Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
ADVANCED TECHNOLOGIES FOR THE GENETIC IMPROVEMENT OF POULTRY (WAS NC-168)
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1001561
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
NC-_old1170
Project Start Date
Oct 22, 2013
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Animal Science
Non Technical Summary
With the advancement of new technologies in genetics and genomics, production of poultry industry can be significantly improved. Genetic lines with distinct resistance to pathogen infection serve as a great model in understanding molecular and cellular mechanisms of host response to infection in poultry. Integration of "omic" data using systems biology approach will enhance our knowledge in pinpoint key genes and signaling pathways affecting economically important traits. New tools and knowledge can be developed to applied in poultry industry and scientific community.
Animal Health Component
25%
Research Effort Categories
Basic
65%
Applied
25%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033220104034%
3043299108033%
3113260109033%
Knowledge Area
303 - Genetic Improvement of Animals; 311 - Animal Diseases; 304 - Animal Genome;

Subject Of Investigation
3220 - Meat-type chicken, live animal; 3299 - Poultry, general/other; 3260 - Poultry meat;

Field Of Science
1040 - Molecular biology; 1090 - Immunology; 1080 - Genetics;
Goals / Objectives
Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices.
Project Methods
Genetic and genomic approaches including microarray, next-generation sequencing etc high-throughput technologies will be used to identify candidate genes and QTL affecting economically important traits in poultry. Systems biology approach will be utilized to integrate "omics" data to understand biological process in chickens.

Progress 10/22/13 to 09/30/18

Outputs
Target Audience:Poultry scientific community, poultry industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students, undergraduate students, and postdoctoral scholar have training in in poultry disease, immunology and genomic analysis. How have the results been disseminated to communities of interest?Oral and poster presentations were given in scientific meetings, and institutes in the US, Ireland, and Africa. Participated in workshop with diverse participants including scientists from institutes, funding agencies, NGO. Oral presentation was given to disadvantaged students and staff in Africa institutes. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? - Harderian gland transcriptome analysis revealed that a limited early response in both Fayoumi and Leghorn lines occurred at 2 dpi. Leghorns eventually had a substantially stronger response at 6 dpi, while Fayoumi had a robust response at the later stages of infection under heat stress. In addition, very few differentially expressed genes overlapped between the lines at each time point suggesting a distinct, line-specific host response to NDV. Especially, GP6 signaling pathway plays significant role in the disease resistance in chickens. - Completed genome-wide association analysis for challenge experiments on Hy-Line Brown: All three replicate trials with over 1,100 challenged birds were completed at UCD and ISU. NDV titers were measured in tears collected at 2 and 6 days post infection. In addition, NDV serum antibody response was measured at 10 days post-infection. The major findings were that the 600K SNP panel and GWAS identified few significant regions associated with the measured phenotypes and these were generally of low genetic effect, emphasizing the highly polygenic nature of the NDV response traits. Additional regions of marginal significance were supported by independent studies that demonstrated differential expression in resistant-susceptible line contrasts of genes that were in the QTL regions.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579; doi:10.3390/genes9120579
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kim, T.H. and H. Zhou. 2018. Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1. Frontiers in Genetics. doi: 10.3389/fgene.2018.00415.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Saelao, P., Y. Wang, K. C, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment. BMC Veterinary Research https://doi.org/10.1186/s12917-018-1583-0
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: K. Rowland. Wolc. J. H. Zhou, R. Gallardo, T. Kelly, A. Dekkers, Lamont. S.J. Genome-Wide Association Study of a Commercial Egg Laying Line Challenged with Newcastle Disease Virus. Front. Genet., 20 August 2018 | https://doi.org/10.3389/fgene.2018.00326.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Kayang, B.B., Amuzu-Aweh, N., Botchway, P.K., Tudeka, C.K., Naazie, A., Aning, K.G., Dekkers, J., Lamont, S.J., Gallardo, R., Kelly, T.R., Bunn, D., & Zhou, H. (2018). Performance of three local chicken ecotypes of Ghana naturally exposed to velogenic Newcastle disease virus. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.846.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Botchway, P.K., Amuzu-Aweh, N., Naazie, A., Aning, K.G., Zhou, H., Dekkers, J., Lamont, S.J., Gallardo, R., Kelly, T.R., Bunn, D., & Kayang, B.B. (2018). Genotypic and phenotypic characterisation of three local chicken ecotypes of Ghana based on principal component analysis and body measurements. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.812.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Amuzu-Aweh, N., Kayang, B.B., Muhairwa, A.P., Botchway, P.K., Naazie, A., Aning, K.G., Gallardo, R., Kelly, T.R., Zhou, H., Lamont, S.J., & Dekkers, J.C.M. (2018). Genetic parameters and genomic regions associated with growth rate and response to Newcastle disease in local chicken ecotypes in Ghana and Tanzania. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.774.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Mushi, J.R., Muhairwa A. P. G.C. Chieanga. P. M Msoffe, Dekkers, J., Lamont, S.J., Gallardo, R., Kelly, T.R., Bunn, D., & Zhou, H. (2018).Phenotypic and genotypic diversity of selected Free Range Local Chickens in Tanzania. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.812.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Muhairwa A. P. G.C. Chieanga. J.R. Mushi, P. M Msoffe, N. Amuzu-Aweh, M. Walugembe, Dekkers, J., Lamont, S.J., Gallardo, R., Kelly, T.R., & Zhou, H. (2018). Investigation of Genetic Resistance to Newcastle Disease in Local Chickens in Tanzania using Natural Challenge by Field Velogenic NDV Strains. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.812.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: G.C. Chiwanga, A. P. Muhairwa, J.R. Mushi, P.L.M Msoffe, R.A. Max, E.N. Amuzu-Aweh, J. Dekkers, R. Gallardo, S.J. Lamont, T. R. Kelly, and H. Zhou. 2018. Viral clearance in Free-range local chicken in Tanzania following challenge by Lentogenic Newcastle Disease virus. Avian Immunology Research Group meeting, Oxford, UK.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Da Silva, A.P., R. Hauck, H. Zhou, R.A. Gallardo. (2018). Understanding Immune Resistance to Different Infectious Bronchitis Virus Genotypes. 67th Western Poultry Disease Conference (WPDC) Salt Lake City, UT.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Deist, Herrmann, R. Gallardo, D. Bunn, J. Dekkers, H. Zhou, S. Lamont. 2018. Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines. Scientific Reports. 8(1):6558. doi: 10.1038/s41598-018-24830-0.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhang J, Kaiser MG, Deist MS, Gallardo RA, Bunn DA, Kelly TR, Dekkers JCM, Zhou H, Lamont SJ. Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines. Sci Rep. 2018 Jan 19;8(1):1278. doi: 10.1038/s41598-018-19754-8.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Princess K. Botchway, Esinam N. Amuzu-Aweh, Muhammed Walugembe, Augustine Naazie, George K. Aning, Perot Saelao, Ying Wang, Huaijun Zhou, Jack Dekkers, Sue J. Lamont, Rodrigo Gallardo, Terra R. Kelly, and Boniface B. Kayang. Genome Wide Association Analysis for Response to Newcastle Disease Virus in Local Chicken Ecotypes of Ghana. Avian Immunology Research Group meeting, Oxford, UK.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Mushi. J.R., A. P. Muhairwa, G.C. Chiwanga, P.L.M Msoffe, J. Dekkers, R. Gallardo, S.J. Lamont, T. R. Kelly, and H. Zhou, M. Walugembe. 2018. Immunological phenotypes of Tanzanian free range local chickens (FRLC) to lentogenic Newcastle disease virus. Avian Immunology Research Group meeting, Oxford, UK.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: K. Rowland. H. Zhou, R. Gallardo, T. Kelly, A. Wolc. J. Dekkers, Lamont. S.J. 2018. Genome-wide association study of complex traits in response to Newcastle disease virus in chickens. Poultry Science Annual Meeting, San Antonio, TX
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Karen Tracy, Perot Saelao, Ying Wang, Rodrigo A. Gallardo, Susan J. Lamont, and Huaijun Zhou. 2018.Dynamics of antiviral response to Newcastle Disease Virus (NDV) and heat stress in chicken spleen. Poultry Science Annual Meeting, San Antonio, TX
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kim, T. H., H. Zhou. 2018. Functional genomics analysis revealed novel genes and pathways modulated by IRF7 in the host innate immune response against avian influenza virus infection in chickens. Gene Expression and Signaling in the Immune System, Cold Spring Harbor, NY
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Karen Tracy, Stephen Preston, Perot Saelao, Ying Wang, Rodrigo A. Gallardo, Susan J. Lamont, Adrian Smith, and Huaijun Zhou. 2018. Immune Repertoire Analysis and the Systemic Immune Response during Newcastle Disease Virus Infection in Chickens. Avian Immunology Research Group meeting, Oxford, UK
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Karen Tracy, Stephen Preston, Perot Saelao, Ying Wang, Rodrigo A. Gallardo, Susan J. Lamont, Adrian Smith, and Huaijun Zhou. 2018. Immune repertoire analysis during Newcastle Disease Virus infection in two genetically distinct chicken lines. The 14th Congress of the International Society for Developmental and Comparative Immunology, Santa Fe, NX, US.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: K. Chanthavixay,Y. Wang, Saelao, P., T.R. Kelly, J.M. Dekkers, R. Gallardo, S.J. Lamont. Zhou, H. 2018. Transcriptome Analysis in Two Inbred Chicken Lines Showing Sex-Differential Response to NDV Infection Under Heat Stress. Plant & Animal Genome XXVI, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Y. Wang, X. Li, Saelao, P., K. Chanthavixay, T.R. Kelly, J.M. Dekkers, R. Gallardo, S.J. Lamont. Zhou, H. 2018. Transcriptome Analysis of Host Response to NDV Infection under Heat Stress in Two Genetically Distinct Chicken Inbred Lines. Plant & Animal Genome XXVI, San Diego, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Saelao, P., Y. Wang, K. Chanthavixay, D. Bunn, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Proteomic Analysis of Liver Tissue from Heat Stressed and Newcastle Disease Virus Infected Inbred Chicken Lines.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: S.J. Lamont., C. Schmidt, and Zhou, H. 2018. Role of Animal Genetic Improvement in Enhancing Food Security? Plant & Animal Genome XXVI, San Diego, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: M. Halstead, Kern, C. P. Saelao, Y. Wang, M. Delany, H. Cheng, Zhou, H. P. J. Ross. 2018. Modification of ATAC-Seq Permits Profiling of Open Chromatin in Cryopreserved Chicken Lung. Plant & Animal Genome XXVI, San Diego, CA
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wilson B. K, T. Kelly, D.A. Bunn, and H. Zhou. 2018. Key criteria and models for implementing a sustainable chicken breeding and distribution program for smallholder poultry producers. Livestock Research for Rural Development. 30 (4), Article #67. Retrieved April 13, 2018, http://www.lrrd.org/lrrd30/4/wils30067.html


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Poultry scientific community, poultry industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students, undergraduate students, and postdoctoral scholar have training in genomics and bioinformatics analysis. How have the results been disseminated to communities of interest?Oral and poster presentations were given in scientific meetings, and institutes in the US, Ireland, and Africa. Participated in workshop with diverse participants including scientists from institutes, funding agencies, NGO. Oral presentation was given to disadvantaged students and staff in Africa institutes. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Identification of genes and signal pathways that are associated with resistance to heat stress and Newcastle disease virus infection in chickens. Development of ChIP-seq and ATAC-seq assays to identify and annotate regulatory elements in poultry genomes. Development of bioinformatic pipeline to functionally annotate poultry genomes.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Deist, Herrmann, R. Gallardo, D. Bunn, J. Dekkers, H. Zhou, S. Lamont. 2017. Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome. BMC Genomics201718:989.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, Y, Saelao, K. Chanthavixay P., R. Gallardo, D,A, Bunn, S.J. Lamont. J.K. Dekkers, T. R. Kelly, Zhou, H. 2017. Physiological Responses to Heat Stress in Two Genetically Distinct Chicken Inbred Lines. Poult. Sci. , pex363, https://doi.org/10.3382/ps/pex363.
  • Type: Other Status: Published Year Published: 2017 Citation: Deist, Herrmann, R. Gallardo, D. Bunn, T. Kelly, J. Dekkers, H. Zhou, S. Lamont. 2017. Novel mechanisms revealed in the trachea transcriptome of resistant and susceptible chicken lines following infection with Newcastle disease virus. Clinical and Vaccine Immunology 24(5). pii: e00027-17. doi: 10.1128/CVI.00027-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: K. Rowland. Deist, M. S. H. Zhou, R. Gallardo, D. Bunn, T. Kelly, A. Wolc. J. Dekkers, Lamont. S.J. 2017. Searching for NDV resistance in the trachea transcriptome. 66th National Breeders Roundtable, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Y. Wang, Saelao, P., Kern, C. K. Chanthavixay, S. Jin, D. Bunn, R. Gallardo, S.J. Lamont. Zhou, H. 2017. Transcriptome Analysis of Host Response to Heat Stress in Two Genetically Distinct Chicken Inbred Lines. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lamont. S.J. Deist, M. S. K. Rowland. J. Zhang. M. Kaiser, J. Dekkers, R. Gallardo, D. Bunn, T. Kelly, H. Zhou, 2017. A bird's-eye view of genetics, genomics, immune response and disease. Conference on Animal Genetics and Disease, Hinxton, UK.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lamont. S.J. Deist, M. S. K. Rowland. J. Zhang. M. Kaiser, J. Dekkers, R. Gallardo, D. Bunn, T. Kelly, H. Zhou, 2017. Searching for NDV resistance in the trachea transcriptome. 66th National Breeders Roundtable, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kern, C. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, T. Kim, P. J. Ross, I. Korf, M. Delany, H. Cheng, Zhou, H. 2017. The Open Chromatin Landscape of the Chicken Genome. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: R. Hauck, B. Crossley, H. Zhou. Gallardo R. A. 2017. Persistence of high and low pathogenic avian influenca in footbath and poultry manure. 66th Western Poultry Disease Conference, Sacramento, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: A.P. Da Silva, R. Hauck, H. Zhou. Gallardo R. A. 2017. MHC and genetic resistance to infectious bronchitis virus. 66th Western Poultry Disease Conference, Sacramento, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Zhang J., M. G. Kaiser, M. S. Herrmann, R. A. Gallardo, D. A. Bunn, H. Zhou, S. J. Lamont. 2017. Transcriptome Analysis Reveals Distinct Immune Responses to Newcastle Disease Virus in Spleen Between Resistant and Susceptible Chicken Lines. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: X. Zhou, Y. Zhang, J. N. Brutman, J.J. Michal, H. Jiang, Y. Wang, P. Ross, M. Delany, H. Zhou, H. Cheng, J. F. Davis, Z. Jiang. 2017, Non-Coding RNAs: Striking Features in Use of Alternative Polyadenylation Sites. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Herrmann, M. S. H. Zhou, R. Gallardo, D. Bunn, T. Kelly, J. Dekkers, S. Lamont. 2017. Battle of the Sexes: Examining Gender Differences on the Trachea, Lung, and Harderian Gland Transcriptomes in Young Chickens. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: N. Trakooljul, Zhou, H. P. J. Ross, I. Korf, M. Delany, H. Cheng, S. Ponsuksili, K. Wimmers. 2017. Comparative DNA Methylome of the Chicken and Pig: An Evolutionary Bridge Between Avian and Mammalian. Plant & Animal Genome XXV, San Diego, CA.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Wang, Y., P. Saelao, Mon K. K. Z., Kim T. H., Kelly T. R., and Zhou H. 2017. Using genetic approaches to improve host responses to environmental stressors. Pp. 323-338. In: Advance in Poultry Welfare Mench J. A. Elsevier, ISBN:978-0-08-100915-4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: K. Rowland. H. Zhou, R. Gallardo, T. Kelly, A. Wolc. J. Dekkers, Lamont. S.J. 2017. Genome-wide association study of complex traits in response to Newcastle disease virus in chickens. 36th Conference for the International Society of Animal Genetics, Dublin, Ireland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: N. Trakooljul, H. Zhou, P. Ross, I. Korf, M. E. Delany, H. H. Cheng, C. Ernst, C. Kern, F. Hadlich, S. Ponsuksili, and K. Wimmers. 2017. Update on DNA methylation datasets of FAANG reference samples for the chicken and pig. 36th Conference for the International Society of Animal Genetics, Dublin, Ireland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Zhou, H. P. J. Ross, Kern, C. P. Saelao, Y. Wang, M. Halstead, K. Chanthavixay, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. K. Tuggle, C. W. Ernst. 2017. Identification of regulatory elements in livestock species. 36th Conference for the International Society of Animal Genetics, Dublin, Ireland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kern, C. P. Saelao, Y. Wang, K. Chanthavixay, I. Korf, C. K. Tuggle, C. W. Ernst P. J. Ross, Zhou, H.. 2017. Genome-wide analysis of H3K4me3 and H3K27me3 in three tissues in pigs. 36th Conference for the International Society of Animal Genetics, Dublin, Ireland.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Poultry scientific community, poultry industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students, undergraduate students, and postdoctoral scholar have training in genomics and bioinformatics analysis. How have the results been disseminated to communities of interest?Oral and poster presentations were given in scientific meetings, and institutes in the US and Africa, New Zealand and China. Participated in workshop with diverse participants including scientists from institutes, funding agencies, NGO. Oral presentation was given to disadvantaged students and staff in Africa institutes. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? § Identification of genes and signal pathways that are associated with resistance to heat stress and Newcastle disease virus infection in chickens § Development of ChIP-seq assay to identify regulatory elements in livestock genomes. § Development of bioinformatic pipeline to functionally annotate livestock genomes.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zar Mon, K. K., P. Saelao, M. M. Halstead, G. Chanthavixay, H.-C. Chang, L. Garas, E. A Maga and H. Zhou. 2016. Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks. Front. Vet. Sci. - Veterinary Infectious Diseases. 2:61. doi: 10.3389/fvets.2015.00061.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tuggle, C., E. Giuffra, S. N. White, L. Clarke, H. Zhou, P. J. Ross, H. Acloque, J. M. Reecy, A. Archibald, R. R. Bellone, M. Boichard, A. Chamberlain, H. Cheng, R. P.M.A. Crooijmans, M. E. Delany, C. J. Finno, M. A. M. Groenen, B. Hayes, J. K. Lunney, J. L. Petersen, G. S. Plastow, C. J. Schmidt, J. Song, M. Watson. 2016. GO-FAANG meeting: a Gathering On Functional Annotation of ANimal Genomes Animal Genetics DOI: 10.1111/age.12466.
  • Type: Other Status: Published Year Published: 2016 Citation: Zhou, H. P. J. Ross, Kern, C. P. Saelao, Y. Wang, J. L. Chitwood, I. Korf, M. Delany, H. Cheng,. 2016. Genome-wide Functional Annotation of Regulatory Elements in chickens. Pp:48-52. The Proceedings of XXV World's Poultry Congress, Beijing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Rowland, K., Zhou, H., Gallardo, R., Bunn, D., Lamont, S. 2016. Genome Wide Association Study for NDV response in chickens. XIVth Avian Immunology Research Group (AIRG) Meeting. Munich, Germany
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhou, H., D,A, Bunn, R. Gallardo, S. J. Lamont, J. C.M. Dekkers, A. Muhairwa, P. Msoffe, B. Kayang, A. Naazie, G. Aning, C. J. Schmidt. 2016. Feed the Future Innovation Lab for Genomics to Improve Poultry Improving Food Security in Africa By Enhancing Resistance to Newcastle Disease and Heat Stress in Chickens. The Proceedings of XXV World's Poultry Congress, Beijing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: genome-wide association study for NDV response in chickens. International Conference on Quantitative Genetics. June 2016; Madison, WI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Herrmann, M. S. H. Zhou, R. Gallardo, D. Bunn, S. Lamont. 2016. Searching for NDV resistance in the trachea transcriptome. 65th National Breeders Roundtable, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Rowland, K., Zhou, H., Gallardo, R., Bunn, D., Lamont, S. 2016. Genetic parameter estimation and genome-wide association study for NDV response in chickens. 65th National Breeders Roundtable, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Herrmann, M. S. H. Zhou, R. Gallardo, D. Bunn, T. Kelly, J. Dekkers, S. Lamont. 2016. Harderian Gland transcriptome responses to Newcastle disease virus in two inbred lines. XIVth Avian Immunology Research Group (AIRG) Meeting. Munich, Germany.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhang J., M. G. Kaiser, M. S. Herrmann, R. A. Gallardo, D. A. Bunn, H. Zhou, S. J. Lamont. 2016. RNA-seq Analysis Reveals Distinct Splenic Response of Two Chicken Lines to Newcastle Disease Virus. 65th National Breeders Roundtable, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhou, H. P. J. Ross, Kern, C. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. K. Tuggle, C. W. Ernst. 2016. Update on Genome-wide Functional Annotation of Regulatory Elements in Livestock Species. 35th Conference for the International Society of Animal Genetics. Salt Lake City, UT.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Kern, C. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, T. Kim, P. J. Ross, I. Korf, M. Delany, H. Cheng, Zhou, H. 2016. Identification of tissue-specific promoters in chickens. 35th Conference for the International Society of Animal Genetics. Salt Lake City, UT.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: M. Halstead, Kern, C. P. Saelao, Y. Wang, Zhou, H. P. J. Ross. 2016. Profiling of open chromatin in chicken tissues using ATAC-seq. 35th Conference for the International Society of Animal Genetics. Salt Lake City, UT.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Y. Wang, Saelao, P., Kern, C. K. Chanthavixay, S. Jin, D. Bunn, R. Gallardo, S.J. Lamont. Zhou, H. 2016. Transcriptome Analysis of Host Response to Environmental Temperature Differences in Two Genetically Distinct Chicken Inbred Lines Challenged with Newcastle Disease Virus Infection. The Proceedings of XXV World's Poultry Congress, Beijing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Gallardo R. A., A.P. Da Silva, R. Hauck, H. Zhou. (2016). MHC and innate immune response as factors providing resistance to infectious bronchitis virus. American Veterinary Medical Association / American Association of Avian Pathologists (AVMA/AAAP) Annual Meeting, San Antoino, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Saelao, P., Y. Wang, K. Chanthavixay, D. Bunn, R. Gallardo, J. Fulton, S.J. Lamont. Zhou, H. 2016. Haplotype Analysis of Candidate Genes Resistance to Newcastle Disease Virus and Heat Stress in chickens. 105th Annual Poultry Science meeting, New Orland.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Poultry scientific community, poultry industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students, undergraduate students, and postdoctoral scholar have training in genomics and bioinformatics analysis. How have the results been disseminated to communities of interest?Oral and poster presentations were given in scientific meetings, and institutes. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? § Identification of genes that are associated with resistance to heat stress and Newcastle disease virus infection in chickens § Identification of potential genes that are associated with avian influenza virus infection. § Development of in vitro knock-out assay for gene functional study of IRF7.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont S, Hu S, Zhou H*, Li N. 2015. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics, 16 :851 (23 October 2015)
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kim, T.H, H. Zhou. 2015. Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown: PLoS One 10.1371/journal.pone.0133450
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Schmid M. et al. H. Zhou. 2015. Third Report on Chicken Genes and Chromosomes. Cytogenet Genome Res 145:78-179 (DOI:10.1159/000430927)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Y. Wang, Saelao, P., D,A, Bunn, R. Gallardo, S.J. Lamont. Zhou, H. 2016. Physiological Responses to Heat Stress in Three Chicken Lines. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Andersson Leif, Archibald L Alan, Bottema D Cynthia, Brauning Rudiger, Burgess C Shane, Burt W Dave, Casas Eduardo, Cheng H Hans, Clarke Laura, Couldrey Christine, Dalrymple P Brian, Elsik G Christine, Foissac Sylvain, Giuffra Elisabetta, Groenen A Martien, Hayes J Ben, Huang S LuSheng, Khatib Hassan, Kijas W James, Kim Heebal, Lunney K Joan, McCarthy M Fiona, McEwan C John, Moore Stephen, Nanduri Bindu, Notredame Cedric, Palti Yniv, Plastow S Graham, Reecy M James, Rohrer A Gary, Sarropoulou Elena, Schmidt J Carl, Silverstein Jeffrey, Tellam L Ross, Tixier-Boichard Michele, Tosser-Klopp Gwenola, Tuggle K Christopher, Vilkki Johanna, White N Stephen, Zhao Shuhong, Zhou Huaijun, The FAANG Consortium. 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16:57. DOI: 10.1186/s13059-015-0622-4
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: 1. Wu G, Liu L, Qi Y, Sun Y, Yang N, Xu G, Zhou H, Li X. 2015. Splenic gene expression profiling in White Leghorn layer inoculated with the Salmonella enterica serovar Enteritidis. Anim Genet. doi: 10.1111/age.12341.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Zhou, H. P. J. Ross, Kern, C. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. K. Tuggle, C. W. Ernst. 2016. Genome-wide Functional Annotation of Regulatory Elements in Livestock Species. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kern, C. P. J. Ross, P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. K. Tuggle, C. W. Ernst. Zhou, H. 2016. Identification of Tissue-Specific Long Non-Coding RNAs in Three Livestock Species. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Saelao, P., Y. Wang, A. Nazmi, D,A, Bunn, R. Gallardo, S.J. Lamont. Zhou, H. 2016. Genome-Wide Identification of Regions Associated with Heat-Tolerance and Newcastle Disease Virus Resistance in Chickens. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: S. Waters, K. Chanthavixay, C. Kern, P. Saelao, Y. Wang, J. L. Chitwood, P. J. Ross, H. Zhou. 2016. Identifying Tissue Specific Long Noncoding RNAs in the Chicken Genome. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: 1. T. H. Kim, C. Lopez, Y. Wang, H. Zhou. 2016. Inducible Overexpression and Targeted Genome Editing of Chicken IRF7 in DF-1 Cell Line. Plant & Animal Genome XXIV, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kern, C. P. J. Ross, P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. K. Tuggle, C. W. Ernst. Zhou, H. 2015. Identification of Tissue-Specific Long Non-Coding RNAs in Three Livestock Species. GO-FAANG Workshop. Washington DC. October 8-9.


Progress 10/22/13 to 09/30/14

Outputs
Target Audience: Poultry scientific community, poultry industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Graduate students, undergraduate students, and postdoctoral scholar have training in genomics and bioinformatics analysis. How have the results been disseminated to communities of interest? Oral and poster presentations were given in scientific meetings, institutes, industry. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? § Identification of genes that are associated with resistance to heat stress and Newcastle disease virus infection in chickens § Identification of potential genes that are associated with avian influenza virus infection. § Development of in vitro overexpression and knock-down assay for gene functional study of IRF7.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Gallardo RA, R. Carrasco-Medanic, H. Zhou, S. Lyu, Y Wang, PR woodcock, and FJ Hoerr. 2014. Effects of Very Virulent Infectious Bursal Disease Virus Reassortants Challenge in Commercial Chickens. Avian Disease
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Kogut, M., C L Swaggerty, H I Chiang, K J Genovese, H He, H Zhou, R Arsenault. 2014. Critical role of glycogen synthase kinase-3? in regulating the avian heterophil response to Salmonella enterica serovar Enteritidis. Frontiers in Veterinary Science accepted.
  • 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. doi: 10.1111/age.12141.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Miller M, C. Robinson, J. Abernathy, R. M. Goto, M. Hamilton, H. Zhou, and M. Delany. 2014. Mapping Genes to Chicken Microchromosome 16 and Discovery of Olfactory and Scavenger Receptor Genes near the Major Histocompatibility Complex. J. Heredity. 105(2):203-15. doi: 10.1093/jhered/est091
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang Y, Lupiani B, Reddy S, S. J. Lamont, Zhou H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Science. 93(2):485-93. doi: 10.3382/ps.2013-03557.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Li J., Q. Li, R. Li, L. Li, Y. Wang, V. Brahmakshatriya, B. Lupiani, S. Reddy, X. Hu, S. Lamont, S. Hu, H. Zhou and N. Li. 2014. Single base resolution DNA methylomes reveal genome-wide methylation differences between avian influenza virus resistant and susceptible chickens before and after virus infection. 34th Conference for the International Society of Animal Genetics. Xi'An, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Wang Y, P. Saelao, Z. Zhao, Lupiani B, Reddy SM, Lamont SJ, Zhou H. 2014. Identification of allele specific expression in chicken lungs following avian influenza virus infection using RNA-Seq. 34th Conference for the International Society of Animal Genetics. Xi'An, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Zhou, H. P. Saelao, J. Abernathy, J. M Pisenti, M. E. Delany. 2014. SNPs associated with adult onset myotonic muscular dystrophy in chickens using 600K SNP array. 34th Conference for the International Society of Animal Genetics. Xi'An, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Kim, T, H and H. Zhou. 2014. Role of IRF7 on Host Response to Poly(I:C) using an Integrative Approach of Over-expression, Knock-down and RNA-seq. XIII Avian Immunology Research Group meeting, Guelph, Canada
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Wang Y, N. Huefner, Lupiani B, Reddy SM, Lamont SJ, Wang, H. Chen, R, Zhou H. 2014. System Biology Analysis of Innate Resistance to Avian Influenza Virus Infection in Two Genetically Distinct Chicken Inbred Lines. Plant & Animal Genome XXII, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Huefner, N. K. Drake, Zhou H. 2014. Animal Systems Biology Analysis and Modeling Center: A Service Center Approach to Computational Systems Biology. Plant & Animal Genome XXII, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gallardo RA, R. Carrasco-Medanic, H. Zhou, S. Lyu, Y Wang, PR woodcock, and FJ Hoerr. 2014. Innate Immune Responses in SPF Chickens Against vvIBDV and vvIBDV Reassortants and Interactions with In-ovo IBDV Vaccines. American Association of Avian Pathologists AVMA Convention 2014, Denver, CO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Zhou, H. Re-annotation of chicken genome using next generation sequencing. 2013. 11th World Congress on Animal Production, Beijing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Kim, T, H and H. Zhou. 2013. Chicken IRF7 over-expressed and knock-downed HD11 cell line establishment applying piggyBac transposon vector system. IX Transgenic Animal Research Conference, Tahoe, CA