Source: IOWA STATE UNIVERSITY submitted to
PHENOMICS FOR GENETIC AND GENOME-ENABLED IMPROVEMENT OF RESILIENCE IN PIGS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1011708
Grant No.
2017-67007-26144
Project No.
IOW05496
Proposal No.
2016-07991
Multistate No.
(N/A)
Program Code
A5171
Project Start Date
Feb 15, 2017
Project End Date
Feb 14, 2021
Grant Year
2017
Project Director
Dekkers, J. C.
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Animal Science
Non Technical Summary
Pork is the most-consumed meat globally, consumption of which is expected to increase over the next decades with international population and income growth. To keep up with demand and provide global food security and safety, pork producers must employ further technological innovation to increase production sustainably. Infectious disease is one of the largest costs associated with pork production and one of the most difficult to manage. In addition, infectious disease in pork production impedes animal welfare, can impact human health and contributes to poor public perception of animal production in terms of animal welfare, food safety and antimicrobial resistance. Although biosecurity and vaccination protocols help to reduce the incidence of disease, maintaining a disease-free status in pork production is not feasible. Thus, additional strategies to reduce the incidence and impact of disease are needed. Disease resilience refers to the ability of an animal to sustain performance in the face of general disease challenge and is determined in part by host genetics. However, genetic selection for improved disease resilience is hampered by the inability to directly measure disease resistance or resilience in the nucleus breeding populations that drive genetic improvement because they are by necessity kept under high biosecurity and face limited disease pressures. New high-throughput phenomic and genomics approaches provide unique prospects to develop measures that can be taken on healthy animals at a young age that are predictive of resistance and resilience when phased with disease in a production environment, which is the overall goal of this proposal. Achievement of this goal will increase the international competitiveness and productivity of the US pork industry and its contributions to global food safety/security by developing genetic improvement strategies that reduce pig deaths and morbidity, and improve production efficiency and animal welfare. This project builds on and complements our previous and ongoing work on resistance to PRRS and PCV2, yet is novel in focusing on overall disease resilience, rather than resistance to specific disease. This project also leverages and builds on a recently initiated and ongoing large-scale international research program that is funded by Genome Alberta, Genome Canada and a consortium of 7 breeding organizations with major market shares in the US, in which 3500 North American commercial crossbred pigs are evaluated for resilience during nursery-grow-finish in a research environment that mimics a production environment with high disease pressure based on natural challenge. The environment that has been created allows for optimal expression of disease resilience, which is being captured by deep phenotyping during grow-finish, including individual daily body weights, feed and water intake, along with disease incidence, mortality, and morbidity. We will use this already established and funded program to apply deep phenotyping approaches on samples collected on all pigs prior to natural challenge, which mimic the non-evasive phenotypes that can be collected on healthy animals in a nucleus breeding program at a young age. Phenotypes collected include high-throughput approaches to interrogate the blood transcriptome, metabolome and proteome, as well as the microbiome of fecal swabs, and in-vitro measures of immune response using blood. These phenotypes will complement additional immune response measures that are being collected through the already funded project. The resulting comprehensive deep phenotypes will be used to develop predictors of disease resilience at both the genetic and phenotypic level. Genetic analyses will be enhanced by utilizing 80k SNP genotypes that will be available on all pigs, allowing for the development of whole genome-enabled selection programs, which is ideal for the use of this information in high-health nucleus breeding programs. Deliverables include methods and tools to evaluate and optimize resilience to disease and strategies for end users to integrate into their programs. Project deliverables will lead to economic benefits for the US through improved performance, lower medication costs, increased international demand for North American breeding stock, and possibly an increase in domestic and export market share owing to consumer preference for pork from higher health and welfare pigs. Producers will derive financial benefits from higher productivity, better market penetration and genetics. Other benefits include a healthier and safer food chain, and vast knowledge generation and translation. End-user recipients such as in particular breeding organizations, are all engaged in the research to ensure the deliverables are transferred directly into the hands of the breeding industry, which will ensure rapid implementation.
Animal Health Component
50%
Research Effort Categories
Basic
0%
Applied
100%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033510108030%
3033510108120%
3043510108010%
3113510108020%
3113510108120%
Knowledge Area
303 - Genetic Improvement of Animals; 311 - Animal Diseases; 304 - Animal Genome;

Subject Of Investigation
3510 - Swine, live animal;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
The overall goal of this project to enhance the ability of pigs to resist and minimize the impact of disease by developing methods to select for disease resilience in high-health nucleus breeding populations.Specific objectives are to:Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease.Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease.Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease.Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection.
Project Methods
This project builds on an ongoing large-scale international research program that is funded by Genome Alberta, Genome Canada and a consortium of 7 breeding organizations with major market shares in the US, in which 3500 North American commercial crossbred pigs are evaluated for resilience during nursery-grow-finish in a research environment that mimics a production environment with high disease pressure based on natural challenge. The environment that has been created allows for optimal expression of disease resilience, which is being captured by deep phenotyping during grow-finish, including individual daily body weights, feed and water intake, along with disease incidence, mortality, and morbidity. We will use this already established and funded program to apply deep phenotyping approaches on samples collected on 960 pigs prior to natural challenge, which mimic the non-evasive phenotypes that can be collected on healthy animals in a nucleus breeding program at a young age. Phenotypes collected include high-throughput approaches to interrogate the blood transcriptome, metabolome and proteome, as well as the microbiome of fecal swabs, and in-vitro measures of immune response using blood. These phenotypes will complement additional immune response measures that are being collected through the already funded project. The resulting comprehensive deep phenotypes will be used to develop predictors of disease resilience at both the genetic and phenotypic level. Genetic analyses will be enhanced by utilizing 80k SNP genotypes that will be available on all pigs, allowing for the development of whole genome-enabled selection programs, which is ideal for the use of this information in high-health nucleus breeding programs.

Progress 02/15/17 to 02/14/21

Outputs
Target Audience:Researchers in animal molecular and quantitative genetics, and in livestock breeding and genetics, both in academia and industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One post-doctoral fellow and one PhD and threeMSstudents workedon the project at Iowa State University, providing unique opportunities for training and professional development. They have each presented their work at one or more scientific conferences. They have also presented their work to the industry collaborators in two workshops, providing unique opportunities to interact with stakeholders (swine breeding industry) and scientists. They have prepared scientific and technical reports on their work. How have the results been disseminated to communities of interest?Presentations at industry and scientific meetings and workshops, industry reports, blogs, and articles, and scientific papers. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Overall impact statement: Animals and livestock contribute 40 percent of the global value of agricultural output and contribute to the livelihoods and food security of almost a billion people worldwide. Advances in animal breeding, genetics, and genomics will facilitate resilience of pigs to disease. Building resilience of pigs to disease is critical to improving livestock production and lowering costs for producers. This project identified multiple bio-markers that can be measured on young healthy pigs that are heritable and genetically correlated with disease resilience. These bio-markers can be used for genetic selection for disease resilience in high-health nucleus breeding populations. Objective 1. Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. In vitro assays were performed on over blood samples from over 1,000 healthy nursery pigs prior to the disease challenge, including 35 cytokines following stimulation and 17 phagocytotic activity measurements. Cytokines generally had relatively low heritability but some had moderate heritability, in particular several IL-6 and IL-8 measures. Several of these had moderately high genetic correlations with growth rate and medical treatment rates under challenge. Most phagocytotic activity measurements had moderate to high (up to 63%) estimates of heritability and some had high positive genetic correlations with growth rate under challenge and high negative genetic correlations with treatment rates and mortality, making them suitable bio-markers to select for disease resilience. Objective 2. Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease. The transcriptome (3'RNAseq), metabolome (NMR), and proteome (Mass Spectometry) was profiled on blood samples from ~940 healthy nursery pigs prior to the natural disease challenge. The level of gene expression of over 14,000 genes was quantified and showed both phenotypic and genetic associations with concurrent and subsequent performance and disease resilience. Genes associated with immune and stress response were unfavorably associated with both pre- and post-challenge traits, while genes associated with heme-related terms had favorable associations with both pre- and post-challenge traits, and genes associated with protein localization and viral gene expression were unfavorably associated with performance and health traits under challenge. The expression of a substantial number of genes was moderately heritable. Abundance was also measured for over 400 proteins and 40 metabolites. Several proteins and metabolites showed moderate heritability and moderate genetic correlations with concurrent and subsequent performance and disease resilience. Objective 3. Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease. Faecal samples were collected on ~960 pigs prior to entry into the natural challenge facility and were sequenced. Data was summarized at the genus level, (ASV/species level data was too sparse for additional analysis). A total of 47 genera were retained after quality control, with 7 showing moderate heritability (>0.2). Faecalibacterium abundance showed some promise, with a heritability of 0.27 and high genetic correlations with mortality and treatment rates, but with large standard errors. Objective 4. Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection. Genomic predictions of breeding values using genomic relationship showed moderate accuracies, around 0.25 for growth rates and around 0.2 for mortality and treatment rates, demonstrating potential for their use in selection. Inclusion of relationship matrices based on the transcriptome, the proteome, and the metabolome substantially increased the accuracy of predicting phenotypes, especially growth rate at the time the blood samples for these -omics measures were taken. Data Management Plan: The data generated under this project includes immune assays, fecal microbiome, and blood transcriptome, proteome, and metabolome data on ~900 young healthy pigs. In combination with SNP genotype and extensive phenotype data of these and another ~2,000 pigs, these data were used to generate scientific publications, as documented, with at least 5 additional publications in preparations. The full complement of data are held in a secure project database (Genome Canada Pig Health database at UAlberta), that was established for the larger Genome Canada funded disease resilience project, with back-up copy of data securely stored with back-up and encryption at Iowa State University. These data were generated on pigs from the seven company members of the PigGen research consortium. Because of the confidentiality of the source of these data, each company is only be able to access to the data of its own pigs, unless a data sharing agreement is established. Data generated under this project will be available to other researchers upon reasonable request to Jack Dekkers and after establishment of a data sharing agreement. The data will be stored for at least 10 years.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Dong, Q., Lunney, J.K., Lim, K.S., Nguyen, Y., Hess, A.S., Beiki, H., Rowland, R.R., Walker, K., Reecy, J.M., Tuggle, C.K. and Dekkers, J.C., 2021. Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus. BMC veterinary research, 17(1), pp.1-21. doi.org/10.1186/s12917-021-02785-1
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: 4. Jeon, R.L., Cheng, J., Putz, A.M., Dong, Q., Harding, J.C.S., Dyck, M.K., Plastow, G.S., Fortin, F., Lunney, J., Rowland, R., PigGen Canada, and Dekkers, J.C.M., 2021. Effect of a genetic marker for the GBP5 gene on resilience to a polymicrobial natural disease challenge in pigs. Livestock Science, 244, p.104399. doi.org/10.1016/j.livsci.2021.104399
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: 1. Sanglard, L.P., Mote, B.E., Willson, P., Harding, J., Plastow, G.S., Dekkers, J. and Ser�o, N.V., 2020. Genomic analysis of IgG antibody response to common pathogens in commercial sows in health-challenged herds. Frontiers in genetics, 11, p.1276. doi.org/10.3389/fgene.2020.593804
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: A.4. Cheng J., A. M. Putz, J. C. S. Harding, M. K. Dyck, F. Fortin, G. S. Plastow, PigGen Canada, and J. C. M. Dekkers. 2021. Genetic parameters of water and feed intake and behavior traits of wean-to-finish pigs under a polymicrobial natural disease challenge model. J. Anim. Sci. Biotech.
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: A.5. Lim K. S., J. Cheng, A. Putz, Q. Dong, X. Bai, C. K. Tuggle, M. K. Dyck, PigGen Canada, F. Fortin, J. C. S. Harding, G. S. Plastow, and J. C. M. Dekkers. 2021. Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience. BMC Genomics.
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: A.6. R. L. Jeon, C. Gilbert, J. Cheng, A. M. Putz, M. K. Dyck, G. S. Plastow, F. Fortin, PigGen Canada, J. C. M. Dekkers, and J. C. S. Harding. 2021. Proliferation of peripheral blood mononuclear cells from healthy piglets after mitogen stimulation as indicators of disease resilience. J. Anim. Sci.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: F.1. Lim K.S., J. Cheng, A. Putz, Q. Dong, C.K. Tuggle, M.K. Dyck, PigGen Canada, F. Fortin, J.C.S. Harding, G.S. Plastow and J.C.M. Dekkers. 2020. Association of the blood transcriptome of healthy piglets with response to natural polymicrobial disease, including PRRS. Virtual North American PRRS Symposium, US.


Progress 02/15/19 to 02/14/20

Outputs
Target Audience: researchers in animal molecular and quantitative genetics, and in livestock breeding and genetics Changes/Problems:There have been some delays in data acquisition. What opportunities for training and professional development has the project provided? One post-doctoral fellow and one PhD and one MSc student are working on the project at Iowa State University, providing unique opportunities for training and professional development. They have each presented their work at one or more scientific conferences, providing unique opportunities to interactwith stakeholders (swine breeding industry) and scientists, and have prepared scientific and technical reports on their work. How have the results been disseminated to communities of interest? Presentations at industry and scientific meetings, industry reports, scientific papers. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. Models are being refined in order to complete estimates of genetic parameters and relationships with subsequent resilience to disease. Objective 2. Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease. Models are being refined in order to complete estimates of genetic parameters and relationships for the transcriptomic, metabolomic, and proteome data with subsequent resilience to disease. Objective 3. Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease. Models are being refined in order to complete estimates of genetic parameters and relationships for the microbiome data with subsequent resilience to disease. Objective 4. Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection. All available data collected on the 920 young healthy pigs will be combined to develop phenotypic and genetic predictors of resilience.

Impacts
What was accomplished under these goals? Overall impact statement: Animals and livestock contribute 40 percent of the global value of agricultural output and contribute to the livelihoods and food security of almost a billion people worldwide. Advances in animal breeding, genetics, and genomics will facilitate resilience of pigs to disease. Building resilience of pigs to disease is critical to improving livestock production and lowering costs for producers. In year 3, all phenomics assays on the ~940 healthy nursery pigs were completed and preliminary phenotypic and genetic analyses were completed. Objective 1. Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. In vitro assays were performed on all available blood 1 samples (n=1,095) from the batches used for the project. In the first test, samples were split into three for challenge with two different antigens along with an untreated control. Supernatants were tested for 9 cytokines (Interleukins 1b, 2, 4, 6, 8, 10, 13, 17 & Interferon gamma) by ELISA. The second test determined phagocytosis capacity of different white blood cells determined by measuring uptake of fluorescently labelled E.coli using cell sorting. Estimation of genetic parameters and relationships with subsequent resilience to disease has identified a small of potential biomarkers. Objective 2. Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease. Samples for transcriptome, metabolome, and proteome work were collected on ~940 health nursery pigs prior to them entering the natural disease challenge facility. RNA was isolated and sequenced for all samples using 3'RNAseq. Phenotypic associations or gene expression profiles with concurrent and subsequent performance under challenge have been completed, as are preliminary genetic analyses. ~940 samples for metabolomics were analyzed by NMR and 44 metabolites reproducibly quantified. Initial estimates of genetic parameters and relationships with subsequent resilience to disease have been completed. The proteome of all 915 samples was quantified using Mass Spectometry. Preliminary phenotypic and genetic analyses have been completed. Objective 3. Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease. Faecal samples were collected on ~960 pigs prior to entry into the natural challenge facility and were sequenced. Data was summarized at the genus level (ASV/species level data was too sparse for additional analysis). A total of 47 genera were retained after quality control with 7 showing moderate heritability (>0.2). The data is now being analyzed for relationships with subsequent resilience measures. 4. Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection. The complete data for these analyses is being compiled.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Cheng, J., Putz, A.M., Harding, J.C., Dyck, M.K., Fortin, F., Plastow, G.S., Canada, P. and Dekkers, J.C., 2020. Genetic analysis of disease resilience in wean-to-finish pigs from a natural disease challenge model. Journal of Animal Science, 98(8), p.skaa244
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Chen, Y., Cortes, L.E.T., Ashley, C., Putz, A.M., Lim, K.S., Dyck, M.K., Fortin, F., Plastow, G.S., Dekkers, J.C. and Harding, J.C., 2020. The genetic basis of natural antibody titers of young healthy pigs and relationships with disease resilience. BMC genomics, 21(1), pp.1-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Jeon, R. L., A. M. Putz, J. Lunney, R.R.R. Rowland, J. C. S. Harding, M. K. Dyck, F. Fortin, G. S. Plastow, PigGen Canada, J. C. M. Dekkers. Effect of Genotype at a GBP5 Marker on Resilience to a Polymicrobial Natural Disease Challenge in Pigs. Plant and Animal Genome, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Lim, K.-S., Q, A. Putz, Q. Dong, C.K. Tuggle, M.K. Dyck, PigGen Canada, F. Fortin, J.C.S. Harding, G. Plastow, and J.C.M. Dekkers, 2020. Quantitative genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience. Plant and Animal Genome, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Cheng, J., A. M. Putz, J. C. S. Harding, M. K. Dyck, F. Fortin, G. S. Plastow, and PigGen Canada, and J. C. M. Dekkers. Genetic parameters of the disease resilience traits in wean-to-finish pigs from a Natural Disease Challenge Model. Banff Swine Symposium, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Chen, Y., S. Longergan, K.-S. Lim, A. Putz, C. Tuggle, M. Dyck, PigGen Canada, F. Fortin, J. Harding, G. Plastow, and J. Dekkers. Protein levels in blood of young healthy pigs as indicators of disease resilience. Plant and Animal Genome, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Chen, Y., Laura, L., Ashley, C., Putz, A.M., Lim, K.S., Dyck, M., Fortin, F., Plastow, G.S., Dekkers, J.C. and Harding, J.C., 2019. 59 The Genetic Basis of Natural Antibody Titers and Relationships with Disease Resilience in Pigs. Journal of Animal Science, 97(Supplement_2), pp.35-36.


Progress 02/15/18 to 02/14/19

Outputs
Target Audience:Swine industry, in particular the swine breeding and genetics industry, scientists. Changes/Problems:Some delays in completion of all assays and initiation of statistical analyses. The need for a 1-year no-cost extension is anticipated. What opportunities for training and professional development has the project provided?One post-doctoral fellow and two PhD students are working on the project at Iowa State University, providing unique opportunities for training and professional development. They have each presented their work at one or more scientific conferences, providing unique opportunities to interactwith stakeholders (swine breeding industry) and scientists, and have prepared scientific and technical reports on their work. How have the results been disseminated to communities of interest?Presentations at industry and scientific meetings, industry reports, scientific papers. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from younghealthy animals as potential predictors of resilience of pigs to disease. Resulting data will be analyzed to estimate genetic parameters and relationships with subsequent resilience to disease. Objective 2. Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthyanimals as potential predictors of resilience of pigs to disease. The RNAseq, metabolome and proteome data will be used to estimate genetic parameters and relationships with subsequent resilience. The proteome analyses on the first 420 samples will be used to determine which proteins to assay on the remaining samples. Objective 3. Determine the genetic control of the gut microbiome of young healthy animals as potential predictors ofresilience of pigs to disease. Microbiome sequencing will be completed and genetic parameters and relationships with resilience will be estimated. Objective 4. Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictorsof resilience to disease using genome-enabled selection. All available data collected on the 920 young health pigs will be combined to develop phenotypic and genetic predictors of resilience.

Impacts
What was accomplished under these goals? Overall impact statement: Animals and livestock contribute 40 percent of the global value of agricultural output and contribute to the livelihoods and foodsecurity of almost a billion people worldwide. Advances in animal breeding, genetics, and genomics will facilitate resilience of pigs to disease. Building resilience of pigs to disease is critical to improving livestock production and lowering costs forproducers. In year 2, samples for the second half of pigs were collected and processed, completing the samples proposed to be collected on ~960 healthy nursery pigs. Objective 1. Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. Supernatants from blood samples following exposure to two antigents were collected for cytokine assays, which have now been completed. Phagocytosis capacity was measured on all samples using fluorescent E.coli. Objective 2. Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood fromyoung healthy animals as potential predictors of resilience of pigs to disease. Samples for transcriptome, metabolome, and proteome work were collected on ~940 health nursery pigs prior to them entering the natural disease challenge facility. RNA was isolated and sequenced for all samples using 3'RNAseq and analyzed for associations between gene expression and subsequent resilience, showing several promising associations and opportunities to use gene expression on young healthy pigs to predict subsequent resilience. ~940 samples for metabolomics and proteomics have been processed and resulting data are awaiting analysis. Objective 3. Determine the genetic control of the gut microbiome of young healthy animals as potential predictorsof resilience of pigs to disease. Faecal samples have been collected on ~960 pigs prior to entry into the natural challenge facility and are being processed for microbiome analyses. Objective 4. Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs aspredictors of resilience to disease using genome-enabled selection. Yet to be initiated.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Putz, A.M., J.C.S. Harding, M.K. Dyck, PigGen Canada, F. Fortin, G.S. Plastow, and J.C.M. Dekkers. 2018. Novel resilience phenotypes from a natural challenge model for disease resilience in wean-to-finish pigs. Frontiers in Genetics. doi: 10.3389/fgene.2018.00660
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Chen, Y., Tibbs, L. E., Ashley, C., Putz, A., Lim, K. S., Dyck, M. K., PgGen Canada, Fortin, F., Plastow, G. S., Dekkers, J., Harding, J. C. S. 2018. The Genetic Basis of Natural Antibody Titers and Relationships with Disease Resilience in Pigs. Proc. North American PRRS Symposium. Chicago, IL. December 1-2, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lim, J., Yang, T., Bai, X., Yang, Z., Newell, M., Goruk, S., Harding, J.C.S., Fortin, F., Dyck, M.K., PigGen Canada, Dekkers, J.C.M., Field, C.J., Plastow, G.S. Hemotological based prediction of disease resilient pigs in a natural challenge model. Advances in Pork Production (2018) 29:Abstract#24
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lim, K.-S., Q, A. Putz, Q. Dong, C.K. Tuggle, M.K. Dyck, PigGen Canada, F. Fortin, J.C.S. Harding, G. Plastow, and J.C.M. Dekkers, 2018. Blood transcriptome in healthy piglets as a potential biomarker to improve disease resilience. Proc. North American PRRS Symposium. Chicago, IL. December 1-2, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Pedersen-Macnab M.K., Seddon Y.M., J.C.S. Harding J.C.S., F. Fortin F., Dekkers J., Dyck M.K., Plastow G.S., PigGen Canada (2019) The effect of environmental enrichment on the immune response and measures of disease resilience and welfare in pigs Advances in Pork Production 30: Abstract 21
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Dekkers, J.C.M. 2019. Genetic improvement of animal health. 2019. Plant and Animal Genome. San Diego.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Dekkers, J.C.M. 2018. Using Genetics to Improve Animal Health. Agricultural Bioscience International Conference, Weifang, China.


Progress 02/15/17 to 02/14/18

Outputs
Target Audience:Swine industry, in particular the swine breeding and genetics industry, scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One post-doctoral fellow and two PhD students have been appointed on the project at Iowa State University, providing unique opportunities for training and professional development. The post-doctoral fellow and one PhD student have presented an abstract at the Plant and Animal Genome meetings in San Diego and also attended the joint meeting of the National Swine Improvement Federation and the PRRS symposium in Chicago in December 2017, providing unique opportunities to interact with stakeholders (swine breeding industry) and scientists. How have the results been disseminated to communities of interest?Presentations at industry and scientific meetings. What do you plan to do during the next reporting period to accomplish the goals?Objective 1... Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. Blood samples were collected on another 480 healthy nursery pigs prior to their entry into the natural disease challenge facility and cytokines and phagocytosis will be measured. Resulting data will be analyzed to estimate genetic parameters and relationships with subsequent resilience to disease. Objective 2... Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease. Samples for transcriptome, metabolome, and proteome work will be collected on another 460 health nursery pigs prior to them entering the natural disease challenge facility. RNA will be isolated and sequenced and analyzed in combination with the first set of 460 to estimate genetic parameters and relationships with subsequent resilience. Metabolome assays will be completed and proteome assays will be initiated. Objective 3... Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease. Faecal samples will be collected on another 460 nursery pigs and all samples will be sequenced for microbiome analyses. Objective 4... Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection. This will be initiated in year 3

Impacts
What was accomplished under these goals? Overall impact statement: Animals and livestock contribute 40 percent of the global value of agricultural output and contribute to the livelihoods and food security of almost a billion people worldwide. Advances in animal breeding, genetics, and genomics will facilitate resilience of pigs to disease.Building resilience of pigs to diseaseis critical to improving livestock production and lowering costs for producers. In year 1, protocols for sample collection and assays were established and samples for the first half of pigs were collected and assays were initiated. Objective 1... Determine the genetic control of in-vitro immune assay-based phenotypes conducted on blood from young healthy animals as potential predictors of resilience of pigs to disease. Blood samples were collected on 587 healthy nursery pigs prior to their entry into the natural disease challenge facility. Supernatants following exposure to two antigents were collected and shipped to INRA, France, for cytokine assays. Phagocytosis capacity was measured on all samples using fluorescent E.coli. Objective 2... Determine the genetic control of transcriptome, metabolome, and proteome profiles of blood from young healthy animals as potential predictors of resilience of pigs to disease. Samples for transcriptome, metabolome, and proteome work were collected on 460 health nursery pigs prior to them entering the natural disease challenge facility. Samples for metabolomics are being processed and samples for proteome work were stored for future analyses. RNA was isolated and sequenced using 3'RNAseq. For that purpose, we collaborated with Lexogen, the manufacturer of the 3'RNAseq kits, to develop and evaluated a 3'RNA library preparation kit that includes a hemoglobin block, such that hemoglobin mRNA, which presents ~50% of all mRNA in blood, is not sequenced and most sequencing resources are directed at other mRNA. Processing of the sequencing data is in progress. Objective 3... Determine the genetic control of the gut microbiome of young healthy animals as potential predictors of resilience of pigs to disease. Faecal samples have been collected on 460 pigs and are being processed for microbiome analyses. Objective 4... Develop and evaluate the use of integrated deep phenotypes obtained on blood from healthy pigs as predictors of resilience to disease using genome-enabled selection. Yet to be initiated.

Publications

  • Type: Other Status: Published Year Published: 2018 Citation: Putz, A.M., Harding, J., Dyck, M.K., Fontin, F., Plastow, G.S. and Dekkers, J., 2018. Novel Resilience Phenotypes from a Natural Disease Challenge Model for Wean-to-Finish Pigs. Animal Industry Report, 664(1), p.71.
  • Type: Other Status: Published Year Published: 2018 Citation: Tibbs, L.E., Ashley, C., Putz, A., Lim, K.S., Dyck, M.K., Fontin, F., Plastow, G.S., Dekkers, J. and Harding, J., 2018. Selection for Increased Natural Antibody Levels to Improve Disease Resilience in Pigs. Animal Industry Report, 664(1), p.69.
  • Type: Other Status: Published Year Published: 2018 Citation: Lim, K.S., Dong, Q., Moll, P., Vitkovska, J., Wiktorin, G., Bannister, S., Daujotyte, D., Tuggle, C.K. and Dekkers, J., 2018. A Globin Blocker to Increase Sequencing Efficiency for QuantSeq 3'mRNA-Seq in Porcine Blood. Animal Industry Report, 664(1), p.73.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Putz, A.M., Harding, J.C.S., Fortin, F., Plastow, G. and Dekkers, J.C.M., 2017. A natural challenge model for disease resilience in wean-to-finish pigs. Journal of Animal Science, 95(supplement2), pp.17-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Dekkers, J.C.M. 2017. Using genetic selection and genomics to combat infectious disease. PRRS-NSIF symposium, https://www.vet.k-state.edu/na-prrs/docs/2017-proceedings.pdf
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lim, KS, Q Dong, P Moll, J Vitkovska, G Wiktorin, S Bannister, D Daujotyte, CK Tuggle, and JCM Dekkers. 2017. A Globin Blocker to Increase Sequencing Efficiency for QuantSeq 3' mRNA-Seq in Porcine Blood. P0447. Plant and Animal Genome. http://www.intlpag.org/2018/images/pdf/PAGXXVI-abstracts-posters.pdf
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Tibbs, L, C. Ashley, A Putz, KS Lim, M Dyck, F Fortin, GS Plastow, PigGen Canada, JCM Dekkers, J Harding. 2018. Selection for increased natural antibody levels to improve disease resilience in pigs. Plant and Animal Genome. https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/32331
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Putz, AM, MK Dyck, PigGen Canada, JCS Harding, F Fortin, GS Plastow, and JCM Dekkers. 2018. Quantifying Resilience Utilizing Feed Intake Data in A Natural Challenge Model for Disease Resilience in Wean-to-Finish Pigs. Novel resilience phenotypes from a natural disease challenge model in wean-to-finish pigsWorld Congress Genetics Applied to Livestock Production, Auckland, New Zealand, https://icarinterbullwcgalp.zerista.com/event/member/452758