Source: IOWA STATE UNIVERSITY submitted to
GENETIC RESISTANCE TO DISEASE IN CHICKENS-UTILIZING NOVEL BIOLOGICAL RESOURCES AND CONTEMPORARY GENETIC APPROACHES TO FURTHER THE UNDERSTANDING OF HOST RESISTANCE MECHANISMS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0223603
Grant No.
(N/A)
Project No.
IOW05275
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2010
Project End Date
Sep 30, 2015
Grant Year
(N/A)
Project Director
Lamont, SU, J.
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Animal Science
Non Technical Summary
There are many compelling reasons to improve the health status of poultry: improved poultry health will improve animal welfare, production efficiency, and profitability of poultry agriculture; and protect the human food supply from possible contamination with harmful microbes and residues of antimicrobial drugs. Scientific approaches that enhance the innate, genetic capabilities of poultry populations to ward off disease are especially desirable, because they are environmentally friendly, permanent, reduce use of antibiotics, and are generally synergistic with the protective effects of vaccination. Iowa State University has developed and maintained unique genetic lines of chickens that are well-suited for in-depth study to discover the genetic mechanisms that contribute to successful resistance to disease in poultry. This project will reproduce and maintain the chicken genetic lines so that they remain available for study, and will produce special populations to characterize resistance to Salmonella, Eimeria and avian influenza. The collaborative studies on pathogen resistance will determine the associations of naturally existing variation of genomic structure and gene expression with resistance traits. These discoveries can be applied in the poultry breeding industry to enhance the genetic resistance to disease of future commercial populations.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033299108010%
3033299109010%
3043299108010%
3043299109010%
3113299108030%
3113299109030%
Goals / Objectives
1) Maintain breeding colonies of chickens unique genetic structure and phenotypes; 2) Characterize the impact of Salmonella infection on liver transcriptome; 3) Determine functional genomic response of diverse chicken lines to challenge with various pathogens.
Project Methods
We will maintain breeding colonies of chickens of unique genetic structure and phenotypes. Chicks will be wingbanded and raised with contemporary groups in floor pens with ad libitum access to water and a nutritionally complete diet. Light cycle will be controlled to manage onset of lay. At sexual maturity, birds will be transferred to individual laying cages. Lines will be maintained with fully pedigreed, artificial insemination matings. Eggs will be marked with parental information, stored to accumulate large full-sib families, and incubated to hatch. As needed for specific trials, additional numbers of eggs or chicks will be produced. Chickens will have a minimal program of vaccinations to protect them from environmentally ubiquitous pathogens. Birds will be blood-typed for line-specific red cell antigens, to help ensure pedigree integrity. Biological resources (semen, ovaries, fertile eggs) will be provided to the USDA National Germplasm Preservation Center for cryopreservation efforts. To obtain a systems-level assessment of changes in gene expression that are associated with infection, we will analyze the transcriptomes of birds from Iowa State University chicken genetic lines that either were or were not infected with pathogens. Number of birds challenged will be sufficient to generate a wide range of phenotypic responses to the infection, which will allow the analysis of the phenotypic extremes (resistant/susceptible) for the microarray, along with samples from non-infected birds. Individual samples of cDNA isolated from various tissues of infected birds and non-infected birds will be analyzed in a pair-wise infected/non-infected design on 44K element Agilent microarrays, with dye-swap incorporated into the design. Statistical analysis will contrast the infected/non-infected response, and account for dye label, slide and batch. Statistically significant differentially expressed genes will be bioinformatically interrogated for pathway and functional group membership and over-represented categories of gene ontology. The output of these studies will be novel information about the gene pathways that are altered in a various tissues or cells upon whole-bird infection with pathogens. This information will highlight targets for genetic selection, vaccine development and additional research topics. Information generated in this project will be promptly and widely disseminated to target audiences of fellow scientist, poultry breeders and poultry producers through presentation at scientific meetings, industry meetings, direct contact with poultry geneticists, and publication of results in peer-reviewed journals. Trainees at various levels (undergrad, graduate and post-doctoral) will be mentored and trained in the conduct of this project. Indicators of success will include presentations and publications based upon the project, and numbers of trainees educated in the project. Long-term success (outside the period of this project) will be use of the new knowledge by the poultry breeding industry to improve genetic resistance traits of commercial populations.

Progress 10/01/10 to 09/30/15

Outputs
Target Audience:Students and researchers in animal and poultry breeding, genetics and genomics; commercial breeders of poultry; animal and poultry health professionals. Changes/Problems:In the final year of the project, the outbreak of high path avian influenza prevented the export of live birds to collaborators. To safeguard the breeding flock, a small number were transferred to another site with higher biosecurity, but the cost to maintain them there is very high so this is not a viable long-term solution. What opportunities for training and professional development has the project provided?Graduate and undergraduate students were mentored and trained in conducting research in this project. Summer interns in a program that targets research experiences to U.S. students of underrepresented groups in STEM were trained in research procedures. Faculty and graduate students participated in national and international scientific conferences. How have the results been disseminated to communities of interest?Results have been disseminated by publication of multiple peer-reviewed journal papers, and presentation of research at scientific conferences and in seminars at other universities. Invited book chapters on relevant subjects have been written. Popular press (industry reports) have been posted on the web. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Improving the health status of poultry will improve animal welfare, production efficiency, and profitability of poultry agriculture, and protect the human food supply from possible microbial contamination and residues of antimicrobial drugs. Approaches that enhance the innate, genetic capabilities of poultry populations to ward off disease are especially desirable because they are environmentally friendly, permanent, reduce use of antibiotics, and are generally synergistic with the protective effects of vaccination. Iowa State University has developed and maintained unique genetic lines of chickens that are well-suited for in-depth study to discover the genetic mechanisms that contribute to successful resistance to disease in poultry. This project reproduced and maintained the chicken genetic lines so that they remain available for study, and produced special populations for research to characterize resistance to a pathogens and to biotic stressors such as moldy feed. The collaborative studies on pathogen resistance helped to determine the associations of naturally existing variation of genomic structure and gene expression with disease-resistance traits. These discoveries can be applied in the poultry breeding industry to enhance the genetic resistance to disease of future commercial populations. This will result in improved animal health and productivity, greater efficiency in commercial poultry production systems, and enhanced food safety. Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their commercial egg-producing and meat-producing lines. The information on genetic variation will also enable fine-mapping and eventual identification of the specific genes in the disease-resistance pathways. The discovery that two of the tested lines differ for response to Avian Influenza (AI) provides a foundation for using these lines for studies of resistance to AI, an important disease. The preliminary observation that chicken lines show variation in glutathione transferase may provide a selection target to enhance resistance to aflatoxicosis. Determining SNP haplotypes in the MHC of well-characterized lines will help to genetically select for enhanced immune response and disease resistance. Maintenance of unique genetic material helps to ensure that natural variation to meet future needs is available. Sharing genetic resources with other researchers enabled a larger portfolio of studies to be initiated at the collaborators' institutions and expanded the scope of collaborative research with which the Iowa station was involved. Objective 1) Maintain breeding colonies of chickens unique genetic structure and phenotypes. Over the project life, the specialized Iowa State University genetic lines of chickens were successfully reproduced and maintained. The breeding colonies included several highly inbred lines, one outbred broiler line, and two advanced intercross lines (AIL) established from the initial cross of a broiler sire with dams of two of the inbred lines (Fayoumi and Leghorn). This labor-intense activity of line reproduction includes design of matings, manual collection of semen and artificial insemination of hundreds of hens twice weekly during the reproductive season, marking the collected eggs, incubating and hatching the eggs in systems to allow full-pedigree tracking, and applying individual identifier bands to each newly hatched chick. Chicks are then raised under good husbandry practices until mature, when they are used to produce the next generation and hatches of chicks for research. As chicks and breeders the birds of the inbred lines are blood-typed to characterize the major histocompatibility complex (MHC) type. Objective 2) Characterize the impact of Salmonella infection on liver transcriptome. Salmonella enterica serovar enteritidis is an enteric bacterium that can contaminate chicken eggs and meat, resulting in production losses and consumer illness. To provide insight into the systemic metabolic effects of S. enteritidis infection, liver samples were harvested 10 days postinfection from broiler hens. Hepatic global gene expression levels were assessed using a chicken 44K Agilent microarray. Forty-four genes were differentially expressed at a significance level of q value < 0.05. One hundred eighty-three genes were differentially expressed at a suggestive significance level of q value < 0.1. A predominance of downregulation existed among significantly differentially expressed genes. Cell cycle and metabolism networks were created from the differentially expressed genes. Mitochondria-mediated apoptosis, electron transport, peptidase activity, vein constriction, cell differentiation, IL-2 signaling, Jak-Stat signaling, B-cell receptor signaling, GDP/GTP exchange, and protein recycling were among the functions of the differentially expressed genes that were down-regulated in response to S. enteritidis. The effects of S. enteritidis infection on the liver transcriptome profiles of broilers reflect a predominance of downregulation of genes with cell cycle and metabolic functions. The most pronounced response was the downregulation of genes that function in metabolic pathways, inflammation, and mitochondria-mediated apoptosis. These results provide insight into important systemic metabolic mechanisms that are active in the chicken liver in response to S. enteritidis infection at 10-days postinfection. Application of this information may allow more rationale development of vaccines, or targeted breeding to increase beneficial allelic variation in the population to enhance natural resistance to bacteria. Objective 3) Determine functional genomic response of diverse chicken lines to challenge with various pathogens. Over the project life, genetic material in the form of live chicks, fertile eggs, or biological samples were shared with many cooperating researchers to conduct joint studies on the impact of genetic variation (provided by the Iowa State University lines) on diseases caused by biotic stressors (pathogens), metabolic diseases (obesity) and abiotic stressor (heat). Adipose tissues of ISU fat and lean lines were determined in collaboration with B. Voy of the University of Tennessee-Knoxville to use different biochemical pathways for metabolism. In collaboration with J. Womack of Texas A&M University and others, ISU genetic lines were shown to differ for the NK-lysin alleles. In collaboration with H. Zhou at University of California-Davis, copy number variation was established between the Fayoumi and Leghorn lines. Also in collaboration with H. Zhou, novel genes and signaling pathways were demonstrated between these lines after avian influenza infection. To expand knowledge of the annotation of genes for the chicken, data of ISU lines was contributed to the avian RNA-seq consortium. In collaborative studies with R. Coulombe at Utah State University, the activity of liver enzymes that detoxify aflatoxins was found to be higher in the Fayoumi line of chickens than other lines. In collaboration with J. Fulton at Hy-Line, International, the use of a 90-SNP panel to define the MHC showed that most of the ISU inbred lines had little within-line variation. In collaboration with H. Lillehoj at the USDA, the MHC-disparate lines were demonstrated to differ for response to necrotic enteritis.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sun, H., Liu, P., Nolan, L.K., and Lamont, S.J. 2015. Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens. BMC Genomics 16:690 DOI 10.1186/s12864-015-1850-4.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kim, D. K., Lillehoj, H.S., Jang, S.I., Lee, S.H., Hong, Y.H., and Lamont, S.J. 2015. Genetically disparate Fayoumi chicken lines show different response to avian necrotic enteritis. J. Poultry Sci. doi.org/10.2141/jpsa.0140203.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Sun, H., Liu, P., Nolan, L.K., and Lamont, S.J. 2015. (accepted) Combined Analysis of Primary Lymphoid Tissues' Transcriptomic Response to Extra-intestinal Escherichia coli (ExPEC) Infection. Dev Comp Immunol.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Sun, H., Liu, P., Nolan, L.K., and Lamont, S.J. (accepted) Novel pathways revealed in bursa of Fabricius transcriptome in response to extraintestinal pathogenic Escherichia coli (ExPEC) infection. PLOS ONE.
  • Type: Journal Articles Status: Under Review Year Published: 2016 Citation: Wang, Y., Huefner, N., Lupiani, B., Sanjay, R.M., Lamont, S.J., and Zhou, H. (in review) RNA-seq analysis revealed novel genes and signaling pathway associated with resistance to avian influenza virus infection in chicken lungs. PLOS ONE.
  • Type: Journal Articles Status: Under Review Year Published: 2016 Citation: Lee, M.O., Jang, H.-J., Rengaraj, D., Yang, S.-Y., Han, J.Y., Lamont, S.J., and Womack, J.E. (in review) Tissue expression and antibacterial activity of host defense peptides in chicken. BMC Immunology.
  • Type: Journal Articles Status: Under Review Year Published: 2016 Citation: Lee, S.H., Dong, X., Lillehoj, H.S., Lamont, S.J., Suo, X., Kim, D.K., Lee, K.-W., and Hong, Y.H. (in review) Comparing immune-response to Eimeria tenella in two genetically B-complex disparate Fayoumi chicken lines. Res Vet Sci.
  • Type: Journal Articles Status: Under Review Year Published: 2016 Citation: Nie, Q., Jia, X., Li, Z., Zheng, X., Xu, H., Sandford, E.E., Zhang, X., Nolan, L.K. and Lamont, S.J. (in review) Systematic discovery of spleen miRNAs involved in host response to avian pathogenic Escherichia coli (APEC) by deep sequencing and integrated analysis. DNA Research.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Students and researchers in animal and poultry breeding, genetics and genomics; commercial breeders of poultry; animal and poultry health professionals. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Two graduate and two undergraduate students were mentored and trained in conducting research in this project. Two summer interns in a program that targets research experiences to U.S. students of underrepresented groups in STEM were trained in research procedures. Faculty and graduate students of the project participated in national and international scientific conferences. How have the results been disseminated to communities of interest? Results have been disseminated by publication of multiple peer-reviewed journal papers, and presentation of research at scientific conferences and in seminars at other universities. Seminars on research were presented to first-year graduate students of several different graduate majors. What do you plan to do during the next reporting period to accomplish the goals? Continue the reproduction, maintenance and characterization of the Iowa State University genetic lines of chickens. Share tissues, isolated DNA, fertile eggs and chicks with collaborating researchers to characterize genetic diversity and relationships with resistance to pathogens and to abiotic stressors. Finalize and submit manuscripts on all completed studies.

Impacts
What was accomplished under these goals? IMPACT. Improving the health status of poultry will improve animal welfare, production efficiency, and profitability of poultry agriculture; and protect the human food supply from possible microbial contamination and residues of antimicrobial drugs. Approaches that enhance the innate, genetic capabilities of poultry populations to ward off disease are especially desirable, because they are environmentally friendly, permanent, reduce use of antibiotics, and are generally synergistic with the protective effects of vaccination. Iowa State University has developed and maintained unique genetic lines of chickens that are well-suited for in-depth study to discover the genetic mechanisms that contribute to successful resistance to disease in poultry. This project reproduced and maintained the chicken genetic lines so that they remain available for study, and produced special populations for research to characterize resistance to a pathogens and to biotic stressors such as moldy feed. The collaborative studies on pathogen resistance helped to determine the associations of naturally existing variation of genomic structure and gene expression with disease-resistance traits. These discoveries can be applied in the poultry breeding industry to enhance the genetic resistance to disease of future commercial populations. This will result in improved animal health and productivity, greater efficiency in commercial poultry production systems, and enhanced food safety. Goal-specific accomplishments: 1) Maintain breeding colonies of chickens unique genetic structure and phenotypes. In the past year, the specialized Iowa State University genetic lines of chickens were successfully reproduced and maintained. This included several highly inbred lines, one outbred broiler line, and two advanced intercross lines (AIL) established from the initial cross of a broiler sire with dams of two of the inbred lines (Fayoumi and Leghorn). This labor-intense activity of line reproduction includes design of matings, manual collection of semen and artificial insemination of hundreds of hens weekly during the reproductive season, marking the collected eggs, incubating and hatching the eggs in systems to allow full-pedigree tracking, and applying individual identifier bands to each newly hatched chick. Chicks are then raised under good husbandry practices until mature, when they are used to produce the next generation and hatches of chicks for research. As chicks and breeders the birds are blood-typed to characterize the major histocompatibility complex (MHC) type. Generations are reproduced at approximately 9 month intervals. 2) Characterize the impact of Salmonella on liver transcriptome of broiler chickens. With the successful accomplishment of this goal in the previous year, we extended studies under this goal to examine the impact of an abioltic stressor (heat) on the liver transcriptome. This goal was completed with the publication describing the detailed results in a paper in the journal, BMC Genomics, and presentation of the work at the World Congress of Genetics Applied to Livestock Production. 3) Determine functional genomic response of diverse chicken lines to challenge with various pathogens. Adipose tissues of ISU fat and lean lines were determined in collaboration with B. Voy of the University of Tennessee-Knoxville to use different biochemical pathways for metabolism, and the results were published this year in a peer-reviewed journal paper. In collaboration with J. Womack of Texas A &M University and many others, ISU genetic lines were shown to differ for the NK-lysin alleles, and the results were published in a peer-reviewed journal. In collaboration with H. Zhou at University of California-Davis, copy number variation was established between the Fayoumi and Leghorn lines, and results were published in a peer-reviewed journal. Also in collaboration with H. Zhou, novel genes and signaling pathways were demonstrated between these lines after avian influenza infection, and the results published in a peer-reviewed journal. To expand knowledge of the annotation of genes for the chicken, data of ISU lines were contributed to the avian RNA-seq consortium, and the paper published in a peer-reviewed journal.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Smith, J., Burt. D.W., and the Avian RNAseq Consortium. 2014. The Avian RNAseq Consortium: a community effort to annotate the chicken genome. Cytogenet Genome Res. doi: http://dx.doi.org/10.1101/012559
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Coble, D. J., Fleming, D.F., Persia, M. P., Ashwell, C.M., Rothschild, M. F., Schmidt, C.J., and Lamont, S.J. 2014. RNA-seq analysis of broiler liver transcriptome reveals novel responses to heat stress. BMC Genomics 15:1084. DOI: 10.1186/1471-2164-15-1084
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lee, M.O., Yang, E., Morisson, M., Vignal. A., Huang, Y.-Z., Cheng, H.H., Muir, W.M., Lamont, S.J., Lillehoj, H.S., Lee, S.H., and Womack, J.E. 2014. Mapping and genotypic analysis of NK-lysin gene in chicken. Genet. Sel. Evol.46:43.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ji, B., Middleton, J.L., Ernest, B., Saxton, A.M., Lamont, S.J., Campagna, S. R., and Voy, B.H. 2014. Genetic leanness in domestic chickens is associated with evidence of increased fatty acid oxidation in white adipose tissue. Physiological Genomics 46:315327.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S.J., Crooijmans, R., and Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Animal Genetics 45:400-411.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang, Y., Lupiani, B., Reddy, S., Lamont, S.J., and Zhou, H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Sci. 93:485-493.


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: Students and researchers in animal and poultry breeding and genetics, commercial breeders of poultry, animal and poultry health professionals. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? One graduate and one undergraduate student were mentored and trained in conducting research in this project. One summer intern in a program that targets research experiences to U.S. students of underrepresented groups in STEM was trained in research procedures. Faculty and graduate students of the project participated in national and international scientific conferences. How have the results been disseminated to communities of interest? Results have been disseminated by publication of peer-reviewed journal papers, and presentation of research at conferences and in seminars at other universities. Seminars on research were presented to first-year graduate students of several different graduate majors. What do you plan to do during the next reporting period to accomplish the goals? Continue the reproduction, maintenance and characterization of the Iowa State University genetic lines of chickens. Share tissues, isolated DNA, fertile eggs and chicks with collaborating researchers to characterize genetic diversity and relationships with resistance to pathogens and to abiotic stressors.

Impacts
What was accomplished under these goals? IMPACT. Improving the health status of poultry will improve animal welfare, production efficiency, and profitability of poultry agriculture; and protect the human food supply from possible microbial contamination and residues of antimicrobial drugs. Approaches that enhance the innate, genetic capabilities of poultry populations to ward off disease are especially desirable, because they are environmentally friendly, permanent, reduce use of antibiotics, and are generally synergistic with the protective effects of vaccination. Iowa State University has developed and maintained unique genetic lines of chickens that are well-suited for in-depth study to discover the genetic mechanisms that contribute to successful resistance to disease in poultry. This project reproduced and maintained the chicken genetic lines so that they remain available for study, and produced special populations for research to characterize resistance to pathogens and to biotic stressors such as moldy feed. The collaborative studies on pathogen resistance helped to determine the associations of naturally existing variation of genomic structure and gene expression with disease-resistance traits. These discoveries can be applied in the poultry breeding industry to enhance the genetic resistance to disease of future commercial populations. This will result in improved animal health and productivity, greater efficiency in commercial poultry production systems, and enhanced food safety. Goal-specific accomplishments: 1) Maintain breeding colonies of chickens unique genetic structure and phenotypes. In the past year, the specialized Iowa State University genetic lines of chickens were successfully reproduced and maintained. This included several highly inbred lines, one outbred broiler line, and two advanced intercross lines (AIL) established from the initial cross of a broiler sire with dams of two of the inbred lines (Fayoumi and Leghorn). This labor-intense activity of line reproduction includes design of matings, manual collection of semen and artificial insemination of hundreds of hens weekly during the reproductive season, marking the collected eggs, incubating and hatching the eggs in systems to allow full-pedigree tracking, and applying individual identifier bands to each newly hatched chick. Chicks are then raised under good husbandry practices until mature, when they are used to produce the next generation and hatches of chicks for research. As chicks and breeders the birds are blood-typed to characterize the major histocompatibility complex (MHC) type. Generations are reproduced at approximately 9 month intervals. 2) Characterize the impact of Salmonella infection on liver transcriptome. This goal was completed with the publication describing the detailed results in a paper in the journal, Genesis, and presentation of the work at the World’s Poultry Congress. 3) Determine functional genomic response of diverse chicken lines to challenge with various pathogens. In collaborative studies with R. Coulombe at Utah State University, the activity of liver enzymes that detoxify aflatoxins was found to be higher in the Fayoumi line of chickens than other lines. In collaboration with J. Fulton at Hy-Line, International, the use of a 90-SNP panel to define the MHC showed that most of the ISU inbred lines had little within-line variation. Adipose tissues of ISU fat and lean lines were determined in collaboration with B. Voy of the University of Tennessee-Knoxville to use different biochemical pathways for metabolism. In collaboration with H. Lillehoj at the USDA, the MHC-disparate lines were demonstrated to differ for response to necrotic enteritis. In collaboration with J. Womack of Texas A &M University, ISU genetic lines were shown to differ for the NK-lysin alleles. In collaboration with H. Zhou at University of California-Davis, copy number variation was established between the Fayoumi and Leghorn lines, also novel genes and signaling pathways were demonstrated between these lines after avian influenza infection.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Coble, D.J., Sandford, E. E., Ji, T., Abernathy, J., Fleming, D., Zhou, H., and Lamont, S.J. 2013. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Genesis 51:357364


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of novel chickens were maintained and reproduced. The Iowa State University chicken genetic lines are of two basic genetic types: (a) highly inbred lines or (b) advanced intercross lines (AIL). The highly inbred lines (75 - 100 generations of sib matings) are of defined MHC type, with the inbreeding of the earliest line starting in 1925. Lines are primarily of egg-type origin, but also include the non-commercial Fayoumi and Spanish lines. A non-inbred broiler line was also maintained. Birds of the MHC-defined lines were serologically typed each generation with line-specific anti-erythrocyte antisera to verify line purity (approximately 900 birds each generation); all birds as chicks and the potential breeders, a second time before mating. A resource population for in-depth characterization of the host genetics of response to Salmonella (Iowa Salmonella Response Resource Population, ISRRP) was been developed over the years by crossing outbred broiler males with females of two distinct, highly inbred lines (Leghorn and Fayoumi). The ISRRP was maintained in AILs, with the F19 generation being hatched in the past year. The continued production of AIL facilitates the opportunities to narrow the confidence intervals (fine-map) around quantitative trait loci (QTL) and to conduct detailed studies on gene expression. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. Genetic lines were distributed to collaborators, as numbers allowed. Fayoumi chicks were shipped to H. Lillehoj (USDA-ARS, Beltsville) to study response to Eimeria challenge, tissues were sent to R. Coulombe (Utah State U) to test for genetic variants in glutathione transferase, and blood/DNA was sent to Janet Fulton (Hy-Line, Intl) to test on an MHC-high-density SNP panel. Multiple graduate students, visiting scholars and undergraduate interns, received instruction and research experience through participation in the project. PARTICIPANTS: Project director is Susan J. Lamont. Participants from Iowa State University were: Michael Kaiser (Research Associate II), Derrick Coble (Ph.D. student in Interdepartmental Genetics), and Hongyan Sun (Ph.D. student in Animal Breeding and Genetics). Academic collaborators included: Texas A and M University (Huaijun Zhou, now at University of California-Davis), and Roger Coulombe (Utah State University). Industry collaborators included Janet Fulton (Hy-Line, Intl.) TARGET AUDIENCES: Animal and poultry health professionals, veterinarians, researchers in animal and poultry breeding and genetics, commercial breeders of poultry. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their commercial egg-producing and meat-producing lines. The information on genetic variation will also enable fine-mapping and eventual identification of the specific genes in the disease-resistance pathways. The discovery that two of the tested lines differ for response to Avian Influenza (AI) provides a foundation for using these lines for studies of resistance to AI, an important disease. The preliminary observation that chicken lines show variation in glutathione transferase may provide a selection target to enhance resistance to aflatoxicosis. Determining SNP haplotypes in the MHC of well-characterized lines will help to genetically select for enhanced immune response an disease resistance. Maintenance of unique genetic material helps to ensure that natural variation to meet future needs is available. Sharing genetic resources with other researchers enabled a larger portfolio of studies to be initiated at the collaborators' institutions and expanded the scope of collaborative research with which the Iowa station was involved.

Publications

  • Coble, D.J., Sandford, E. E., Ji, T., Abernathy, J., Fleming, D., Zhou, H., and Lamont, S.J. 2012. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Genesis (on line) DOI: 10.1002/dvg.22351
  • Lian, L., Ciraci, C., Chang, G., Hu, J., and Lamont, S.J. 2012. NLRC5 knockdown in chicken macrophages alters response to LPS and poly (I:C) stimulation. BMC Vet. Res. 8:23 doi:10.1186/1746-6148-8-23
  • Coble, D.J., Sandford, E.E., Ji, T., Abernathy, J., Fleming, D., Zhou, H., Lamont, S.J. 2012. Impacts of Salmonella Enteritidis infection on liver transcriptome in broilers. Proc. 2012 World's Poultry Congress, July 2012, Brazil. Abstract sp27.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of novel chickens were maintained and reproduced. The Iowa State University chicken genetic lines are of two basic genetic types: (a) highly inbred lines or (b) advanced intercross lines (AIL). The highly inbred lines (50 - 100 generations of sib matings) are of defined MHC type, with the inbreeding of the earliest lines starting in 1925. Lines are primarily of egg-type origin, but also include the non-commercial Fayoumi and Spanish lines. A non-inbred broiler line was also maintained. Birds of the MHC-defined lines were serologically typed each generation with line-specific anti-erythrocyte antisera to verify line purity (approximately 900 birds each generation); all birds as chicks and the potential breeders, a second time before mating. A resource population for in-depth characterization of the host genetics of response to Salmonella (Iowa Salmonella Response Resource Population, ISRRP) has been developed over the years by crossing outbred broiler males with females of two distinct, highly inbred lines (Leghorn and Fayoumi). The ISRRP was maintained in AILs, with the F18 generation being hatched in the past years. The continued production of AIL facilitates the opportunities to narrow the confidence intervals (fine-map) around quantitative trait loci (QTL) and to conduct detailed studies on gene expression. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. Genetic lines were distributed to collaborators, as numbers allowed. Fayoumi fertile eggs were shipped to collaborator H. Zhou (Texas A and M University) to study response to avian influenza virus and Fayoumi chicks to H. Lillehoj (USDA-ARS, Beltsville) to study response to Eimeria challenge. Multiple graduate students, visiting scholars and undergraduate interns, received instruction and research experience through participation in the project. PARTICIPANTS: Project director is Susan J. Lamont. Participants from Iowa State University were: Michael Kaiser (Research Associate II), Derrick Coble (Ph.D. student in Interdepartmental Genetics), and Erin Sandford (Ph.D. student in Interdepartmental Genetics). Academic collaborators included: Texas A and M University (Huaijun Zhou, now at Univeristy of California-Davis), USDA-ARS (Hyun Lillehoj), and University of Tennessee - Knoxville (Brynn Voy). TARGET AUDIENCES: Animal and poultry health professionals, veterinarians, researchers in animal and poultry breeding and genetics, commercial breeders of poultry. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their commercial egg-producing and meat-producing lines. The information on genetic variation will also enable fine-mapping and eventual identification of the specific genes in the disease-resistance pathways. Assessing the liver transcriptome broadens the picture of systemic response to infection in the chicken. Maintenance of unique genetic material helps to ensure that natural variation to meet future needs is available. Sharing genetic resources with other researchers enabled a larger portfolio of studies to be initiated at the collaborators' institutions and expanded the scope of collaborative research with which the Iowa station was involved.

Publications

  • Chuammitri, P., Redmond, S. B., Kimura, K., Andreasen, C. B., Lamont, S. J., and Palic, D. 2011. Heterophil functional responses to dietary immunomodulators vary in genetically distinct chicken lines. Vet. Immunol. Immunopathol, doi:10.1016/j.vetimm.2011.05.019
  • Coble, D. J., Redmond, S.B., Hale, B., and Lamont, S. J. 2011. Distinct lines of chickens express different splenic cytokine profiles in response to Salmonella enteritidis challenge. Poultry Sci. 90:1659-1663.
  • Kumar, S., Ciraci, C., Redmond, S., B., Chuammitri, P., Andreasen, C., B., Palić, D., and Lamont, S.J. 2011. Immune response gene expression in spleens of diverse chicken lines fed dietary immunomodulators. Poultry Sci. 90:1009-1013.
  • Redmond, S.B., Chuammitri, P., Andreasen, C. B., Palic, D., Lamont, S.J. 2011. Genetic control of chicken heterophil function in advanced intercross lines: associations with novel and with known Salmonella resistance loci and a likely mechanism for cell death in extracellular trap production. Immunogenetics 63: 449-458. DOI 10.1007/s00251-011-0523-y
  • Redmond, S.B., Chuammitri, P., Andreasen, C. B., Palic, D., Lamont, S.J. 2011. Proportion of circulating chicken heterophils and CXCLi2 expression in response to Salmonella enteritidis are affected by genetic line and immune modulating diet. Vet. Immunol. Immunopath. 140: 323-328.
  • Coble, D.J., Redmond, S.B., Hale, B., and Lamont, S.J. 2011. Distinct lines of chickens express different splenic cytokine profiles in response to Salmonella enteritidis challenge. Proc. 100th Annual PSA Meeting, St. Louis, Missouri. July 2011.
  • Coble, D.J., Sandford, E., Abernathy, J., Zhou, H., and Lamont, S.J. 2011. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Plant & Animal Genome XIX, January 2011, San Diego, CA. (URL: http://www.intl-pag.org/19/abstracts/P07a_PAGXIX_718.html)
  • Redmond, S.B., Chuammitri, P., Andreasen, C. B., Palic, D., Lamont, S.J. 2011. Genome-wide analysis of chicken heterophil functional response to Salmonella on advanced intercross lines reveals associations with known resistance loci, novel loci, and a likely mechanism for cell death through extracellular trap production. Plant & Animal Genome XIX, January 2011, San Diego, CA.
  • Wang Y., V. Brahmakshatriya, B. Lupiani, S. Reddy, B. S. Lamont, H. Zhou. 2011. Identification of differentially expressed microRNAs associated with Avian Influenza Virus Infected in two genetically distinct Chicken Lines. Proc. Plant & Animal Genome XIX, January 2011. San Diego, CA.