015
Project Director
Patience, J. F.
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Animal Science
Non Technical Summary
The rationale behind the proposed research and extension activities is that an improved understanding of the biology of pigs selected for better feed efficiency (FE) will identify new technologies and improved management procedures that can be applied by the U.S. pork industry. Feed represents 55% to 60% of the total cost of raising a pig to market. An aggressive extension effort to ensure existing technologies are broadly applied by the industry to improve FE provides a practical and industry focused foundation for this project. Concurrently, the proposed research program will provide essential new information regarding the uptake and retention of nutrients in relation to improved FE and whether pigs selected for efficiency under low fiber high energy diets and without major stressors, maintain their superiority in environments similar to those encountered in commercial production systems. This research will help to identify metabolic pathways that are important for the efficient use of feed for meat production. A unique strength is the collection of multiple types of molecular data on unique lines of pigs. We will use this to develop tools to improve FE through the use of biomarkers to identify highly efficient pigs. As an outcome of the proposed investigations, we expect to determine how highly efficient pigs achieve their metabolic advantage. Collectively, our findings will extend our fundamental knowledge of the efficient use of feed in pigs, and help identify specific pathways and targets on which selection and management strategies can be established to reduce the cost of production, reduce demands on feed resources and increase the net income of pork producers and industry. Interwoven throughout the project is an aggressive and innovative extension effort with a two-pronged approach: increase awareness -- and thus adoption -- of existing technology on FE, and communicate and encourage adoption of new technologies developed by the research proposed herein. This integration of extension and research activities will raise the awareness and maximize the application of FE technologies. Success on a topic as complex as FE requires multiple disciplines functioning in a concerted and coordinated fashion. Our research and extension group includes geneticists, biochemists, nutritionists, physiologists, meat scientists, microbiologists, pathobiologists, behaviorists, biostatisticians and extension and management specialists. Thus, this project is uniquely positioned to address the program area priority of improved feed efficiency, and more specifically, to "improve biological nutrient use efficiency" of swine. This project also addresses the Global Food Security Challenge Area by increasing the quantity of pork that can be produced with the same or fewer resources. Another major benefit of this project is the development of a cadre of highly trained personnel to support continued advances in the future. Enhanced feed efficiency in the U.S. pork industry will lead to improved global competitiveness, improved profitability, and more sustainable global food supplies.
Animal Health Component
(N/A)
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3023510100010%
3023510101030%
3023510102010%
3023510104010%
3023510108030%
3023510109010%
Knowledge Area
302 - Nutrient Utilization in Animals;

Subject Of Investigation
3510 - Swine, live animal;

Field Of Science
1080 - Genetics; 1020 - Physiology; 1010 - Nutrition and metabolism; 1090 - Immunology; 1000 - Biochemistry and biophysics; 1040 - Molecular biology;
Goals / Objectives
Our long term goal is to increase nutrient utilization and feed efficiency, to strengthen the competitiveness of the pork industry and to reduce its demand on grains and proteins, through focused and integrated initiatives in both research and extension. Our overall objective is to utilize a multi-disciplinary approach that integrates 1) research in swine genomics, quantitative genetics, transcriptomics, proteomics, nutrition, immunology, bioinformatics, statistics, microbiology, physiology, and behavior, 2) innovative extension approaches, and 3) extensive undergraduate and graduate research opportunities. An important foundation of the project is access to unique lines of pigs that have been divergently selected for reduced residual feed intake (RFI), a measure of feed efficiency. These lines provide the unique capability to identify the genetic, metabolic and physiological differences in pigs varying in feed efficiency. To achieve our overall objective and goal, we will focus on 5 specific objectives: Objective 1: Quantify the performance of pigs selected for increased feed efficiency under corn-soybean diets when fed lower quality by-product ingredients (higher fiber, lower fat). Objective 2: Evaluate the ability of pigs selected for increased efficiency to cope with behavioral, physiological and immunological stressors. Objective 3: Develop industry-ready tools to easily and effectively identify and select more efficient pigs. Objective 4: Increase pork producers' awareness of the factors influencing feed efficiency and strategies available to achieve improvement. Objective 5: Ensure the rapid and effective implementation of new technologies to improve feed efficiency both nationally and internationally. While our major focus uses the Yorkshire RFI selection lines developed at Iowa State University, we will also integrate our results with those obtained from a similar selection experiment on European Yorkshires at INRA in France, led by one of the co-PD's, Dr. Helene Gilbert. We will also utilize industry breeding lines in aspects of the proposed work. Completion of the research activities outlined herein will improve our understanding of critical genes, genetic variants, proteins and pathways that control feed efficiency and develop methods to identify animals with superior feed efficiency. By incorporating tools of the new biology, new information and management procedures will provide dramatic advances, and a fully integrated extension initiative will help to ensure rapid and effective adoption by the pork industry. These advances will enhance feed efficiency at the farm level and thus contribute to increased global food security and sustainability. Our approach to integrate diverse disciplines, utilize undergraduate, graduate and post-graduate student training, and implement a strong extension program will result in technological advances and development of a cadre of well trained scientists, technical specialists and pork producers to support continued success in the future.
Project Methods
This project represents a true multi-disicplinary approach to a complex subject and includes experts in geneticists, biochemists, nutritionists, physiologists, meat scientists, microbiologists, pathobiologists, behaviorists, biostatisticians and extension and management specialists. The project is divided into 5 objectives, 3 of which involve research and 2 extension. The first objective will quantify the performance of pigs selected for enhanced feed efficiency, to help determine the biological and metabolic basis of their superiority. Performance will not only include classical growth measurements, but also meat quality assessments, nutrient utilization and microbial populations in the gastrointestinal tract. The second objective will evaluate the ability of pigs selected for superior feed efficiency to cope with behavioral, physiological and immunological stressors. This research will involve challenge studies with specific disease organisms commonly found in the American pig industry, as well as studies of behavior and physiology. The third objective will involve multi-level genetic analysis of the pigs selected for better feed efficiency to allow development of industry-ready tools for easy selection of superior animals by suppliers of breeding stock to pork producers. This will require identification of key molecular pathways or networks associated with improved feed efficiency as well as development of a practical classifier to predict feed efficient pigs. This objective will require the use of sophisticated tools in molecular genetics, including identification of SNPs, association analysis and molecular pathway analysis. The extension objectives, numbers 4 and 5, will adopt a wide array of communication vehicles and techniques, recognizing the persons within the target audience have unique preferences for learning and adopting new information. Thus, classical approaches such as factsheets, conferences and symposia will be blended with web-based tools, social network technologies and on-farm demonstration projects. Perhaps most critically, the whole project will involve close co-operation with, and involvement of, persons within the American pork industry, to provide guidance, direction and feedback on our progress. Breeding companies will be involved in evaluating the new technologies to ensure their practical relevance, and demonstration projects will allow producers to see first-hand how the new knowledge can assist them in improving their own farming operations.

Progress 04/01/11 to 03/31/17

Outputs
Target Audience:Primary target audiences are 1) pork producers, 2) feed and genetics suppliers to the pork industry, 3) consultants, including veterinarians, 4) extension and related workers, and 5) the academic community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Specific symposia on focused topics directly affecting feed efficiency, such as dietary fat and dietary fiber, were held in 2015 and 2017, respectively; directed specifically at nutritionists employed by feed companies or pork producers; they were attended by about 90 people. Academic training was done with undergraduate and graduate students and post-doctoral training. Below is a list of students and categories for individuals who had the opportunity to obtain training in research and extension throughout all 5 objectives of this project. Jennifer Young, Former - Post doc, Direct - Manage RFI lines, data analysis. Jenelle Dunkelberger, PhD-completed, Direct - Effect of PRRS challenge on RFI lines; help with data collection. Emily Mauch, PhD, Direct - Effect of high fiber diet on RFI lines; help with data collection. Nick Serao, Post doc, Indirect - assist with data collection. Wan-Ling Hsu, Post doc-completed, Direct - Quantitative genetic analyses of selection response and genetic parameters. Dinesh Thekkoot,PhD - completed, Indirect - GWAS for lactation efficiency, help with data collection. Andrew Hess, PhD-completed, Indirect - assist with data collection. Emily Waide, PhD-completed, Indirect - assist with data collection. Nick Boddicker, PhD - completed, Indirect - assist with data collection. Yi Zhang,Visiting Scholar - completed, Indirect - Genotype analyses; assist with data collection. Boxing Sun, Visiting Scholar - completed, Indirect - Data analysis; assist with data collection. Alyssa Dannen. Joel Steckelberg. Kelsey Wahlberg, Undergraduate,Indirect - assist with data collection and entry and sample collection, storage, and processing. Martine Schroyen, Post doc, Indirect- process RNA samples in Obj 3A. Ziyanda Mpetile, MS, Direct- help collect blood samples, analyze data in Obj 3A, B. Thesis: Determine the effect of RFI selection on immune traits. Haibo Liu, PhD, Direct- process RNA and metabolomic samples, help analyze data in Obj 3A. Thesis: Identification of biomarkers for feed efficiency using a systems biology approach. Kristina Feye, PhD, Direct- process samples, help analyze data in Obj 3B. Thesis: The effect of Immune stress on feed efficient animals. J. Kyle Grubbs, Post doc, Direct- process serum sample, analyze protein data in Obj 3A. Project: the identification of protein as biomarkers differentially expressed in efficient versus non-efficient animals. Austin Putz, Undergraduate, Direct- process RNA samples in Obj 3A. Project: the isolation and globin depletion of RNA samples from whole blood collected from high and low efficient animals. Yet Nguyen, PhD, Direct: analyze RNA data. Josh Flohr,M.S. and Ph. D., Direct assistance/training. Jon De Jong, M.S. and Ph.D., Direct assistance/training. Jeremiah Nemechek, Ph.D., Direct assistance/training. Kyle Coble, Ph.D., Indirect assistance/traning. Amanda Graham, M.S., Indirect assistance/training. Devin Goehring, M.S., Indirect assistance/training. Chad Paulk, Ph.D., Indirect assistance/training. Miriam Ayuso Hernando, Visiting scholar, Involved with data collection and review of fact sheets for the project. Nestor Gutierrez, Post Doc, Indirect assistance/training. Jesus Acosta, Msc., Indirect assistance/training. Trey Kellner, Ph.D., Direct - Demonstration project. Kyle Grubbs, Post-Doc, Direct assistance/training. Jordy Berger, Undergraduate, Indirect assistance/training. Emily Benedict, Undergraduate, Indirect assistance/training. Roslyn Punt, Undergraduate, Indirect assistance/training. Emily Arkfeld, MSc., Direct assistance/training. Shannon Cruzen, Ph.D., Indirect - Protein metabolism in muscle in response to selection for RFI. Jessie Colpoys, Ph.D., Direct- Behavioral and physiological stress responses of RFI lines. Johanna Sholar, Undergraduate, Indirect- assist with data analysis. Chloe Wasendorf, Undergraduate, Indirect- assist with data analysis. Jennie Schubert, Undergraduate, Indirect- assist with data collection. Ashley Woodley, Undergraduate, Indirect- assist with data collection. Adrianne Kaiser, Undergraduate, Indirect- assist with data collection. Sarah Myers, Undergraduate, Indirect- assist with data collection. Venkatesh Mani,PhD. - completed, Indirect - assist with sample analysis in Objectives 1 & 2. Dana van Sambeek,MSc. - completed, Indirect - assist with sample analysis in Objectives 1 & 2. Emma Helm, MSc. - on going, Direct - assistance and training. Amanda Outhouse, MSc. - completed, Direct - assistance and training. Brian Patterson, MSc., Indirect- assist with sample analysis in Objectives 1 & 2. Erin Lewis, Undergraduate, Indirect- assist with sample analysis in Objectives 1 & 2. Andrea Gisch, Undergraduate, Indirect- assist with sample analysis in Objectives 1 & 2. Calvin Hartz, Undergraduate, Indirect- assist with sample analysis in Objectives 1 & 2. Erin Laughlin, Undergraduate, Direct- assist with sample analysis in Objectives 1 & 2. Anoosh Rakhshandeh, Former Post doc, Direct - Objective 2 - conducted LPS challenge work. Jentry Fane, Undergraduate, Indirect assistance/training. Shelby Curry, PhD., Direct - assist with lab sample analysis in Objective 2. Bree Adamic, Undergraduate, Indirect assistance/training. Anna Clifton, Undergraduate, Indirect assistance/training. How have the results been disseminated to communities of interest?Results found through this project have been published in scientific journals, presented in international conferences and published in non-technical language at the Swine Feed Efficiency website. A number of these documents has been translated to Spanish to reach non-native speakers in rural areas. An effort from Kansas State University has been created for audio/digital dissemination through podcast (found at the project's website). What do you plan to do during the next reporting period to accomplish the goals? Continued summary of impact... Results indicated that responses to selection for feed efficiency (FE), as measured by RFI, under a standard high energy diet may not fully translate into similar increases in efficiency under poorer diets, although such selection is also not expected to result in detrimental effects on efficiency on poor diets.Thus, breeding programs need to consider the diet that production animals are fed. On the LEHF diet, the low RFI pigs had more lean tissue and less fat growth than the high RFI pigs, while eating less and gaining similarly, yet had similar FE. RFI shows promise as a selection tool for improved FE without compromising pork quality, even when fed low energy diets. When evaluation behavior and immune responses, neuroendocrine axes and metabolic differences may explain observed line differences in behavior and body composition and may have implications for selection techniques and reducing swine stress though handling and facility design. Immune responses contradict the widely held belief that selection for efficiency increases susceptibility to disease and indicates that selection for FE can be conducted in the high-health conditions of nucleus farms, without detrimental effects on growth under less optimal conditions, as present in the field. As an important unanticipated result of this PRRS challenge study of the RFI lines, we identified pigs in the RFI lines that harbor mutations in the Artemis gene, which causes them to exhibit an impaired adaptive immune system (lack of B and T cells), which is known as Severe Combined Immune Deficiency (SCID). While SCID is known to occur in several species, including humans (bubble boy), this was the first know natural mutation that causes SCID ever identified in pigs. This finding has now led to our development of SCID pigs as an important biomedical model, with funding from NIH. Feed efficiency conferences were held in 2011 and 2015 with total attendance of 414 at the former and 501 at the latter. Attendees represented a strong cross-section of the pork industry, including producers and suppliers of goods and services to the industry. The specialized conference for the genetics sector was rolled into the final feed efficiency conference, with special sessions devoted to that target audience. Train the trainer sessions were held in conjunction with the National Pork Board Educator Conference, the Leman Conference and the AASV Annual Meeting. "Feed Efficiency in Swine" was published in 2012 and became widely recognized as the best single source of information on the current state of art on feed efficiency. The website www.swinefeedefficiency.com provides a single source for information on the project, including publications, presentations and some excellent decision-making tools developed at Kansas State University. Plans are progressing to have this website maintained into the future, even though the term of the contract has been completed. Decision tools were developed at Kansas State University on an array of topics to assist producers in correctly applying new information on such topics as feed particle size, feeder adjustment and diet recommendations. A survey was conducted early in the project to determine the level of knowledge and understanding about feed efficiency existed in the industry. This information was then use to develop and implement various technology transfer activities, as areas of deficiency were identified. A multidisciplinary approach to understand Feed Efficiency as a multi-factorial component of pork production was extremely valuable to make it possible for PI to contribute with their expertise in different projects. Students and industry were highly beneficiated by this interaction with unique training opportunities and results that impact on day to day production practices.

Impacts
What was accomplished under these goals? A multidisciplinary approach to solve feed efficiency (FE) in pigs made collaboration and training unique to PIs, students and the pork industry. During the past 6 years, researchers were able to investigate divergently genetically selected pig lines to understand and recommend practical approaches on management, nutrition and breeding decisions. Pigs selected for improved FE should perform better when fed a higher quality diet, but may not be more susceptible to disease or behavior stress.Practical tools were generated from this grant from a molecular level (biomarkers) all the way to management practices (decision tools). The grant became well known by the industry for its conferences, publications and trained students' work. As a result, the genetics sector can adopt enhanced selection methodologies to improve the genetic quality of the US herd. Nutritionists can easily adopt the numerous recommendations for enhancing FE. Pork producers can similarly adopt the improved production methods to improve feed efficiency. The net impact on the efficiency of the U.S. pig herd will be substantial, thus reducing dependence on feed grain resources. Obj1: Performance traits measured feeding low energy-high fiber (LEHF) diets were genetically similar but not same as performance traits when feeding, with genetic low correlations for residual feed intake (RFI). Results indicated that responses to selection for FE, under a standard high energy diet may not fully translate into similar increases in efficiency under poorer diets, such selection is also not expected to result in detrimental effects on FE on poor diets. Breeding programs must consider diet for production. On LEHF diet, low RFI (LRFI) had more lean tissue and less fat growth than high RFI (HRFI), while eating less and gaining similarly, had similar FE. LRFI had greater digestibility of diet, in particular on LEHF diet, which may explain part of line differences in FE. Both line and diet impacted carcass composition, with minimal effects on pork quality and sensory characteristics. RFI shows promise as a selection tool for improved FE without compromising pork quality, even when fed low energy diets. Obj2: LRFI did not negatively impact barrow stress responsiveness. A hormonal stress challenge study indicated genetic selection for LRFI resulted in decreased blood cortisol and a significant increase in insulin following a glucose tolerance test. Differences may explain observed line differences in behavior and body composition and may have implications for selection techniques and reducing swine stress though handling and facility design. Lines were challenged with lipopolysaccharide (LPS), LRFI had lower endogenous endotoxin and inflammatory markers, and enhanced activities of antimicrobial enzymes. HRFI and LRFI had similar febrile and pro-inflammatory response. Immune stimulation affected apparent ileal digestibility and apparent total tract digestibility of dietary nutrients may be a major source of differences in FE. Altogether, genetic selection for LRFI reduced total tract digestive capacity of growing during immune system stimulation. LRFI under high-health conditions, were not more affected by infection with PRRS during growing period. In contrast, growth rate LRFI were less impacted by PRRS and had lower levels of viremia and an increase in antibody levels. Obj3: We have identified both RNAs and proteins that are differentially expressed between RFI lines. We identified 1,972 differentially expressed genes (DEG), and validated 24 of 37 DEG tested in these samples using a different technique; however, only 25% of genes were validated in a separate set of 24 animals not extreme for RFI value. Five DEG were significantly associated with RFI phenotype of individual animals. In summary, post-weaning blood transcriptome was different between low and HRFI, and identified DEG provided potential new insights into molecular basis of RFI. While observed relationship between post-weaning blood gene expression and RFI phenotype measured during grow-finish phase was not strong, DEG provide a preliminary list for developing predictive biomarkers for RFI.We used two-dimensional difference in-gel electrophoresis and mass spectrometry to assay for differences between lines for abundance in serum proteins. Three proteins had significant RFI line differences and are being validated as protein biomarkers for RFI.We used RNAseq data created in this project with other public data and generated a high-quality assembly of genes expressed in porcine blood.Blood was collected during Immune System Stimulation (ISS) of older pigs using bacterial component LPS. 103 genes were differentially expressed between lines, 19 showed line differences in post-weaned pig project described above; this overlap is highly significant and provides preliminary validation for differences between two ISU RFI lines. These genes would be strongest candidates for validation studies as RNA biomarkers to predict RFI phenotype in other populations. GWAS found RFI to be affected by many genes with small effects, this is consistent with results for RFI in other populations and species. Genomic prediction across lines, utilizing all genetic markers on panel, did show a reasonable level of accuracy, and therefore opportunities for its use in genetic selection of RFI. GWA of performance lines under LEHF diet also showed a highly polygenic genetic architecture for RFI with limited overlap of signals with performance on HELF diet. Genomic prediction was shown to have some predictive ability across diets. HRFI and LRFI lines that were subjected to PRRS challenge of obj 2 were genotyped using 60k SNP panel. Lines were found not to segregate for chromosome 4 region (GBP5) that has been found to be associated with host response to PRRS.As an unanticipated result of this PRRS challenge study of RFI lines, we identified in RFI lines that harbor mutations in the Artemis gene, which exhibits an impaired adaptive immune system, known as Severe Combined Immune Deficiency (SCID). While SCID is known to occur in several species, this was the first know natural mutation that causes SCID identified in pigs. This has now led to our development of SCID pigs as a biomedical model, with funding from NIH. SNP data from the ISU RFI lines were merged with SNP genotypes from Large White lines that were divergently selected for RFI at INRA in France to characterize population differences and selection signatures. ISU and INRA populations were found to be distinct. These data are currently used for joint GWA studies. Obj 4 - 5: FE conferences in 2011 and 2015 with total attendance of 414 and 501, from pork industry. A specialized conference for genetics sector was rolled into final feed efficiency conference, with special sessions devoted to target audience. Train the trainer sessions were held in conjunction with the National Pork Board Educator Conference, the Leman Conference and the AASV Annual Meeting."Feed Efficiency in Swine" was published in 2012 and became widely recognized as a source of information on FE. Website provides information on the project, including publications, presentations and excellent decision-making tools developed at K-State University. A total of 13 factsheets were published. Demonstration projects to provide practical information related to feed efficiency and encourage adoption by industry. Decision tools were developed at K-State University on an array of topics to assist producers.A survey was conducted early in the project to determine the level of knowledge and understanding about feed efficiency existed in the industry. This information was then use to develop and implement various technology transfer activities, as areas of deficiency were identified. The results of this project can be readily adopted by various segments of the US pork industry.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Nemechek, J.E., M.D. Tokach, K.F. Cobel, C.W. Hastad, J.M. DeRouchey, S.S. Dritz, and R.D. Goodband. 2014. Effects of corn particle size and diet form on finishing pig growth performance and carcass characteristics.� J. Anim. Sci. 92 (Suppl.2):123
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Tuggle, C.K., E.J. Powell, D. Rajao, C. Loving, K. Feye, J. Cunnick, P.C. Gauger, A. Vincent, E.H. Waide, and J.C.M. Dekkers. Characterizing the Iowa State University Severe Combined Immune Deficient (SCID) Pig. Plant and Animal Genome XXIII, Abstract W832, January 2015. https://pag.confex.com/pag/xxiii/webprogram/Paper14535.html
  • Type: Other Status: Published Year Published: 2016 Citation: Azarpajouh, S., Colpoys, J.D., Gabler, N.K., Johnson, A., Dekkers, J., Rakhshandeh, A., and Abell, C. 2016. Effect on Gilt Behavior and Postures when Selected for Residual Feed Intake Selection in Response to a Lipopolysaccharide Challenge," Animal Industry Report, Iowa State University. AS 662, ASL R3110.
  • Type: Other Status: Published Year Published: 2016 Citation: Colpoys, J. D., Annen, J., Martens, K. Gabler, N. K.; and Johnson, A. 2016.Stalled Gilt Behavior when Provided with Novel Flavors on Rope Environmental Enrichment," Animal Industry Report, Iowa State University AS 662, ASL R3112.
  • Type: Other Status: Published Year Published: 2012 Citation: Flohr, J.R., M.D. Tokach, J.M. DeRouchey, J.F. Patience, R.D. Goodband, S.S. Dritz, and J.L. Nelssen. 2012. Feed efficiency in swine: A survey of current knowledge. Kansas Swine Industry Day Report of Progress 1074.
  • Type: Other Status: Published Year Published: 2015 Citation: Grubbs, K., Tuggle, C.K., Dekkers, J. C. M.; Nguyen, Y.T., Huff-Lonergan, E.J., Nettleton, D.S., and Lonergan, S. M. 2015. Development of Protein Biomarker Identification Protocols. Animal Industry Report, Iowa State University AS 661, ASL R2940.
  • Type: Other Status: Published Year Published: 2015 Citation: Liu, H., Nguyen, Y., Nettleton, D., Dekkers, J., Tuggle, C. Differentially expressed genes in blood from young pigs between two swine lines divergently selected for feed efficiency: potential biomarkers for improving feed efficiency. 2015 Industrial report.
  • Type: Other Status: Published Year Published: 2015 Citation: Hsu, W., J.M. Young, E.D. Mauch, and J.C.M. Dekkers. 2015 Analysis of ten generations of selection for residual feed intake in Yorkshire pigs. Iowa State University Animal Industry Report 2015.
  • Type: Other Status: Published Year Published: 2014 Citation: Mauch, E.D., J.M. Young, J.F. Patience, N.K. Gabler, and J.C.M. Dekkers. 2014. Effect of low energy, high fiber diets on�pigs selected for residual feed intake. A.S. Leaflet R2917. Iowa State University Animal Industry Report 2014.
  • Type: Other Status: Published Year Published: 2015 Citation: Steckelberg, J.R., E.D. Mauch, A.M. Dannen, N.V.L. Ser�o, and J.C.M. Dekkers. 2015. Pigs selected for residual feed intake �� during the grow-finish phase are also more efficient during the nursery phase. Iowa State University Animal Industry Report 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Boettcher, A.N., Powell E.J., Cunnick J.E., Loving C.L., Tuggle C.K.� 2016. Porcine SIRPA recognition of human CD47: Implications for human hematopoietic stem cell transplantation into SCID pigs.� 45th Annual Autumn Immunology Conference, November 18-21. Chicago, Illinois.
  • Type: Other Status: Published Year Published: 2014 Citation: De Jong, J.A., J.M. DeRouchey, M.D. Tokach, R.D. Goodband, J.C. Woodworth, S.S. Dritz, J. Erceg, L. McKinney, and G. Smith. 2014. Formation of fines during the pelleted feed manufacturing process and the resulting differences in nutrient composition of fines and pellets. Kansas Swine Industry Report of Progress 1110.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Flohr, J.R., M.D. Tokach, J.M. DeRouchey, J.F. Patience, R.D. Goodband, S.S. Dritz and J.L. Nelssen. 2012. Feed efficiency in swine: A survey of current knowledge. Proc. Kansas Swine Day 2012. pp. 1-16.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gabler, N.K. (2014) Gary Allee Symposium: The he longitudinal impact of PRRS on metabolism, whole body protein accretion and feed. ASAS-ADAS Midwest Animal Science Meeting, Des Moines, IA. March 17-19, Abstract # 60.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gabler, N.K. (2014) Porcine reproductive and respiratory syndrome virus impact on pig feed efficiency and tissue accretion. Nottingham Feed Conference, University of Nottingham June 24-25, Sutton Bonington Campus, UK.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gabler, N.K. What are the nutritional and metabolic costs of immune system activation in pigs? Midwest Animal Science Meeting, Non-ruminant Nutrition Symposium 2017. ASAS Midwestern Section and ADSA Midwest Branch Meeting. Omaha, NE, March 13-15, 2017
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Gabler, N.K. and W. Schweer. Impact of nutrition on disease susceptibility and the impact of disease on nutrient utilization. Pig Feed Quality Conference 2016. March 31-April 2, Bangkok, Thailand.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Graham, A. B., J. A. De Jong, J. M. DeRouchey, M. D. Tokach, S. S. Dritz, R. D. Goodband, and J. C. Woodworth. 2015. Effects of Creep Feed Pellet Diameter on Suckling and Nursery Pig Performance. �Kansas Agricultural Experiment Station Research Reports: Vol. 1: Iss. 7.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Helm, E., A. C. Outhouse , K. Schwartz , J. C. M. Dekkers , S. M. Lonergan , and N. K. Gabler. Impact of Lawsonia intracellularis-Mycoplasma hyopneumoniae Dual Challenge on Growth Performance of Pigs Divergently Selected for Residual Feed Intake. ASAS Midwestern Section and ADSA Midwest Branch Meeting. Omaha, NE, March 13-15, 2017
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Liu, H., T.P.L. Smith, D.J. Nonneman, J.C.M. Dekkers, C.K. Tuggle. 2016. A comprehensive porcine blood transcriptome. 35th Conference�of the International Society for Animal Genetics.�July 28 - August 1,�Salt Lake City, UT. Abstract �#P3033.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Liu, H., N. T. Yet, D. Nettleton, J. C. M. Dekkers, and C. K. Tuggle. 2016. Post-Weaning Blood Transcriptomic Differences Between Yorkshire Pigs Divergently Selected for Residual Feed Intake. Proceedings of Plant and Animal Genome XXIV.� San Diego, CA, USA. Abstract #W915.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Powell, E., J. Cunnick, S. Knetter, E. Waide, J.C.M. Dekkers, C.K. Tuggle. 2014.�Increased numbers of functional NK cells in pigs with Severe Combined Immune Deficiency (SCID) caused by natural mutations in the Artemis gene. 34th Conference�of the International Society for Animal Genetics.�July 28 - August 1, �in Xian, China. Abstract �#abs490.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Powell, E.J., A.N. Boettcher, L. Varley, J. Cunnick, M. Sauer, A. Putz, M. Schroyen, S. Charley, C.K. Tuggle. 2016. Contact hypersensitivity testing shows long-term hapten-specific memory associated with increased liver NK cell populations up to 32 days post-sensitization. 45th Annual Autumn Immunology Conference November 18-21. Chicago, Illinois.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Outhouse, A., J. Grubbs, C.K. Tuggle, N. Gabler, A. Rakhshandeh, S. Lonergan. Immune system stimulation by repeated lipopolysaccharide infections alters Longissimus dorsi sarcoplasmic protein in pigs. Reciprocal Meat Conference, Lincoln, NE June 14-17, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Schroyen, M. K. M. Feye, Y. T. Nguyen, A. Rakhshandeh, N. K. Gabler, D. Nettleton, J. C. M. Dekkers, and C. K. Tuggle. 2016. Towards robust blood biomarkers for residual feed intake in pigs. 35th Conference�of the International Society for Animal Genetics.�July 28 - August 1,�Salt Lake City, UT. Abstract �#P3011.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Tuggle, C.K., D. Rajao, C. Loving, P.C. Gauger, E. H. Waide, J.C.M. Dekkers, and A. Vincent. 2014. �Inability of Severe Combined Immune Deficient (SCID) pigs to control IAV replication despite innate immune activation. Vaccines Against Antigenically Variable Viruses Iowa State University meeting, Ames, IA. June 18-19, 2014. (Abstract #32).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Waide, E.H., C.K. Tuggle, N.M. Ellinwood, J.W. Ross, J.C.M. Dekkers. 2014. Not all SCID pigs are created equally: two natural mutations cause Severe Combined Immunodeficiency (SCID) in pigs. The International Plant & Animal Genome XXI Conference. January 11-15, 2014, San Diego, California. (Abstract # P0598).
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nguyen, Y., D. Nettleton, H. Liu, and C.K. Tuggle. 2015. Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates. J. Agricultural, Biological, and Environmental Statistics. 20:577-597.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Colpoys, J. D., C. E. Abell, N. K. Gabler, A. F. Keating, S. T. Millman, J. M. Siegford., J. M. Young, A. K. Johnson. 2015. Feed efficiency effects on barrow and gilt behavioral reactivity to novel stimuli tests. J. Anim. Sci. 93(3): 1267-1275
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Dunkelberger, J.R., N.J. Boddicker, N.V.L. Serao, J.M. Young, R.R.R. Rowland, and J.C.M. Dekkers. 2015. Response of pigs divergently selected for residual feed intake to experimental infection with the PRRS virus. Livestock Sci. 177: 132-141
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ewen, C.L., A.G Cino-Ozuna, H. He, M.A. Kerrigan, J.C. Dekkers, C.K. Tuggle, R.R. Rowland, C.R. Wyatt. 2014. Analysis of blood leukocytes in a naturally occurring immunodeficiency of pigs shows the defect is localized t oB and T cells. Vet Immunol and Immunopat. 162 (3-4) DOI: 10.1016/j.vetimm.2014.10.003
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Flohr, J.R., M.D. Tokach, J.M. DeRouchey, R.D. Goodband, S.S. Dritz, J.L. Nelssen, and J.F. Patience. 2014. Feed Efficiency: An assessment of current knowledge from a voluntary subsample of the swine industry. J. Extension. 52:6RIB6.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Graham, A.B., R. D. Goodband, M. D. Tokach, S. S. Dritz, J. M. DeRouchey, S. Nitikanchana, and J. J. Updike. 2014. The effects of low-, medium-, and high-oil distillers dried grains with solubles on growth performance, nutrient digestibility, and fat quality in finishing pigs. J. Anim Sci. 92:3610-3623
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Harris, A.J., J.F. Patience, S.M. Lonergan, J.C.M. Dekkers and N.K. Gabler. 2012. Improved nutrient digestibility and retention partially explains feed efficiency gains in pigs selected for low residual feed intake. J Anim Sci 90: 164-166.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu, H., Nguyen, Y., Nettleton, D., Dekkers, J., Tuggle, C. 2016 Post-Weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake. BMC Genomic. doi: 10.1186/s12864-016-2395-x.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Liu, H., T.P.L. Smith, D.J. Nonneman, J.C.M. Dekkers, C.K. Tuggle.� �2017. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics, in press.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nguyen, Y., Nettleton, D., Liu, H., Tuggle, C. K. 2015. Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates. Journal of Agricultural, Biological, and Environmental Statistics. 20:577-597.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Powel, E.J., J.E. Cunnick, S.M. Knetter, C.L. Loving, E.H. Waide, J.C. Dekkers and C.K. Tuggle. 2016. NK cells are intrinsically functional in pigs with Severe Combined Immunodeficiency (SCID) caused by spontaneous mutations in the Artemis gene Vet. Immunol Imunopathol. doi:10.1016/j.vetimm.2016.04.008. Epub 2016 Apr 19
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rajao, D.S., C.L. Loving, E.H. Waide, P.C. Gauger, J.C. Dekkers, C.K. Tuggle and A.L. Vincent. 2017. Pigs with severe combined immunodeficiency are impaired in controlling influenza A virus infection. J. Innate. Immun. 9(2): 193-202.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Rakhshandeh, A., J.C.M. Dekkers, B.J. Kerr, T.E. Weber, J. English and N.K. Gabler. 2012. Effect of immune system stimulation and divergent selection for residual feed intake on digestive capacity of the small intestine in growing pigs. J Anim Sci 90: 233-235.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Waide, E.H., J.W. Ross, R.R. Rowland, C.R. Wyatt, A.B. Evans, D.M. Thekoot, N.J. Boddicker, N.V. Serao and C.K. Tuggle. 2015 Not all SCID pigs are created equally: Two independent mutations in the Artemis gene cause SCID in pigs. J Immunol. 195(7) 3171-3179.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Arkfeld, E. K., E. R. Benedict, R. C. Johnson, J. M. Young, D. M. Thekkoot, J. K. Grubbs, S.M. Cruzen, N. K. Gabler, J. C. M. Dekkers, S. M. Lonergan, E. Huff-Lonergan. 2013. Composition and quality of carcasses from pigs selected for divergent residual feed intake. Meat Science 93:25.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Arkfeld, E. K., E. R. Benedict, R. C. Johnson, J. M. Young, J. F. Patience, J. C. M. Dekkers, N. K. Gabler, S. M. Lonergan, E. Huff-Lonergan. 2013. Divergent selection for residual feed intake impacts carcass composition of pigs on high or low energy diets. J. Anim. Sci. 91(Suppl.2):9.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Arkfeld, E.K., J. E. Berger, E. R. Hamman, J. M. Young, R. C. Johnson, C. A. Fedler, K. Prusa,� J. F. Patience,� J. C. M. Dekkers, N. K. Gabler, S. M. Lonergan, E. Huff-Lonergan. 2014. Effect of diet and selection for residual feed intake on sensory quality and postmortem proteolysis of pork loin. Meat Science Meat Science 101:123. doi:10.1016/j.meatsci.2014.09.059.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Arkfeld, E.K., E. R. Benedict, R. C. Johnson, J. M. Young, J. F. Patience, J.C.M. Dekkers, N. K. Gabler, S. M. Lonergan, and E. Huff-Lonergan. 2014. Effects of divergent selection for residual feed intake and diets varying in energy and fiber content on pork loin protein degradation and sensory quality. Meat Science 96:470(doi:10.1016/j.meatsci.2013.07.102).
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: De Jong, J.A, J.M. DeRouchey, M.D. Tokach, R.D. Goodband, S.S. Dritz, and C.W. Hastad. 2014. Effects of corn particle size, complete diet grinding, and diet form on 11- to 20-kg nursery pig growth performance and caloric efficiency. J. Anim. Sci. 92 (Suppl.2):133
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Flohr, J.R., M.D. Tokach, J.M. DeRouchey, J.F. Patience, R.D. Goodband, S.S. Dritz and J.L. Nelssen. 2012. Feed efficiency in swine: A survey of current knowledge. Proc. Kansas Swine Day 2012. pp. 1-16.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Gabler, N.K., J.K. Grubbs, A. Harris, S.M. Cruzen, E. Huff-Lonergan, J.F. Patience, J.C.M. Dekkers and S.M. Lonergan. 2012. The physiological basis defining feed efficiency differences in pigs selected on residual feed intake. Ann. Mtg., American Society of Animal Science, Phoenix, AZ.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gabler, N. K., and W. P. Schweer. 2014. Porcine reproductive and respiratory syndrome virus and pig feed efficiency and tissue accretion In: P. C. Garnsworthy and J. Wiseman (eds.) Recent Advances in Animal Nutrition p125-138. Context Leicestershire, United Kingdom.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Huff-Lonergan, E., S. M. Lonergan, S. Cruzen, K. Grubbs, J. Dekkers, N. Gabler, J. Selsby, and L. Baumgard. 2014. Use of proteomics for livestock improvement. Journal of Animal Science 92(E-Suppl.2):190.�
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Nemechek, J.E., M.D. Tokach, E. Fruge, E. Hansen, S.S. Dritz, R.D. Goodband, J.M. DeRouchey, and J.L. Nelssen. 2013. Effect of pellet quality and feeder adjustment on growth performance of nursery pigs. J. Anim. Sci. 91 (Suppl. 2): (Abstr.).


Progress 04/01/15 to 03/31/16

Outputs
Target Audience:Primary target audiences are 1) pork producers, 2) feed and genetics suppliers to the pork industry, 3) consultants, including veterinarians, 4) extension and related workers, and 5) the academic community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We continue to train undergraduate and graduate students with the support of this grant. We have also had the opportunity to train and expose the industry and scientific community with multiple events on Year 5 as listed bellow: Project Wrap-Up Conference for the Pork and Related Industries: This conference was held in October, 2015, in Omaha, NE. More than 500 people registered for the event, representing 19 different countries, 25 US states and 22 different universities. It was estimated that about 50% of the total US sow herd was represented at the conference. The program included 38 speakers making 41 different presentations. The conference was a huge success, and many attendees asked when the next conference might be held. Specialized Conference for the Genetics Industry:This conference was embedded in the Wrap-Up Conference. Train the Trainer Conference:A Train the Trainer Conference was held as part of the national swine extension meeting in 2015. The target audience in this instance was extension personnel. In addition, a session was held as a pre-conference symposium at the American Association of Swine Veterinarians Annual Meeting, held in late February, 2016. The target audience was veterinarians and feed industry personnel, who as a group have a great deal of direct contact with pork producers. This event was extremely well attended and feedback was very positive. A presentation at the Leman Conference in September, 2016 will also share the results of demonstration projects undertaken as part of this project. Smaller specialized conferences have also proven to be extremely popular. Last year, a specialized conference on dietary fat was held in Ames, IA, with excellent results; its target audience was feed industry nutritionists, a group who has a very large influence on the composition of diets fed to the U.S. swine herd. Website on Feed Efficiency:The website has been created (www.swinefeedefficiency.com) and populated with information that is currently available. Visitors to the website can access decision-making tools, published papers, abstracts and conference proceedings (when allowed by copyright), information about the AFRI project, factsheets, podcasts, popular press articles, presentations and decision tools. This website also carries all of the presentations from the 2015 ICFES. How have the results been disseminated to communities of interest?During year 5 of our project, we were able to use 4 channels of distribution of information: Website - our website has been updated constantly and every PD has used it's address to "advertise" our results to the industry. All presentations and proceedings from the ICFES 2015 have been published on our website. Podcasts - our group from Kansas State University has used its podcast to promote results from our demonstration projects. Conferences - students and PDs have been in multiple conferences presenting data from this project. Factsheets: printed material has been distributed with help of extension specialist from KSU and ISU. What do you plan to do during the next reporting period to accomplish the goals?Research Objective #1: Quantify the performance of pigs selected for increased FE under corn-soybean diets when fed lower quality by-product ingredients (higher fiber, lower fat). Microbial data are still under analysis at University of Saskatchewan. Genomic DNA testing for part of the samples is still underway and with that, design of pyrosequencing strategy and assignment of MID tags, preparation of genomic DNA samples for pyrosequencing, including amplification and purification of cpn60 Universal Target using appropriate MID tagged primers and complete qPCR enumeration of selected major taxonomic groups have not been concluded. Research Objective 3: Develop industry-ready tools to easily and effectively identify and select more efficient pigs. Objective 3A: Development of a practical classifier to predict feed efficient pigs. We have initiated higher-throughput protein blot analyses to test the value of three proteins for predicting RFI status and we expect to complete these ISU-specific analyses by the end of the current grant period. A significant issue is that we are testing only our ISU lines, and demonstration of proteins or RNAs consistently predictive of RFI in another swine population would magnify the value of these biomarkers. As described above, we have initiated collaboration with Helene Gilbert and co-workers at INRA, France, who have developed similar RFI selection lines and have access to animals for sample collection. We are discussing the experimental design for such sample collection within their lines so that we can attempt to validate both our RNA and protein biomarker findings. Objective 3B:Identification of key molecular pathways or networks that integrate FE with stress responses in pigs.For several reasons (decreased sequencing costs, the failure to see blood RNA differences due to ISS at 168 hours, and the observation of tissue protein differences at this time point), we have performed RNAseq and miRNAseq analysis of liver, spleen, small intestine andL. dorsi. These analyses are ongoing, but we clearly see RNA expression in liver that distinguishes both line and ISS treatment groups. We expect to complete the RNA portion of this work by the end of the grant period and to write a manuscript in the no-cost extension period. We will also use the additional time to perform an analysis of the miRNA expression patterns in these tissues, and attempt to integrate the RNA and miRNA patterns so that we have a more comprehensive view of the RNA differences in response to ISS in the two RFI lines. Also, development of new mass spectrometry technologies on our campus have provided the opportunity to make proteome wide comparisons using the LS MS/MS approach for whole liver extracts. This approach is more sensitive and provides more resolution. Now that the ISU Protein Facility has solved their equipment upgrade issues, we will analyze liver cytoplasmic proteins with the high-throughput methods available. Preliminary evidence shows that abundance and identity of over 400 proteins per 2-hour run will be possible. Using existing samples from Objective 3B, we are in a position to extend our understanding of the proteome response to stress response. Importantly, we will integrate the proteome data with RNA expression to define the physiological pathways involved in FE and response to stress. Objective 3C: Genome-Wide Association Analyses to identify SNPs associated with FE and RFI.Following tasks need to be done to complete this objective: GWAS on the high fiber diet and identification of genomic regions that show genotype by diet interactions; Combined GWAS with the INRA data; Genotyping founders on the 650K SNP panel (added objective); Impute all genotyped animals up to 650K (added objective); Repeat GWAS and genomic prediction analyses with 650K data. Objective 3E: Develop and validate FE SNPs in commercial populations.To be completed: Genomic prediction analyses with external population. Objective 4: Increase pork producers' awareness of the factors influencing feed efficiency and strategies available to achieve improvement. Extension Objective 5: Ensure the rapid and effective implementation of new technologies to improve feed efficiency both nationally and internationally.It is anticipated that another specialized conference, on the topic of fiber, will be held in the extension period. A great deal of interest in such an event has been expressed by the industry. Again, the target audience will be feed industry nutritionists, who have a very large influence on the composition of diets fed to the U.S. swine herd. Covering fat and fiber will provide a great deal of training on two aspects of the pig diet, which have a large impact on feed efficiency as well as economic efficiency. In the extension year, translation into Spanish will be completed, and additional factsheets based on project research will be completed. One more demonstration project can be completed in the extension year.

Impacts
What was accomplished under these goals? The project is under the final year of it's course, all objectives are being finalized, and manuscripts are being finished. The research knowledge created through this multidisciplinary approach was presented to the swine industry October 2015 on the International Conference on Feed Efficiency in Swine. Producers and technical support related personnel now have tools and information to understand how animals selected for feed efficiency behave on a physiological, behavioral and nutritional level. Final studies being conducted will try to answer questions on a molecular level. An effort to disseminate information to pork producers through conferences and training as part of our extension objectives is within the last period of this grant. Following are accomplishment broken down by project objectives. Research Objective #1: Quantify the performance of pigs selected for increased FE under corn-soybean diets when fed lower quality byproduct ingredients (higher fiber, lower fat) Objective 1A, B and C.We are finalizing the manuscript drafts and publications, and these objectives are completed.Objective 1D: Microbial populations. Intestinal content and mucosal samples have been collected and microbial populations sequenced. Microbial data is still under analyses at University of Saskatchewan. Research Objective#2: Evaluate the ability of pigs selected for increased efficiency to cope with behavioral, physiological and immunological stressors. All manuscripts proposed for this objective have been published or are in the process of being published. Research Objective 3: Develop industry-ready tools to easily and effectively identify and select more efficient pigs. Objective 3A: Development of a practical classifier to predict feed efficient pigs. We have identified both RNAs and proteins that are differentially expressed between the RFI lines, and three papers have been submitted on these projects. Objective 3B:Identification of key molecular pathways or networks that integrate FE with stress responses in pigs.We have completed the liver protein and blood RNAseq data collection for Obj 3B; Preliminary results indicate that there are few whole blood RNA differences between the lines due to Immune System Stimulation (ISS) treatment either acutely (2-24 hrs treatment) or by 168 hrs. Objective 3C: Genome-Wide Association Analyses to identify SNPs associated with FE and RFI.All proposed genotyping using the 60K SNP panel has been completed and GWAS analyses have been conducted. This has not resulted in the identification of QTL with large effects, which might be due to the polygenic nature of RFI. Objective 3D: Identify SNPs Associated with Response to PRRS Infection.This objective has been completed. Objective 3E: Develop and validate FE SNPs in commercial populations.The original plan was to develop a small genotyping panel with SNPs that were identified to be significant in the RFI lines. Because of the apparent polygenic nature of RFI, this objective will not be pursued as such. Extension Objective 4: Increase pork producers' awareness of the factors influencing feed efficiency and strategies available to achieve improvement. Extension Objective 5: Ensure the rapid and effective implementation of new technologies to improve feed efficiency both nationally and internationally. The majority of the activities have been completed. Objectives 4 & 5: Activity #3: Website on Feed Efficiency The website for this project,www.swinefeedefficiency.comis in progress.Activity #5: Factsheets on Feed Efficiency. Factsheets are the primary vehicle for us to we use to reach the segment of the pig industry that works on a daily basis with pigs. In other words, these are the foot soldiers who care for pigs and often have great influence on overall production efficiency, but who are unlikely to attend conferences or visit websites. The factsheets are being translated into Spanish to enhance communication with Hispanic employees. Activity #7: Demonstration Projects. Demonstration projects have proven to be a very popular component of this extension effort. One project remains in process. Activity #10: Train-the Trainer-Conference:Maximizing the multiplier effect of train-the-trainer efforts is also a very effective extension tool. While traditional extension personnel associated with universities and other public institutions have been served in this regard, the growing role of agribusiness in extending new technology also needs to be recognized.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Arkfeld, E. K., J. M. Young, R.C. Johnson, C.A Fedler, K. Prusa, J. F. Patience, J. C. M. Dekkers, N. K. Gabler, S.M. Lonergan, E. Huff-Lonergan. 2015. Composition and quality characteristics of carcasses from pigs divergently selected for residual feed intake on high or low energy diets. Journal of Animal Science 93:2530-2545.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Colpoys, J. D., A.K. Johnson, N. K. Gabler. 2016. Daily feeding regimen impacts pig growth and behavior. Physiol Behav. 2016 Mar 5. pii: S0031-9384(16)30090-7. doi: 10.1016/j.physbeh.2016.03.003. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Colpoys, J. D., C. E. Abell, N. K. Gabler, A. F. Keating, S. T. Millman, J. M. Siegford., J. M. Young, A. K. Johnson. 2015. Feed efficiency effects on barrow and gilt behavioral reactivity to novel stimuli tests. J. Anim. Sci. 93(3): 1267-1275
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Grubbs, J.K., C.K. Tuggle, J.C.M. Dekkers, N.J. Boddicker, Y.T. Nquyen, E. Huff-Lonergan, D. Nettleton, S.M. Lonergan.2015. Investigation of the efficacy of albumin removal procedures on porcine serum proteome profile. Journal of Animal Science. doi: 10.2527/jas2014-8559
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mpetile Z, Young JM, Gabler NK, Dekkers JC, Tuggle CK. 2015. Assessing peripheral blood cell profile of Yorkshire pigs divergently selected for residual feed intake. J Anim Sci. 2015 Mar;93(3):892-9.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nemechek, J.E., M.D. Tokach, S.S. Dritz, E.D. Fruge, E.L. Hansen, R.D. Goodband, J.M. DeRouchey, and J. C. Woodworth. 2015. Effects of diet form and feeder adjustment on growth performance of nursery and finishing pigs. J. Anim. Sci. 93:41724180.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nemechek, J.E., M.D. Tokach, S.S. Dritz, R.D. Goodband, J.M. DeRouchey, and J.C. Woodworth. 2016. Effecs of diet form and particle size on growth performance and carcass characteristics of finishing pigs. Anim. Feed Sci. Tech.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Schweer W.P., S.C. Pearce, E. Burrough, K Schwartz, K.J. Yoon, C. Sparks, and N.K. Gabler. 2016. The effect of PRRSV and PEDV challenge on growing pigs I: Growth Performance and digestibility. Journal of Animal Science 94:2:514-522.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Schweer W.P., S.C. Pearce, E. Burrough, K Schwartz, K.J. Yoon, C. Sparks, and N.K. Gabler. 2016. The effect of PRRSV and PEDV challenge on growing pigs II: intestinal integrity and function. Journal of Animal Science 94:2:523-532.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Flohr, J. R., J. C. Woodworth, M. D. Tokach, S. S. Dritz, J. M. DeRouchey, and R. D. Goodband. 2016. Development of equations to predict the influence of floor space on average daily gain, average daily feed intake, and gain-to-feed ratio of finishing pigs. J. Anim. Sci. 94 (Suppl.2):15 (Abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Flohr, J. R., J. C. Woodworth, M. D. Tokach, S. S. Dritz, J. M. DeRouchey, R. D. Goodband, and G. Gourley. 2016. Evaluating the effects of floor space allowance and pig removal from a group on the growth of finishing pigs. J. Anim. Sci. 94 (Suppl.2):16 (Abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: DeJong, J. A., J. M. DeRouchey, M. D. Tokach, S. S. Dritz, R. D. Goodband, and J. C. Woodworth. 2016. Effects of creep feed pellet diameter on suckling and nursery pig performance. J. Anim. Sci. 94 (Suppl.2):213 (Abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: De Jong, J. A., J. M. DeRouchey, M. D. Tokach, R. D. Goodband, J. C. Woodworth, C. K. Jones, C. R. Stark, L. McKinney, G. Smith, and J. A. Erceg. 2015. Formation of fines during the pelleted feed manufacturing process and the resulting differences in nutrient composition of fines and pellets J. Anim. Sci. 93 (Suppl.2):140 (Abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: De Jong, J. A., J. M. DeRouchey, M. D. Tokach, R. D. Goodband, S. S. Dritz, and M. Allerson. 2015. Evaluating strategic pellet feeding regimens on finishing pig performance, stomach morphology, and carcass characteristics. J. Anim. Sci. 93 (Suppl.2):386 (Abstr.).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Grubbs, J.K., C.K. Tuggle, J.C.M. Dekkers, S.M. Lonergan. 2015 Comparison of Albumin Depleted and Whole Serum Samples for Biomarker Identification. Journal of Animal Science. 92(E-Suppl 2):577
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Grubbs, J.K., C.K. Tuggle, J.C.M. Dekkers, S.M. Lonergan. 2016 Identification of Potential Serum Biomarkers for Feed Efficiency in Young Pigs. Journal of Animal Science. 92(E-Suppl 2):187.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Haibo Liu, Yet Nguyen, Dan Nettleton, Jack Dekkers, Chris Tuggle. Identification of early blood differentially expressed genes between two pig lines divergently selected for feed efficiency: Potential biomarkers for feed efficiency. 2015 Midwest ADSA-ASAS Annual Meeting. Des Moines, IA. March 15-18, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Hsu, W., J.M. Young, E.D. Mauch, and J.C.M. Dekkers. 2015. Estimates of genetic parameters and response to 10 generations of selection for residual feed intake in Yorkshire pigs. ADSA�-ASAS Joint Midwest Meeting. Des Moines, IA. 16 March 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Outhouse, A. C., J. K. Grubbs, C. K. Tuggle, N. K. Gabler, A. Rakhshandeh, and S. M. Lonergan. 2015. Immune system stimulation by repeated lipopolysaccharide injection alters liver cytoplasmic protein profile in pigs.?J. Anim. Sci 93(Suppl. 2):20
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Tuggle, C.K., E.J. Powell, D. Rajao, C. Loving, K. Feye, J. Cunnick, P.C. Gauger, A. Vincent, E.H. Waide, and J.C.M. Dekkers. Characterizing the Iowa State University Severe Combined Immune Deficient (SCID) Pig. Plant and Animal Genome XXIII, Abstract W832, January 2015.
  • Type: Other Status: Published Year Published: 2015 Citation: Graham, A. B., J. A. De Jong, J. M. DeRouchey, M. D. Tokach, S. S. Dritz, R. D. Goodband, and J. C. Woodworth. 2015. Effects of Creep Feed Pellet Diameter on Suckling and Nursery Pig Performance. Kansas Agricultural Experiment Station Research Reports: Vol. 1: Iss. 7.
  • Type: Other Status: Published Year Published: 2015 Citation: Flohr, J. R., M. D. Tokach, John F. Patience, G. Gourley, J. M. DeRouchey, S. S. Dritz, J. C. Woodworth, and R.D. Goodband. 2015. Re-evaluating Floor Space Allowance and Removal Strategy Effects on the Growth of Heavyweight Finishing Pigs. Kansas Agricultural Experiment Station Research Reports: Vol. 1: Iss. 7.
  • Type: Other Status: Published Year Published: 2015 Citation: Flohr, J. R., M. D. Tokach, S. S. Dritz, J. C. Woodworth, J. M. DeRouchey, and R. D. Goodband. 2015. Using Meta-analyses to Generate Alternative Prediction Equations for the Space Requirements of Finishing Pigs. Kansas Agricultural Experiment Station Research Reports: Vol. 1: Iss. 7.
  • Type: Other Status: Published Year Published: 2015 Citation: De Jong, J. A., J. M. DeRouchey, M. D. Tokach, S. S. Dritz, R. D. Goodband, and M. Allerson. 2015. Evaluating Pellet and Meal Feeding Regimens on Finishing Pig Performance, Stomach Morphology, Carcass Characteristics, and Economics. Kansas Agricultural Experiment Station Research Reports: Vol. 1: Iss. 7.
  • Type: Other Status: Published Year Published: 2015 Citation: Sholar, J., Colpoys, J. D., Gabler, N. K., Keating, A. F., Millman, S. T., Siegford, J.; and Johnson, A. K. 2015. Approachability to a Human in Gilts Divergently Selected for Feed Efficiency, Animal Industry Report, Iowa State University. AS 661, ASL R3016.
  • Type: Other Status: Published Year Published: 2015 Citation: Mauch, E. D., Gabler, N. Sera?o, N. V. L., Weber, T. E., Patience, J. F., Kerr, B. and Dekkers, J. C. M. 2015. Effect of Low Energy, High Fiber Diets on Digestibility Traits in Pigs Selected for Residual Feed Intake," Animal Industry Report, Iwoa State University. AS 661, ASL R3033.
  • Type: Other Status: Published Year Published: 2015 Citation: http://www.swinefeedefficiency.com/podcasts


Progress 04/01/14 to 03/31/15

Outputs
Target Audience: Primary target audiences are 1) pork producers, 2) feed and genetics suppliers to the pork industry, 3) consultants, including veterinarians, 4) extension and related workers, and 5) the academic community. Changes/Problems: With the efficiency of our grant budget two activities have been extended to expand knowledge and outreach of our project. Since the Genetics Conference will be done in combination with the II International Feed Efficiency in Swine (October 2015), funds are being used as a training opportunity with a one-day symposium on lipids for swine; the objective of this symposium is to expand and distribute knowledge on the incorporation of lipids into swine diets.We are also expanding the number of demonstration projects with the funds freed up by savings in other extension activities. What opportunities for training and professional development has the project provided? Nick Serao - Post doc - Indirect - assist with data collection Wan-Ling Hsu - Post doc - Direct - Quantitative genetic analyses of selection response and genetic parameters Martine Schroyen - Post doc - Indirect- process RNA samples in Obj 3A J. Kyle Grubbs - Post doc - Direct- process serum sample, analyze protein data in Obj 3A Project: the identification of protein as biomarkers differentially expressed in efficient versus non-efficient animals Nestor Gutierrez - Post Doc - Indirect assistance/training Shelby Curry - PhD. - Direct - assist with lab sample analysis in Objective 2 Yet Nguyen - PhD - Direct: analyze RNA data Chad Paulk - PhD - Indirect assistance/training Trey Kellner - PhD - Direct - Demonstration project Kristina Feye - PhD - Direct- process samples, help analyze data in Obj 3B. Thesis: The effect of Immune stress on feed efficient animals Kyle Coble - PhD - Indirect assistance/training Jessie Colpoys - PhD - Direct- Behavioral and physiological stress responses of RFI lines Jeremiah Nemechek - PhD - Direct assistance/training Josh Flohr - MS and PhD - Direct assistance/training Jon De Jong - MS and PhD - Direct assistance/training Haibo Liu - PhD - Direct - process RNA and metabolomic samples, help analyze data in Obj 3A. Thesis: Identification of biomarkers for feed efficiency using a systems biology approach Jenelle Dunkelberger - PhD - Direct - Effect of PRRS challenge on RFI lines; help with data collection Emily Mauch - MSc - Direct - Effect of high fiber diet on RFI lines; help with data collection Amanda Graham - MS - Indirect assistance/training Devin Goehring - MS - Indirect assistance/training Miriam Ayuso Hernando - Visiting scholar Involved with data collection and review of fact sheets for the project. Jesus Acosta - MSc - Indirect assistance/training Joel Steckelberg - Undergraduate - Indirect - assist with data collection and entry and sample collection, storage, and processing Kelsey Wahlberg - Undergraduate - Indirect - assist with data collection and entry and sample collection, storage, and processing Austin Putz - Undergraduate - Direct- process RNA samples in Obj 3A Project: the isolation and globin depletion of RNA samples from whole blood collected from high and low efficient animals. Jordy Berger - Undergraduate - Indirect assistance/training Emily Benedict - Undergraduate - Indirect assistance/training Roslyn Punt - Undergraduate - Indirect assistance/training Johanna Sholar - Undergraduate - Indirect- assist with data analysis Chloe Wasendorf - Undergraduate - Indirect- assist with data analysis Jennie Schubert - Undergraduate -Indirect- assist with data collection Ashley Woodley -Undergraduate - Indirect- assist with data collection Adrianne Kaiser -Undergraduate -Indirect- assist with data collection Jentry Fane - Undergraduate - Indirect assistance/training Bree Adamic - Undergraduate - Indirect assistance/training Anna Clifton - Undergraduate - Direct - assistance/training Alyssa Dannen - Undergraduate - Indirect - assist with data collection and entry and sample collection, storage, and processing -Direct assistance/training - if a student is or was involved with this AFRI grant for Full thesis or thesis chapter -Indirect assistance/training - if a student is or was involved with this AFRI grant by helping other students or researcher How have the results been disseminated to communities of interest? During year 4 of our project, there were able to able to use 4 channels of distribution of information: Website - our website has been updated constantly and every PD has used it's adress to "adverstise" our results the industry. Podcasts - our group from Kansas State University has used its podcast to promote results from our demosntration projects. Conferences - students and PDs have been in multiple conferences presenting data from this project. Fact Sheets - Fact sheets have been printed in a booklet format and distruted to industry and farmers. What do you plan to do during the next reporting period to accomplish the goals? Objective 1: Objectives 1A and 1B - Growth performance and feed efficiency/Meat quality: Finalize analysis of the line by diet experiment and write manuscript. Finish gene and protein abundance analysis on metabolism samples. Objective 1C - Metabolism: Finish statistically analyzing the total tract digestibility data and its relationship with the performance data in 1A. Objective 1D - Microbial populations: Extract and purify genomic DNA for all samples. Design pyrosequencing strategy and assign MID tags. Prepare genomic DNA samples for pyrosequencing, including amplification and purification of cpn60 Universal Target using appropriate MID tagged primers. Complete qPCR enumeration of selected major taxonomic groups. Objective 2: Objective 2A - Behavioral Studies: Completed. Objective 2B - Appetite regulation and ACTH challenge: Complete this sub objective by finishing drafting the ACTH manuscript and submit for scientific review and publication. To analyze the data collected feeding frequency and appetite regulation study and write up the manuscript. Objective 2C - E. coli Endotoxin Challenge: Complete this objective by finishing drafting and submit the manuscript for scientific review and publication. Objective 2D - PRRS Challenge: Completed. Objective 3: Objective 3A - Practical Classifier: We will further analyze the RNA-seq variants to find genes carrying different polymorphisms between lines and identify allele-specific expression of genes. To build a practical classifier for pig feed efficiency, we will quantitate a subset of the confirmed differentially expressed genes among large number of pigs from each line and diet combination, as well as confirm line-specific RNA-seq variants. We will finish identification of selected differentially expressed proteins, and begin testing of antibodies for confirmation of identified proteins via high-throughput methods such as Westerns or ELISA methods. Serum samples will be assayed for metabolites. Thyroid hormone assays will be run and analyzed. Objective 3B - A targeted systems immunology analysis of the LPS stimulated will be executed. This analysis will also include the RNAseq data, miRNA Sequencing and cytokine levels in blood (IL1β, IL4, IL6, IL8, IL10, TNFα, INFγ, INFα on the Aushon Ciraplex 9plex). The metabolite analysis of hours 0 and 168 for LRFI and HRFI samples will be completed. Data will be uploaded into MetaPA and analyzed for enrichment analysis. Proteins identified as changed in response to stress will be integrated with existing data on FE in pigs. A manuscript with these data will be completed and submitted. Objective 3C - Association Analysis: Comprehensive GWAS and genomic prediction analyses will be conducted across lines, diets and generations. Data on pathways and gene expression will be integrated. Higher density genotyping or sequencing of founders, followed by imputation for advanced GWAS and genomic prediction will be explored. Joint analysis of selection signatures with the INRA RFI lines. Objective 3D - completed. Objective 3E - use of industry data - Because of the implementation of extensive high density genotyping for genomic selection in industry data and the polygenic nature of RFI, the decision was made not to pursue development of a small SNP chip. Instead, funds will be used for additional genotyping or sequencing in the RFI lines and accuracies of genomic prediction from the RFI lines to other populations (INRA RFI lines and industry populations) will be evaluated. Objectives 4 and 5: Second International Conference in planning stage, will combine the specialized genetics conference into this conference. Added a special conference on dietary fat, which will be held to address this important topic as it relates to feed efficiency. Project Website: Content of feed efficiency website continue to be expanded as new materials and new information from research become available. Decision Tools: Additional decision tools will be developed in year 4, including an interactive feed efficiency decision tree. Demonstration Projects: As previously planned, another demonstration projects will be conducted on commercial pig farms to highlight technologies that improve feed resource utilization. The results of the demonstration project on the use of dietary fat to improve feed efficiency will be summarized and presented to the pork industry. "Train the Trainer" sessions will be held to educate Extension specialists and veterinarians on the latest feed efficiency information to allow them to use the information to train producers.

Impacts
What was accomplished under these goals? The research undertaken in this 5-year project takes advantage of two divergently selected genetic lines at Iowa State University. The lines have been selected for low or for high residual feed intake (RFI). The selection process involves measuring the feed intake on individual pigs, as well as their average daily gain and backfat thickness. The feed intake expected to be needed to support this gain and fat accretion is estimated and individual pigs are selected. If their feed intake is higher than expected, these are less efficient pigs and are called high RFI. Pigs who achieved this performance on less feed than expected are more efficient pigs and are called low RFI. Overall we are observing that pigs that have been selected for improved feed efficiency are performing in a similar fashion in terms of challenges to the immune system, behaviorally, and in meat quality as pigs with lower efficiency. Objective 1 All Year 4 graduate students and a postdoctoral research associate are in place. Growth performance and feed efficiency: Data, including growth performance, feed intake, body weight gain, nutrient digestibility and feed efficiency have been collected on all 4 replicates of this experiment and statistical analyses to evaluate the effect of line and its interaction with diet has been completed for replicates 1-3. Assessment of line differences in protein accretion at Texas Tech University is nearly complete. Data have also been collected to evaluate line differences in growth, feed intake, and feed efficiency in the nursery. Meat quality: completed and manuscript has been submitted. Metabolism: Digestibility samples have been collected and analyses completed for nutrient and energy balance across the two lines of pigs (high and low feed efficiency). Microbial populations: Intestinal content and mucosal samples have been collected following euthanasia of 60 pigs used in the metabolism study under Objective 1C. Analysis is in progress. Objective 2 Behavioral studies: Indirect stress response data from Rep 1 and 2 were analyzed and results were presented at the ASAS Midwest and Joint Annual Meetings. The manuscripts are published. Appetite regulation and ACTH challenge: All laboratory analyses were completed and the data were statistically analyzed. The ACTH challenge data were presented at the ASAS Midwest Meeting and a manuscript is in preparation. A feeding frequency and appetite regulation study has been conducted. E. coli endotoxin challenge: Conducted gene expression analysis on tissues from this study using the Fluidigm 48.48 Gene Expression Chip. All data have now been collected and analyzed for this objective and a manuscript is being drafted. Results have been presented at scientific and industry meetings. PRRS challenge: Analysis of growth and viremia data from the PRRS challenge has been completed; a manuscript has been completed and submitted. Objective 3 Practical classifier: Data have been collected. From second half of samples, extremes of populations based on RFI data in each line and under each diet were selected (2x2 factorial, eight pigs each). RNA isolation from blood was sequenced. Specific genes of interest have been selected for further verification by qPCR. Tests of the effect of depleting serum albumin prior to quantitative analysis using two-dimensional gels were completed and a manuscript submitted. A total of three proteins have been identified as potential classifiers. Currently, a manuscript is in preparation with regards to these classifiers. In addition, a manuscript has been accepted. Statistical comparison of complete blood counts traits as a measure of immunity between the two lines has been completed, and a manuscript has been accepted. Integrate FE with stress responses: We developed an optimal experimental design to prepare and sequence the RNA for all 80 samples. High-quality RNA has been prepared for all samples and all samples have been depleted of high abundance RNAs for alpha- and beta-globin. This depletion is being validated via a Fluidigm 48.48 Gene Expression Chip. In addition to this validation, a targeted Fluidigm analysis of the samples being sequenced has been designed to evaluate some known RFI differences, classical TLR4 signal transduction and response elements, and compare to human and murine data sets. This analysis is underway. A metabolite analysis of hours 0 and 168 for LRFI and HRFI samples will be initiated using the Absolute IDQ p180 metabolite kit. The results have yielded a few interesting interactions, including RFI*Time and RFI*Treatment interactions specific to protein and lipid metabolism. Longissimus dorsi muscle and liver tissue protein samples were prepared for proteomic analysis. The initial stages of this proteomic analysis are complete. Several proteins have been identified in the liver as being changed in abundance in response to a stress response. Association analysis: DNA was isolated from all pigs that completed replicates 1 through 3 of the line by diet experiment and they have been genotyped using the PorcineSNP60 chip by GeneSeek Inc. Preliminary GWAS and genomic prediction analyses have been completed. Results show that RFI is a polygenic trait with few large effects but with reasonable genomic prediction accuracies across lines. A preliminary analysis of selection signatures has been completed. Identify SNPs for response to PRRS: The RFI lines were found not to segregate for the chromosome 4 region that has been found to be associated with host response to PRRS in the PRRS Host Genomics Consortium. A GWAS has been completed and found no strong effects. Integrate FE with stress responses: A total of 79 samples will be sequenced using directional mRNA Sequencing. Samples selected include HRFI and LRFI 0,2,6, and 24 hour stimulated samples and 0 and 168 hour stimulated and unstimulated RFI pigs. Identification and confirmation of proteins changed in response to stress will continue. Proteins in the liver have been identified and proteins in the longissimus dorsi muscle are in the process of being identified. A manuscript is being prepared on the associationwith the proteomic changes in response to stress well-being. Association Analysis: Animals from replicate 4 will be genotyped. Objectives 4 and 5 Project Website: Domain names for the website have been secured, design has been finalized and website is active. Website has been linked to Iowa State University and Kansas State University websites. An awareness campaign for the website is occurring. Decision Tools: We have developed a series of decision tools to help farmers determine the cost and benefit of adopting certain technologies or tools to improve feed efficiency. 13 factsheets have been created and published and additional ones (1 to 2 pages) are being developed. Factsheets were disseminated directly to producers, through popular press, the website and through the awareness campaign and were translated to Spanish for future publication. Demonstration Projects: As previously planned, additional demonstration projects were conducted on commercial pig farms to highlight technologies that improve feed resource utilization. Additional demonstration projects are planned for the next year.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Colpoys, J. D., C.E Abell, J. M. Young, A.F. Keating, N. K. Gabler, S. T. Millman, J. M. Siegford, A.K. Johnson. 2014. Effects of genetic selection for residual feed intake on behavioral reactivity of castrated male pigs to novel stimuli tests. App. Anim. Behav. Sci. 159:34-40.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: E. K. Arkfeld, J. E. Berger, E. R. Hamman, J. M. Young, R. C. Johnson, J. F. Patience, J. C. M. Dekkers, N. K. Gabler, S. M. Lonergan and E. Huff-Lonergan. (2014) Pork quality characteristics of loins from pigs divergently selected for residual feed intake on high or low energy diets. ASAS-ADAS Midwestern Sectional Meeting, Des Moines, IA. March 17-19, Abstract # 311.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Colpoys, J. D., N. K. Gabler, C. E. Abell, A. F. Keating, S. T. Millman, J. M. Siegford, A. K. Johnson. 2014. Selection and breeding for improved feed efficiency alters gilt behavioral responsiveness to a novel object. J. Anim. Sci. 92(E-Suppl. 2):25.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Colpoys, J. D., D. M. van Sambeek, L. L. Anderson, J. C. M. Dekkers, A. K. Johnson, F. R. Dunshea, N. K. Gabler. 2014. Response of swine divergently selected for feed efficiency to a glucose tolerance test. J. Anim. Sci. 92(E-Suppl. 2):160-161.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Grubbs, J.K., C.K. Tuggle, J.C.M. Dekkers, S.M. Lonergan. (2014) Comparison of Albumin Depleted and Whole Serum Samples for Biomarker Identification. Journal of Animal Science 92(E-Suppl 2):577.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Grubbs, J.K., C.K. Tuggle, J.C.M. Dekkers, S.M. Lonergan. (2014) Identification of Potential Serum Biomarkers for Feed Efficiency in Young Pigs. Journal of Animal Science 92(E-Suppl 2):187.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Haibo Liu, Christopher K. Tuggle. Improving Porcine Transcriptome Annotation By Integrating EST, mRNAs and Whole Blood RNA-Seq Data. International Plant & Animal Genome XXIII. San Diego, CA. January 915, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Mauch, E.D., J.M. Young, J.F. Patience, N.K. Gabler, and J.C.M. Dekkers. 2014. Effect of a low energy, high fiber diet challenge on Yorkshire pigs selected for residual feed intake. 10th World Congress on Genetics Applied to Livestock Production. Vancouver, BC, Canada. 17 August 2014.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Mauch, E.D., J.M. Young, J.F. Patience, N.K. Gabler, and J.C.M. Dekkers. 2014. Effect of low energy, high fiber diets on divergent residual feed intake lines in swine. Journal of Animal Science [E-Supplement]:122. ADSA�-ASAS Joint Midwest Meeting. Des Moines, IA. 19 March 2014.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Mauch, E.D., N.K. Gabler, T.E. Weber, J.F. Patience, B.J. Kerr, and J.C.M. Dekkers. 2015. The effect of divergent selection for residual feed intake on digestibility of control and low energy, high fiber diets. ADSA�-ASAS Joint Midwest Meeting. Des Moines, IA. 16 March 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Ser�o, N.V.L., E.D. Mauch, W. Hsu, A. Wolc, M.F. Rothschild, and J.C.M. Dekkers. 2015. Genomic prediction accuracies of residual feed intake (RFI) and component traits of feed efficiency in pigs divergently selected for RFI. ADSA�- ASAS Joint Midwest Meeting. Des Moines, IA. 16 March 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Sholar, J. F., J. D. Colpoys, N. K. Gabler, A. F. Keating, S. T. Millman, J. M. Siegford, A. K. Johnson. 2014. Gilt approachability to a human when selected for feed efficiency. J. Anim. Sci. 92(E-Suppl. 2):114.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Steckelberg, J.R., E.D. Mauch, A.M. Dannen, N.V.L. Ser�o, and J.C.M. Dekkers. 2015. Differences in feed efficiency during the nursery phase of pigs divergently selected for residual feed intake during grow-finish phase. ADSA�-ASAS Joint Midwest Meeting. Des Moines, IA. 16 March 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Schweer, W. P., J. F. Patience, L. A. Karriker, J. C. Sparks, G. G. Gourley, M. Fitzsimmons, K. Schwartz, T. E. Burkey and N. K. Gabler. (2014) PRRSv reduces feed efficiency and tissue accretion rates in grow-finisher pigs. ASAS-ADAS Midwestern Sectional Meeting, Des Moines, IA. March 17-19, Abstract # 82.
  • Type: Other Status: Published Year Published: 2014 Citation: Colpoys, J. D., A. Johnson, N. Gabler, A. Keating, S. Millman, J. Siegford. 2014. Barrow behavioral responsiveness to a human or novel object when fed low versus high energy diets. Animal Industry Report, Iowa State University. R2915.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: W. Schweer, K. J. Yoon, K. Schwartz, N. K. Gabler (2014) The impact of a PRRS-PED Virus Co-Infection on Grower Pig Performance. Conference proceedings page number 17, published by Veterinary Continuing Education Volume 41 Allen D. Leman Conference, St. Paul, MN, USA Sept. 13-16.
  • Type: Websites Status: Published Year Published: 2014 Citation: Swine podcasts: http://www.asi.k-state.edu/species/swine/podcasts.html


Progress 04/01/13 to 03/31/14

Outputs
Target Audience: Our primary target audiences are 1) pork producers, 2) feed and genetics suppliers to the pork industry, 3) consultants, including veterinarians, 4) extension and related workers, and 5) the academic community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Student training: Student Name; Degree in progress*; Student Participation#; PD contact Amanda Graham; M.S.; Indirect assistance/training; Mike Tokach and Joel DeRouchey Devin Goehring; M.S.; Indirect assistance/training; Mike Tokach and Joel DeRouchey Josh Flohr; M.S. and Ph. D.; Direct assistance/training; Mike Tokach and Joel DeRouchey Jon De Jong; M.S. and Ph. D.; Direct assistance/training; Mike Tokach and Joel DeRouchey Ziyanda Mpetile; MS; Direct – help collect blood samples, analyze data in Obj 3A, B. Thesis: Determine the effect of RFI selection on immune traits; Chris Tuggle Emily Mauch; MSc; Direct – Effect of high fiber diet on RFI lines; help with data collection; Jack Dekkers Emily Arkfeld; MSc.; Direct assistance/training; Elizabeth Lonergan Dana van Sambeek; MSc.; Indirect – assist with sample analysis in Objectives 1 & 2; Nicholas Gabler Jeremiah Nemechek; Ph.D.; Direct assistance/training; Mike Tokach and Joel DeRouchey Kyle Coble; Ph.D.; Indirect assistance/traning; Mike Tokach and Joel DeRouchey Chad Paulk; Ph.D.; Indirect assistance/training; Mike Tokach and Joel DeRouchey Kyle Grubbs; Ph.D.; Direct assistance/training; Steve Lonergan Jessie Colpoys; Ph.D.; Direct – Behavioral and physiological stress responses of RFI lines; Anna Johnson and Nicholas Gabler Jenelle Dunkelberger; PhD; Direct – Effect of PRRS challenge on RFI lines; help with data collection; Jack Dekkers Dinesh Thekkoot; PhD; Indirect – GWAS for lactation efficiency, help with data collection; Jack Dekkers Andrew Hess; PhD; Indirect – assist with data collection; Jack Dekkers Emily Waide; PhD; Indirect – assist with data collection; Jack Dekkers Haibo Liu; PhD; Direct – process RNA and metabolomic samples, help analyze data in Obj 3A. Thesis: Identification of biomarkers for feed efficiency using a systems biology approach; Chris Tuggle Kristina Feye; PhD; Direct – process samples, help analyze data in Obj 3B. Thesis: The effect of Immune stress on feed efficient animals; Chris Tuggle Yet Nguyen; PhD; Direct: analyze RNA data; Dan Nettleton Nick Boddicker; PhD – completed; Indirect – assist with data collection; Jack Dekkers Nick Serao; Pos doc; Indirect – assist with data collection; Jack Dekkers Jennifer Young; Post doc; Direct – Manage RFI lines, data analysis; Jack Dekkers Martine Schroyen; Post doc; Indirect– process RNA samples in Obj 3A; Chris Tuggle J. Kyle Grubbs; Post doc; Direct– process serum sample, analyze protein data in Obj 3A. Project: the identification of protein as biomarkers differentially expressed in efficient versus non-efficient animals; Chris Tuggle Austin Putz; Undergraduate; Direct – process RNA samples in Obj 3A. Project: the isolation and globin depletion of RNA samples from whole blood collected from high and low efficient animals.; Chris Tuggle Jordy Berger; Undergraduate; Indirect assistance/training; Steve Lonergan Emily Benedict; Undergraduate; Indirect assistance/training; Steve Lonergan Roslyn Punt; Undergraduate; Indirect assistance/training; Steve Lonergan Johanna Sholar; Undergraduate; Indirect –assist with data analysis; Anna Johnson Chloe Wasendorf; Undergraduate; Indirect – assist with data analysis; Anna Johnson Jennie Schubert; Undergraduate; Indirect – assist with data collection; Anna Johnson Ashley Woodley; Undergraduate; Indirect –assist with data collection; Anna Johnson Adrianne Kaiser; Undergraduate; Indirect – assist with data collection; Anna Johnson Calvin Hartz; Undergraduate; Indirect –assist with sample analysis in Objectives 1 & 2; Nicholas Gabler Erin Laughlin; Undergraduate; Direct –assist with sample analysis in Objectives 1 & 2; Nicholas Gabler Yi Zhang; Visiting Scholar; Indirect – Genotype analyses; assist with data collection; Jack Dekkers Boxing Sun; Visiting Scholar; Indirect – Data analysis; assist with data collection; Jack Dekkers Miriam Ayuso Hernando; Visiting scholar; Involved with data collection and review of fact sheets for the project.; Mike Tokach and Joel DeRouchey *Degree in progress: -Undergraduate -Graduate (M.Sc.) -Graduate (Ph.D.) -Graduate (M.Sc. and Ph.D.) -Post doc -Visiting Scholar #Student participation: -Direct assistance/training - if a student is or was involved with this AFRI grant for Full thesis or thesis chapter – please include a summary title of project -Indirect assistance/training - if a student is or was involved with this AFRI grant by helping other students or researcher -For post-docs or Visiting Scholar, please include a summary title of the project or task involved related to the project. How have the results been disseminated to communities of interest? International Conference on Feed Efficiency in Swine Was held in November, 2011 in Omaha, NE. Total attendance was 414, well above the expected 200 to 300, and represented 18 nations, 23 U.S. states and 10 U.S. universities. Of the 177 surveys received after the meeting, 98.9% stated that the meeting met or exceeded their expectations. The objective of this event was to provide to the swine industry in one event, the full range of knowledge on the topic of feed efficiency. Pork industry survey on feed efficiency Was undertaken to determine the current state of knowledge about feed efficiency within the pork industry. A complementary survey will be completed at the end of the 5-year project, to gage improvement in knowledge and attitudes about feed efficiency in swine. Feed Efficiency in Swine Book published in July, 2012 by Wageningen Academic Publishers, with chapters written by the speakers at the above mentioned conference. Project Website Website has been developed to serve as a repository of information on feed efficiency. The site can be accessed at http://www.swinefeedefficiency.com/. It contains decision tools, publications, presentations and a list of events, all related to feed efficiency in swine. Factsheets A total of 13 factsheets have been written and posted on the project website, covering a range of topics related to feed efficiency in swine. The factsheets are written to provide practical information to readers. Presentations Numerous talks on swine feed efficiency have been presented by the extension partners of this project at a variety of industry meetings Numerous abstracts of research completed on this project have been presented at regional, nation and international conferences. Field Demonstrations Three field demonstrations have been completed. These demonstrations showed: Difference in feed efficiency, energy value and economic return from feeding dried distiller grains with solubles with different fat levels. Influence of reducing particle size and pelleting of diets for finishing pigs on feed efficiency, growth performance, and economic return. Influence of fine grinding of the corn or complete diet and pelleting on performance and economic return with nursery pigs. Scientific data have been presented at the following: Journals: BioResearch Veterinary Pathology Journal of Animal Sciences Meat Science Conferences (abstracts) Midwest Section, American Society of Animal Science, Des, Moines, IA. Reciprocal Meat conference, Fargo, ND. International Congress of Meat Science and Technology. Annual Meeting, American Society of Animal Science, Phoenix, AZ. 12th International Symposium on Digestive Physiology of the Pig. Keystone, CO. International Plant & Animal Genome XX Conference, San Diego, CA. Experimental Biology Conference. April 20-24, 2013, Boston, MA. Poultry Science Association Annual Meetings. San Diego, CA. Allen d. Leman Swine Conference, St. Paul, MN. World Congress of Genetics Applied to Livestock Production, Leipzig, Germany Iowa State University Swine Day, Ames, IA. Reports Kansas Swine Industry Day Reports Animal Industry Reports, Iowa State University What do you plan to do during the next reporting period to accomplish the goals? Research Objective #1: Quantify the performance of pigs selected for increased feed efficiency under corn-soybean diets when fed lower quality by-product ingredients (higher fiber, lower fat). Objectives 1A and 1B – Growth performance and feed efficiency/Meat quality: Write a manuscript on line differences observed in the first two replicates of the line by diet experiment. Complete data collection on the 3rd replicate. Finish the last of the meat quality assays and joint analysis that will be added to the manuscript that has been drafted. Complete breeding of sows to produce and complete the 4th replicate of the line by diet experiment. Complete and submit manuscript summarizing meat quality research to the Journal of Animal Science. Replicates 3 and 4 of the line by diet experiment will be completed and analyzed. Finish gene and protein abundance analysis on metabolism samples. Objective 1C – Metabolism: Digestibility samples have been collected and assayed. We are currently doing a joint analysis on the nutrient and energy digestibility data and the pig performance data across the two lines of pigs (high and low feed efficiency) and diets (low energy, high fiber verses high energy, low fiber). Objective 1D – Microbial populations: Extract and purify genomic DNA for all samples. Design pyrosequencing strategy and assign MID tags. Prepare genomic DNA samples for pyrosequencing, including amplification and purification of cpn60 Universal Target using appropriate MID tagged primers. Complete qPCR enumeration of selected major taxonomic groups. Research Objective #2: Evaluate the ability of pigs selected for increased efficiency to cope with behavioral, physiological and immunological stressors. Objective 2A – Behavioral Studies: Indirect stress response data sets from replicate 1 need to be evaluated for the two behavioral tests: the human approach/avoidance test and the novel object test. Analyze all data on Replicate #2 (pigs born in July-August). Indirect stress responses field data will finish being collected and analyzed from Rep 2. Objective 2B – Appetite Regulation and ACTH challenge: Submit the manuscript from this objective for peer-review publication. Objective 2C – E. coli Endotoxin Challenge: Finalize gene abundance data and complete joint analyses on digesta, blood and tissues collected from this objective. Complete this objective by finishing all data analyses, drafting and submitting the manuscript for scientific review and publication. Objective 2D – PRRS Challenge: Analysis of antibody data will be finalized. Research Objective #3: Develop industry-ready tools to easily and effectively identify and select more efficient pigs. Objective 3A – Practical Classifier to predict feed efficient pigs: RNASeq data on rep 2 will be collected and analyzed. We will finish identification of selected differentially expressed proteins by further analysis of the second co-hort, and begin testing of antibodies for confirmation of identified proteins via high-throughput methods such as Westerns or ELISA methods. Serum samples will be assayed for metabolites. Thyroid hormone assays will be run and analyzed. Objective 3B – Integrate FE with stress responses: Remove globin transcripts and sequence RNA from samples from Objective 2C. Perform statistical analyses to identify genes different between lines in response to the LPS stress. Initiate analysis of serum proteins responding to LPS stimulation using 2D-DIGE methods. Objective 3C – Genome-Wide Association Analyses to identify SNPs associated with FE and RFI: An initial genome-wide association study (GWAS) analysis will be conducted once replicate 3 has been completed (by March 2014). Pigs from the 4th replicate will be genotyped and a GWAS, using all four replicates and in combination with all data on previous generations, will be conducted. Objective 3D – Identify SNPs Associated with Response to PRRS Infection: Data from the PRRS challenge will be combined with data from the PRRS CAP project and a joint GWAS analysis will be conducted to identify regions associated with host response to PRRS and identify regions that show an interaction with line. Objective 3E – Develop and validate FE SNPs in commercial populations. Plans for this objective will be finalized, in collaboration with industry partners. Objectives 4: Increase pork producers’ awareness of the factors influencing feed efficiency and strategies available to achieve improvement. Extension Objective 5: Ensure the rapid and effective implementation of new technologies to improve feed efficiency both nationally and internationally. Activity 2 – Book on Feed Efficiency: Previously completed. Book is available for general sales. Activity 3 – Project Website: Content of feed efficiency website will continue to be expanded as new materials and new information from research become available. Updates on the website are planned for every 2 months. Awareness campaign will continue to progress. Activity 4 – Decision Tools: An updated list of decision tools will be posted at the website. Activity 5 – Factsheets: Additional factsheets (1 to 2 pages each) will be developed and disseminated directly to producers and through popular press to lower feed efficiency. Factsheets will be translated into Spanish. Activity 7 – Demonstration Projects: As previously planned, additional demonstration projects were conducted on commercial pig farms to highlight technologies that improve feed resource utilization. As previously planned, two additional demonstration projects will be conducted on commercial pig farms to highlight technologies that improve feed resource utilization.

Impacts
What was accomplished under these goals? Objective #1:To determine if feeding lower-quality diets affects genetic differences in feed efficiency (FE) and total tract nutrient and energy digestibility. We have collected data on the first 2 replicates of this experiment. On a high-energy low-fiber (HELF) diet, compared to the High RFI line (HRFI), the Low RFI line (LRFI) had more lean tissue and less fat growth, while eating less and gaining similarly and thus having greater FE. On low-energy high-fiber (LEHF) diet across lines, pigs consistently had lower FE, weight gain, and backfat than pigs fed HELF diet. However, average daily feed intake and loin muscle area had conflicting results between generation 8 and 9. Within lines, compared to the HELF diets, pigs fed a LEHF diet had lower FE and less fat while gaining less weight. On the LEHF diet, compared to the HRFI, the LRFI had more lean tissue and less fat growth, while eating less and gaining similarly, yet had similar FE. Change in effect on FE from the HELF diet is likely due to larger line differences in feed consumed on the HELF diet. FE advantages selected for when fed one diet may not be seen when the diet is altered. However, LRFI line was never worse than HRFI line, even when low energy diets were fed. An evaluation of meat quality is also being tested. The objective was to evaluate the contribution of protein turnover pathways to FE. These results indicate that selection for LRFI may indirectly select for reduced protein degradation and turnover. This could contribute to greater efficiency, resulting in decreased cost of production. A reduction in live muscle proteolysis could have a negative impact on meat quality, decreased tenderness and therefore reduced quality. Data were collected to determine meat quality changes due to diet and line. Both line and diet impacted carcass composition, with minimal effects on pork quality and sensory characteristics. RFI shows promise as a selection tool for improved efficiency without compromising pork quality, even if fed low energy diets. Objective #2: To evaluate if pigs selected for better FE through low RFI respond differently to stressors. Early data indicate that long term genetic selection for reduced RFI resulted in decreased behavioral responsiveness during human approach and novel object tests. Selectively breeding for improved FE did not negatively impact barrow stress responsiveness. These data may have implications for livestock handling and facility design. ACTH challenge study has been completed. Data indicate that long term genetic selection for reduced RFI resulted in decreased blood cortisol before and after an ACTH challenge and a significant increase in insulin following a glucose tolerance test. These neuroendocrine axes and metabolic differences may explain selection line differences in behavior and body composition. These data may have implications for selection techniques and reducing swine stress though handling and facility design. To examine the impact of immunological stress on feed intake and metabolism, pigs from each line have been repeatedly challenged with lipopolysaccharide (LPS) while in metabolism crates. Additionally, we are examining the interaction between innate and febrile response and nutrient and energy digestibility and metabolism. The objective of this study was to analyze the effect of PRRS on lines of pigs divergently selected for low and high residual feed intake. The challenge demonstrated that selection for increased FE based on RFI does not increase the impact of PRRS infection on serum viremia and weight gain. Evidence shows that growth of the more efficient pigs was less affected by PRRS than that of the inefficient line. Preliminary results demonstrate a similar ability of the two lines to mount an antibody response to the PRRS virus. Objective #3: The goals of the research proposed under objective 3 are to identify and develop SNPs and biomarkers that can be measured in blood at a young age and are predictive of FE during the growing phase, and find pathways and networks that differentiate feed efficient pigs. 3A – Practical Classifier to identify feed efficient pigs: The required samples of the first objective and data on both cohorts of samples totaling 360 pigs have been collected. Extremes of populations based on RFI data in each line and under each diet were selected. Protein spots have been picked from the gel and have been sequenced to identify the protein. Specific proteins have been identified and further verification by Western blot has been initiated. Statistical comparison of complete blood counts traits as a measure of immunity between the two lines has been completed. We have found that the two lines are highly significantly different for number and components of red blood cells, as well as number and cell types in the whole blood cell component of blood. We have initiated a preliminary test of metabolomics analysis; we are currently evaluating the value of these data and plan to ship Objective 3A samples to the collaborator or potentially choose a different group for collection of these data. 3B – Integrate FE with stress responses: High quality RNA has been isolated from the 80 samples, and globin depletion testing has been initiated. Sufficient RNA is available for both RNA sequencing and follow-up qPCR verification. 3C – Genome-Wide Association Analyses to identify SNPs associated with FE and RFI: DNA was isolated from all pigs that completed replicates 1 and 2 of the line by diet experiment and they have been genotyped using the PorcineSNP60 chip by GeneSeek Inc. Tissues from the third replicate are currently being prepared for submission to GeneSeek Inc. for genotyping. Once this genotyping has been completed, genome-wide association study analyses will be conducted to identify genetic markers associated with FE. 3D – Identify SNPs Associated with Response to PRRS Infection: The RFI lines were found not to segregate for the chromosome 4 region that has been found to be associated with host response to PRRS in the PRRS Host Genomics Consortium. Objectives 4 & 5: The goals of the two extension objectives are to increase awareness and adoption of existing technologies and of new information and technologies developed by the research objectives. Activity 1, 2 and 6 – completed. Project Website: Domain names for the website have been secured, design has been finalized and thewebsite is active. Website material has been included to achieve awareness of FE in swine. Visitors to the website are able to obtain information on the overall goal of this grant as well as progress information and tools that are being developed through this 5-year project. An awareness campaign for the website is underway. This campaign is an attempt to promote the Swine FE domain as a reliable source of information on this topic. We have initiated work to integrate activities of Objectives 1-3 with this website to quickly share the progress and results of the research objectives to the public. Decision Tools: We have developed a series of decision tools to help farmers determine the cost and benefit of adopting certain technologies or tools to improve FE (i.e. calculators, feeder adjustment techniques, premix and diet recommendations). Additional decision tools were developed in year 3 (Ex. Economics of reduced-oil DDGS). Factsheets: 13 factsheets have been created and published and additional ones (1 to 2 pages) are being developed. Factsheets were disseminated directly to producers through popular press, the website and through the awareness campaign. One-third of the fact sheets have been translated to Spanish and will be included in the website. Demonstration Projects: As previously planned, additional demonstration projects were conducted on commercial pig farms to highlight technologies that improve feed resource utilization. Additional demonstration projects are planned for the next year.

Publications

  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Mauch, E.D., J.M. Young, J.F. Patience, N.K. Gabler, J.C.M. Dekkers. 2014. Effect of Low Energy, High Fiber Diets on Divergent Residual Feed Intake Lines in Swine. P607, Plant and Animal Genome Meetings, January, 2014.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Dekkers, J.C.M. 2013. What do SCID, RFI, and PRRS have in common? Poultry Breeders Roundtable. May, 2013, St. Louis.
  • Type: Other Status: Published Year Published: 2013 Citation: AS-Leaflet-R2810 Behavioral Fear Response to a Novel or Human Stimuli in Barrows Selected for Feed Efficiency (Authors: Jessica Jenkins, Anna Johnson, Nicholas Gabler, Aileen Keating, Suzanne Millman, Janice Siegford).
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Onteru, S.K., D.M. Gorbach, J.M. Young, D.J. Garrick, J. Dekkers, and M.F. Rothschild. 2013. Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig. PLOS One 8(6):e61756. doi:10.1371/journal.pone.0061756.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Gilbert, H, and J.C.M. Dekkers. 2013. Improvement of feed efficiency: lessons from residual feed intake studies in pigs: part 1. European Assoc. Animal Production Annual meeting. Invited presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Onteru, S.K., D.M. Gorbach, J.M. Young, D.J. Garrick, J. Dekkers, and M.F. Rothschild. 2013. Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig. Plant and Animal Genome XXI, Abstract, January 2013.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Dunkelberger, J.R., N.J. Boddicker, J.M. Young, R.R.R. Rowland, and J.C.M. Dekkers. 2013. Pigs Selected for Increased Feed Efficiency are less affected by experimental infection with the PRRSv. 2013 PRRS Symposium, Dec. 2013.
  • Type: Other Status: Published Year Published: 2013 Citation: AS-Leaflet-R2814 Evaluation of the Responsiveness of Swine Divergently Selected for Feed Efficiency to an Exogenous Adrenocorticotropin Hormone (ACTH) Challenge (Authors: Jessica Jenkins, Nicholas Gabler, Lloyd Anderson, Jack Dekkers, Anna Johnson, Frank Dunshea).
  • Type: Other Status: Published Year Published: 2013 Citation: AS-Leaflet-R2816 Genome Wide Association Studies for Residual Feed Intake Traits in Pigs (Authors: Suneel Onteru, Danielle Gorbach, Jennifer Young, Dorian Garrick, Jack Dekkers, Max Rothschild).
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Cruzen, S. M., A. J. Harris, K. Hollinger, R. M. Punt, J. K. Grubbs, J. T. Selsby, J. C. M. Dekkers, N. K. Gabler, S. M. Lonergan, E. Huff-Lonergan. 2013. Evidence of decreased muscle protein turnover in gilts selected for low residual feed intake. Journal of Animal Science 91:2133-2140.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mani, V., A. J. Harris, A. F. Keating, T. E. Weber, J. C. M. Dekkers and N. K. Gabler. 2013. Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake. Journal of Animal Science 91:2141-50.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ros-Freixedes, R., L. J. Sadler, S.K. Onteru, R. M. Smith, J. M. Young, A.K. Johnson, S. M. Lonergan, E. Huff-Lonergan, J. C. M. Dekkers, and M. F. Rothschild. 2014. Relationship between gilt behavior and meat quality using principal component analysis. Meat Science 96:264-269.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Flohr, J.R., M.D. Tokach, J.L. Nelssen, S.S. Dritz, J.M. DeRouchey, R.D. Goodband, and J.F. Patience. 2013. Feed efficiency of swine  a survey of current knowledge. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jenkins, J.D., A.K. Johnson, L.L. Anderson, J.C.M. Dekkers, N.K. Gabler and F.R. Dunshea. 2013. Response of swine divergently selected for feed efficiency to an exogenous adrenocorticotopin hormone (ACTH) challenge. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Dunkelberger, J. R., N. J. Boddicker, J. M. Young, R. R. R. Rowland, and J. C. M. Dekkers. 2013. Pigs Selected for Increased Feed Efficiency are less affected by experimental infection with the PRRSv. Proc. A. D. Leman Swine Conference. University of Minnesota, College of Veterinary Medicine, Minneapolis, MN (p186).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Young, J., J. Patience, N. Gabler and J. Dekkers. 2013. The effect of feeding low energy high fiber diets on performance of pigs divergently selected for residual feed intake. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Gabler, N. K. 2013. The impact of PRRSV on feed efficiency, digestibility and tissue accretion in grow-finisher pigs. Allen d. Leman Swine Conference, September 14-17, St. Paul, MN.


Progress 04/01/12 to 03/31/13

Outputs
OUTPUTS: Overall, the project is progressing very well under all five objectives. Indeed, many objectives entered activities projected for year 3 due to the progress being made in earlier activities. Many Co-PIs on the project traveled to France to meet with colleagues at INRA to share information and ideas. By all accounts, the visit was a major success and plans are in place to have our INRA colleagues visit Ames in 18 to 24 months. OUTPUTS: Obj. 1A and B: We are continuing to analyze the growth and carcass performance data from Rep 1 of high versus low RFI pigs fed either a high or low energy diet. Total tract digestibility is being analyzed. Rep 2 is underway. Obj. 1D: Mucosal scrapping and luminal contents have been collected and are being characterized for microbial analysis. Obj. 2A: Rep 1 of human and novel approach test has been completed and further analyzed. Observations and video data for Rep 2 of this objective are currently being collected. Obj. 2B: Data analysis from the intravenous glucose tolerance test and ACTH challenge on eight high and eight low RFI gilts has been completed; manuscript is in preparation. Obj. 2C: Data collection and lab analysis on the impact of immune system stimulation (ISS) and genetic selection for RFI on apparent ileal digestibility (AID) of nutrients and energy, and on intestinal nutrient transport and barrier function has been completed; manuscript is being prepared. Obj. 2D: Viremia assays have been completed for pigs challenged for with the PRRS virus. Analysis is underway. Obj. 3A: We have collected the blood samples on all needed pigs (>500 samples), one year early. For cohort 1, we have calculated RFI data and selected 24 samples for RNA sequencing. All 24 samples have been globin-depleted to maximize sequence data coverage and quality controlled by Q-PCR. Libraries have been made and are being sequenced. We have initiated analysis of the Complete Blood Count data in Cohort 1 to look for correlations with RFI data. In cohort 2, 180 pigs have been selected and are being measured for RFI. Obj. 3C: Parities 1 and 2 of the ninth generation of the RFI lines was produced, evaluated, and selection and mating decisions were made to breed generation 10. Tissues for DNA from the second replicate have been collected for genotyping. Genome-wide association analyses are planned following completion of replicate 2 in year 3. Obj. 4 and 5: Feed Efficiency in Swine book published in July, 2012 by Wageningen Academic Publishers, with 13 chapters (275 pages) written by the speakers from the International Feed Efficiency in Swine Conference. Project Website has been developed to serve as a repository of information on feed efficiency. The site can be accessed at http://www.swinefeedefficiency.com/. It contains decision tools, publications, presentations and a list of events, all related to feed efficiency in swine. A total of 13 factsheets have been written and posted on the project website, covering a range of topics related to feed efficiency in swine. The factsheets are written to provide practical information to readers. PARTICIPANTS: Iowa State University PI: Dr. John Patience: Oversight of overall project, leadership of Obj. 4&5, scientific input in Obj. 1&2. CoPIs: Dr. Nicholas Gabler: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Jack Dekkers: Leadership of Obj. 3, scientific input in Obj. 1&2; contributed to Obj 4&5; Dr. Elisabeth Huff Lonergan: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Steven Lonergan: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Lloyd Anderson: Scientific input in Obj. 1, 2&3; Dr. Anna Johnson: Leadership of Obj. 2, scientific input in Obj. 1&3; Dr. Chris Tuggle: Leadership of Obj. 3, scientific input in Obj. 1&2; Dr. Max Rothschild: Scientific input in Obj. 1,2&3; Dr. Dan Nettleton: Leadership of Obj. 3; Dr. John Mabry: Contributed to Obj. 4&5; Dr. Peng Liu. Undergraduate Students: Austin Putz, Dana van Sambeek, Jessica Jenkins, Anne Cox, Jentry Fanning, Rosslyn Punt, Emily Benedict, Kirstin Adams. Graduate Students: Emily Arkfeld, Venkatesh Mani, Shannon Cruzen, Analia Roca, Dinesh M. Thekkoot, Nick Boddicker, Andrew Hess, Emily Waide, Ziyanda Mpetile, Dana van Sambeek, Jessica Jenkins. Post-doctoral scholars and Technical staff: Dr. Martine Schroyen, Dr. Anoosh Rakhshandeh, Dr. Jennifer Young, Dr. Kyle Grubbs, Dr. Ed Steadham, Martha Jeffrey, Dr. Boxing Sun (visiting scientist Jilin University, China), Dr. Yi Zhang (visiting scientist China Agricultural University, Beijing), Suneel Onteru, Dr. Tinghua Huang. Kansas State University: Dr. Bob Rowland: Leadership of Obj. 2; Dr. Joel DeRouchey: Leadership of Obj. 4&5; Dr. Mike Tokach: Leadership of Obj. 4&5 Hyatt Frobose (Ph.D), Devin Goehring (M.S.), Josh Flohr (M.S.), Nick Shelton (Ph.D.), Kyle Coble (Ph.D.), Jeremiah Nemechek (Ph.D), Amanda Graham (M.S.), Kari Beth Langbein (M.S.), and Matt Asmus (M.S.).. USDA: Dr. Brian Kerr: Scientific input in Obj. 1&2. INRA: Dr. Helene Gilbert: Scientific input in Obj. 3. The University of Melbourne: Dr. Frank Dunshea: Scientific input in Obj. 1&2. TARGET AUDIENCES: Pork producers, industries affiliated with the pork industry and extension personnel: Feed Efficiency in Swine book, factsheets, decision tools,presentations at conferences, survey results. Other academics: Feed Efficiency in Swine book; laboratory instruction. Graduate students including students and post-doctoral fellows: Feed Efficiency in Swine book, laboratory instruction. PROJECT MODIFICATIONS: Due to the budget cut in year one, Obj. 1C has been eliminated.

Impacts
Data from Objectives 1 and 2 indicate that that selection for efficiency under a standard high energy diet may not translate into increased efficiencies under poorer diets, although such selection is also not expected to result in detrimental effects on efficiency on poor diets. These results must be validated by replication, which is underway. The feeding of a low energy high fiber diet, compared to a standard high energy low fiber diet, resulted in reduced growth rates and backfat, but had no detrimental effects on sensory quality of the meat. Obj. 2A: Long-term selection for RFI and FE may alter pig behavior and approachability. This in turn may impact how we manage, handle and move pigs. However, the differences between lines are not large. Obj. 2B: Divergent selection for RFI resulted in altered pre- and post-ACTH induced cortisol responses in finisher gilts. The high RFI pigs tended to be more responsive to this stress challenge, but recovered equally as well as pigs selected for low RFI. Therefore, the ability of livestock to recognize and cope with stress may relate to RFI selection and feed efficiency. Obj. 2C: Feed efficiency is not explained by improved intestinal integrity in production pigs. However, low RFI pigs have lower endogenous endotoxin and inflammatory markers, and enhanced activities of antimicrobial enzymes. This may partially contribute to differences in the feed efficiency between the lines. Irrespective of immune system stimulation, high and low feed efficiency pigs both mounted a similar febrile and proinflammatory response. Additionally, immune stimulation affected both apparent ileal digestibility and apparent total tract digestibility of dietary nutrients in pigs and may be a major source of feed efficiency variation. Altogether, genetic selection for LRFI reduces the total tract digestive capacity of growing pigs during immune system stimulation. Obj. 2D: Pigs selected for increased feed efficiency based on residual feed intake under high-health conditions, do not appear to be more affected by infection with the PRRS virus during the growing period, based on rate of growth following experimental infection. This indicates that selection for feed efficiency can be conducted in the high-health conditions of nucleus farms, without detrimental effects on growth under less optimal conditions, as present in the field. Obj. 3: Globin depletion of blood RNA was successful and this is expected to improve depth RNA sequence data collected by the end of the period and into the next period. Obj. 4 and 5: The book Feed Efficiency in Swine provides a comprehensive treatise on our current knowledge on the subject at both the basic and applied level. The survey confirmed the need for an aggressive and comprehensive extension effort as the level of awareness of existing knowledge is disappointing. The factsheets will greatly help to address this deficiency as will the other materials on the website. The response to the conference, the book and the extension materials confirms the tremendous interest that the pork industry has in acquiring new knowledge on feed efficiency.

Publications

  • Arkfeld, E.K., E.R. Benedict, R.C. Johnson, J.M. Young, D.M. Thekkoot, J.K. Grubbs, S.M. Cruzen, N.K. Gabler, J.C.M. Dekkers, S.M. Lonergan and E. Huff-Lonergan. 2012. Composition and quality of carcasses from pigs selected for divergent residual feed intake. Reciprocal Meat Conference, Fargo, ND.
  • Boddicker, N.J., D.J. Garrick, J.M. Reecy, R.R.R. Rowland, J.K. Lunney and J.C.M. Dekkers. 2012. Genetic architecture of response to experimental porcine reproductive and respiratory syndrome virus infection. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Jenkins, J.D., A.K. Johnson, L.L. Anderson, J.C.M. Dekkers, N.K. Gabler and F.R. Dunshea. 2013. Response of swine divergently selected for feed efficiency to an exogenous adrenocorticotopin hormone (ACTH) challenge. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Rakhshandeh, A., J.C.M. Dekkers, B.J. Kerr, T.E. Weber and N.K. Gabler. 2013. Impact of systemic immune system stimulation on intestinal integrity and function in pigs. Experimental Biology Conference. April 20-24, 2013, Boston, Massachusetts.
  • Young, J., J. Patience, N. Gabler and J. Dekkers. 2013. The effect of feeding low energy high fiber diets on performance of pigs divergently selected for residual feed intake. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Jenkins, J., N. Gabler, L. Anderson, J. Dekkers, A. Johnson and F. Dunshea. 2013. Evaluation of the responsiveness of swine divergently selected for feed efficiency to an exogenous adrenocorticotropin hormone (ACTH). Animal Industry Report, Iowa State University. AS-Leaflet-R2814.
  • Jenkins, J., A. Johnson, N. Gabler, A. Keating, S. Millman and J. Siegford. 2013. Behavioral fear response to a novel or human stimuli in barrows selected for feed efficiency. Animal Industry Report, Iowa State University. AS-Leaflet-R2810.
  • Onteru, S., D. Gorbach, J. Young, D. Garrick, J. Dekkers and M. Rothschild. 2013. Genome wide association studies for residual feed intake traits in pigs. Animal Industry Report, Iowa State University. AS-Leaflet-R2816.
  • Thekkoot, D.M., J. Young, Z-Q. Du, S. Onteru, M. Rothschild and J.C.M. Dekkers. 2013. Whole genome association study for lactation feed efficiency in Yorkshire sows selected for residual feed intake during finishing. Animal Industry Report, Iowa State University. AS-Leaflet-R2821.
  • Young, J., J. Patience, N. Gabler and J. Dekkers. 2013. Feed intake, feed efficiency, and growth of pigs selected for divergent RFI fed high versus low energy diets. Animal Industry Report, Iowa State University. AS-Leaflet-R2831.
  • Swine feed efficiency not always linked to net income. J.F.Patience, Iowa State University. 2012.
  • Swine feed efficiency genetic impact. J.W.Mabry, Iowa State University. 2012.
  • Swine feed efficiency particle size testing methodology. T.L.Steinhart, Iowa State University. 2012.
  • Swine feed efficiency influence of particle size. T.L.Steinhart, Iowa State University. 2012.
  • Swine feed efficiency influence of pelleting. T.G.Miller, Iowa State University. 2012.
  • Swine feed efficiency influence of temperature. T.G.Miller, Iowa State University. 2012.
  • Swine feed efficiency decision tree. M.D.Tokach, Kansas State University. 2012.
  • Swine feed efficiency influence of market weight. D.R.Stender, Iowa State University. 2012.
  • Swine feed efficiency effect of dietary energy on feed efficiency. R.M.Euken, Iowa State University. 2012.
  • Swine feed efficiency influence of ractopamine. M.P.Storlie, Iowa State University. 2012.
  • Swine feed efficiency impact of feeder design and management. R.M.Euken, Iowa State University. 2012.
  • Swine feed efficiency influence of amino acids. M.P.Storlie, Iowa State University. 2012.
  • Swine feed efficiency influence of sow feed on whole farm efficiency. D.R.Stender, Iowa State University. 2012.
  • Flohr, J.R., M.D. Tokach, J.M. DeRouchey, J.F. Patience, R.D. Goodband, S.S. Dritz and J.L. Nelssen. 2012. Feed efficiency in swine: A survey of current knowledge. Proc. Kansas Swine Day 2012. pp. 1-16.
  • Patience, J.F. 2012. Feed Efficiency in Swine. Editor. Wageningen Academic Publishers, Wageningen, The Netherlands.
  • Tokach, M.D., R.D. Goodband, J.M. DeRouchey, S.S. Dritz and J.L. Nelssen. 2012. Feed and barn management strategies that maximize feed efficiency. Page 41-62 in Feed Efficiency in Swine. J.F. Patience, ed. Wageningen Academic Press, Wageningen, The Netherlands.
  • Patience, J.F. 2012. The influence of dietary energy on feed efficiency in grow-finish swine. Page 101-129 in Feed Efficiency in Swine. J.F. Patience, ed. Wageningen Academic Press, Wageningen, The Netherlands.
  • Young, J.M. and J.C.M. Dekkers. 2012. The genetic and biological basis of residual feed intake as a measure of feed efficiency. Page 153-166 in Feed Efficiency in Swine. J.F. Patience, ed. Wageningen Academic Press, Wageningen, The Netherlands.
  • Mani, V., A.J. Harris, A.F. Keating, T.E. Weber, J.C.M. Dekkers and N.K. Gabler. 2013. Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake1. J Anim Sci doi:10.2527/jas.2012-6053.
  • Rakhshandeh, A., J.C.M. Dekkers, B.J. Kerr, T.E. Weber, J. English and N.K. Gabler. 2012. Effect of immune system stimulation and divergent selection for residual feed intake on digestive capacity of the small intestine in growing pigs. J Anim Sci 90: 233-235.
  • Basel, M.T., S. Balivada, A.P. Beck, M.A. Kerrigan, M.M. Pyle, J.C.M. Dekkers, C.R. Wyatt, R.R.R. Rowland, D.E. Anderson, S.H. Bossmann, and D.L. Troyer. 2012. Human Xenografts are not rejected in a naturally occurring immunodeficient porcine line: a human tumor model in pigs. BioResearch Open Access. 1:63-68.
  • Cruzen, S.M., A.J. Harris, K. Hollinger, J.T. Selsby, N.K. Gabler, S.M. Lonergan and E. Huff-Lonergan. 2012. Gilts selected for low residual feed intake have potential for decreased protein degradation. International Congress of Meat Science and Technology. Montreal, Canada.
  • Rakhshandeh, A., B.M. Adamic, J.M. Young, D.M. Thekkoot, T.E.Weber, J.C.M. Dekkers, and N.K. Gabler. 2012. Effect of selection for residual feed intake on sow performance I: Milk composition. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Cino Ozuna, A.G., R.R.R. Rowland, J.C. Nietfeld, J.C.M. Dekkers, and C.R. Wyatt. 2012. Preliminary findings of a previously unrecognized porcine primary immunodeficiency disorder. Veterinary Pathology doi:10.1177/0300985812457790.
  • Rakhshandeh, A., J.C.M. Dekkers, B.J. Kerr, T.E. Weber, J. English and N.K. Gabler. 2012. Effect of immune system stimulation and divergent selection for residual feed intake on digestive capacity of the small intestine in growing pigs. 12th International Symposium on Digestive Physiology of the Pig. Keystone, CO.
  • Thekkoot, D.M., R.A. Kemp, and J.C.M. Dekkers. 2012. Genetic parameters for growth performance and residual feed intake in a commercial line of Duroc pigs. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Wade, E.H., N. Boddicker, Z. Jiang, J.J. Michal, R. Rowland, J.K. Lunney and J.C.M. Dekkers. 2012. Analysis of candidate gene SNP on piglet response to experimental infection with PRRSv. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Arkfeld, E.K., E.R. Benedict, R.C. Johnson, J.M. Young, J.F. Patience, J.C.M. Dekkers, N.K. Gabler, S.M. Lonergan and E. Huff-Lonergan. 2013. Divergent selection for residual feed intake impacts carcass composition of pigs on high or low energy diets. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.
  • Adamic, B.M., A. Rakhshandeh, J.M. Young, D.M. Thekkoot, T.E.Weber, J.C.M. Dekkers, and N.K. Gabler. 2012. Effect of selection for residual feed intake on sow performance I: Lactation efficiency and reproductive performance. Ann. Mtg., Midwest Section, American Society of Animal Science, Des Moines, IA.


Progress 04/01/11 to 03/31/12

Outputs
OUTPUTS: Obj. 1A and B: 172 FireFeeder and 192 group penned low and high residual feed intake (RFI) gilts and barrows, fed either a high or low energy diet, had performance data collected. Total tract digestibility of nutrients and energy were determined and meat quality data were collected from a commercial packing plant. Obj. 1D: Mucosal scrapping and luminal contents have been collected and are awaiting characterization. Obj. 2A: Rep 1 of human and novel approach test was completed. 1600 minutes of video are being reviewed for latency to approach, time spent in zones, investigative behaviors and pig head position in relation to the human or cone. Obj. 2B: We have placed catheters and conducted both an intravenous glucose tolerance test and ACTH challenge on eight high and eight low RFI gilts. All the blood lab work has been completed and we are currently conducting statistical analysis on this work to determine insulin sensitivity and cortisol responses between the lines. Obj. 2C: The impact of immune system stimulation (ISS) and genetic selection for RFI on apparent ileal digestibility (AID) of nutrients and energy, and on intestinal nutrient transport and barrier function has been initiated. Obj. 2D: All animal work to evaluate line differences under PRRS challenge has been completed and 60k genotyped. Efficient line tends to grow faster under challenge. Obj. 3A: We have collected the blood samples and RFI data on the first 180 of 360 pigs, one year early. Obj. 3B: We have collected all required blood samples, physiological data and tissues from the Immune System Stimulation experiment (Obj. 2A,B); these animals were selected out of the Obj. 3A population so we have ties to the early samples. Obj. 3C: Pigs from the first replicate of the diet by line experiment have been 60k genotyped. Genetic evaluation, selection and matings to produce the next generation of the RFI lines have been completed. Genomic DNA was isolated from a total of 312 pigs from generations 4 and 7 of the ISU RFI lines. These samples were genotyped on a genome wide basis using the PorcineSNP60 BeadChip at GeneSeek Inc., Lincoln, NE. Initial genome wide association analyses (GWAS) were performed by combining the genotypes and phenotypes of these animals with the genotypes and phenotypes of the 730 animals that were used in the previous SNP association analyses. Obj. 4 and 5: International Conference on Feed Efficiency in Swine successfully completed, with more than 400 people from 18 countries attending. Forty percent of the U.S. sow herd was represented at the meeting. Feed Efficiency in Swine has gone to the printer and will be released in July; it contains 13 chapters and 275 pages. Project website is up and running and can be found at http://www.swinefeedefficiency.com/. New content is being added as new information becomes available. Survey of pork industry to determine the current level of knowledge and degree of adoption of information on feed efficiency has been completed and results are being analyzed. Decision tools have been developed: feeder adjustment cards, fat calculator, DDGS calculator, optimal market weight calculator, feed budget and spreadsheet. PARTICIPANTS: Iowa State University PI: Dr. John Patience: Oversight of overall project, leadership of Obj. 4&5, scientific input in Obj. 1&2. CoPIs: Dr. Nicholas Gabler: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Jack Dekkers: Leadership of Obj. 3, scientific input in Obj. 1&2; contributed to Obj 4&5; Dr. Elisabeth Huff Lonergan: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Steven Lonergan: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Lloyd Anderson: Scientific input in Obj. 1, 2&3; Dr. Anna Johnson: Leadership of Obj. 2, scientific input in Obj. 1&3; Dr. Chris Tuggle: Leadership of Obj. 3, scientific input in Obj. 1&2; Dr. Max Rothschild: Scientific input in Obj. 1,2&3; Dr. Dan Nettleton: Leadership of Obj. 3; Dr. John Mabry: Contributed to Obj. 4&5; Dr. Peng Liu. Undergraduate Students: Brianna Adamic, Dana van Sambeek, Jessica Jenkins, Susan Herr, Jennifer English, Rosslyn Punt. Graduate Students: Emily Arkfeld, Venkatesh Mani, Kyle Grubbs, Analia Roca, Dinesh M. Thekkoot, Nick Boddicker, Andrew Hess, Emily Waide, Danielle Gorbach, Ziyanda Mpetile. Post-doctoral scholars and Technical staff: Dr. Anoosh Rakhshandeh, Dr. Jennifer Young, Dr. Ed Steadham, Martha Jeffrey, Dr. Boxing Sun (visiting scientist Jilin University, China), Dr. Yi Zhang (visiting scientist China Agricultural University, Beijing), Suneel Onteru, Dr. Tinghua Huang. Kansas State University: Dr. Bob Rowland: Leadership of Obj. 2; Dr. Joel DeRouchey: Leadership of Obj. 4&5; Dr. Mike Tokach: Leadership of Obj. 4&5. USDA: Dr. Tom Weber: Leadership of Obj. 1&2, scientific input in Obj. 3; Dr. Brian Kerr: Scientific input in Obj. 1&2. INRA: Dr. Helene Gilbert: Scientific input in Obj. 3. The University of Melbourne: Dr. Frank Dunshea: Scientific input in Obj. 1&2. TARGET AUDIENCES: Pork producers: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book. Industries affiliated with the pork industry: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book. Extension personnel: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book. Other academics: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book. Post doctoral fellows: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book; laboratory instruction. Graduate students: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book; laboratory instruction. Undergraduate students: International Conference on Feed Efficiency in Swine; Feed Efficiency in Swine book; laboratory instruction; internships. PROJECT MODIFICATIONS: Due to the budget cut in year one, Obj. 1C has been eliminated.

Impacts
Preliminary research from Objs. 1A & B, demonstrates that reducing RFI results in leaner pork carcasses and tends to result in less marbling in pork. As expected, lipopolysaccharide (LPS) immune system stimulation (ISS) increased eye temperature (ISS- vs. ISS+; 37.6 vs. 38.4 degrees C, SE 0.04), plasma levels of haptoglobin (2.6 vs. 3.5 g/L, SE 0.38) and interleukin-1&#946; (1 vs. 152 ng/L, SE 35), indicating effective ISS (P < 0.05). No effects of line or its interaction with ISS on apparent ileal digestion of crude protein (CP) and organic matter (OM), transepithelial resistance (TER) and active glucose (GLU) transport were observed (P > 0.10). However, ISS decreased and tended to decrease AID of CP (ISS- vs. ISS+; 83 vs. 74 %, SE 3; P < 0.05) and OM (88 vs. 79 %, SE 4; P < 0.08), respectively. No effect of ISS on TER was observed (P > 0.10). Relative to ISS-, active GLU transport was greater in ISS+ pigs (7 vs. 11 A/cm2, SE 1.5; P < 0.05), indicating increased intestinal GLU absorption during ISS. Collectively, these results suggest that intestinal digestive capacity is affected by ISS but not by genetic selection for RFI. Initial results from the PRRS challenge confirm our hypothesis that pigs selected for efficiency are able to withstand immunological stressors better or at least as well. Initial GWAS studies using several models showed associations of RFI with important genomic regions on SSC2, 3, 4, and 9. However, further statistical analyses need to be performed as planned in the second year. Completion of the pork industry survey will enhance our knowledge of the level of knowledge possessed by the pork industry on information on feed efficiency and its adoption will become available when the analysis of the survey is completed. The International Conference on Feed Efficiency in Swine provided people in the pork industry with absolutely up-to-date information on the many factors that can influence feed efficiency, and how feed efficacy can be enhanced at the level of the individual farm.

Publications

  • Mani, V., Weber, T.E., Baumgard, L.H., and Gabler, N.K. (2012). Endotoxin, Inflammation and Intestinal Function in Livestock. J. Anim. Sci. 90(5):1452-1465.
  • Onteru, S.K., Gorbach, D.M., Young, J.M., Garrick, D.J., Dekkers, J., and Rothschild, M.F. (2012). A validation of whole genome association analyses for residual feed intake in the pig. The International Plant & Animal Genome XX Conference. January 14-18, 2012, San Diego, California. P0624.
  • Jenkins, J., Johnson, A.K., Gabler, N.K., and Siegford, J. (2011). NOT and HAT for barrows selected for feed efficiency. Iowa State University Science with Practice Post Fair. December 2011, Ames, IA.