Progress 01/01/12 to 08/14/13
Outputs
Target Audience: The target audience for this project is the poultry genetic scientific community and those with an interest in chicken immunology and/or food safety research. Changes/Problems: There were no major problems to report. We did, however, make a change in one approach for our last goal. This goal was to use an array CGH platform to validate some of our findings in a commercial population of broiler chicken. We changed technologies from an array approach to a high-throughput sequencing approach. This approach is more powerful than using an array, as we were able to sequence to a high coverage, while the array was only able to cover a portion of the genome and is based on hybridization dynamics. What opportunities for training and professional development has the project provided? TRAINING: This project involved several laboratory techniques in which students and visiting scientist were trained. As this project also involved animal trials, training was provided to students and scientists on proper handling and surgical procedures. The PD was further trained by the mentor on array and sequencing technical methods as well as bioinformatics methods. PROFESSIONAL DEVELOPMENT: Professional development was provided for as the PD was afforded the opportunity to present data at major conferences. This also presented networking opportunities for the PD as well as further learning about the USDA grant process at the PD meeting in Washington D.C. How have the results been disseminated to communities of interest? This information has been disseminated as both oral and poster presentations at several major conferences. Information is further disseminated by publication in peer-reviewed journals. Genetic maps, custom array platforms, array data and sequencing data will be released to the public upon publication and/or submitted to public repositories. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
MAJOR ACTIVITIES COMPLETED: A candidate pool of Copy Number Variants (CNVs) in four genetic chicken lines (two inbred and two broiler lines) has been identified through the use of the Agilent chicken 244K array Comparative Genomic Hybridization (aCGH). We took those candidate CNVs and built a custom Agilent aCGH platform to saturate the identified CNVs with probes in order to reduce the spacing, referred to here as fine-mapping, of the chromosomal aberrant regions closer to the Quantitative Trait Loci (QTL) affecting genetic resistance to Campylobacter colonization. The original line A and line B broiler samples were then analyzed by the custom Agilent aCGH. We now have a list of candidate CNVs that have been fine-mapped from the original 244K platform. We have since aligned this data with existing data (including but not limited to gene expression information, gene ontologies, QTL databases) and created a genetic map in which these regions might be associated with Campylobacter colonization resistance. We have further validated a selected number of these identified CNV regions using alternative experimental approaches including quantitative and digital PCR. Lastly, we challenged a random population of broiler chicken from a commercial source with Campylobacter jejuni and determined which chickens have differences in colonization load, in order to validate our finding in a closed genetic line with those chickens used in industry. We then sequenced high-colonizing and low colonizing broilers from this population and determined significant CNVs and single nucleotide variants. We aligned this data to our previous genetic line array data to discover overlaps and validate variants associated with Campylobacter colonization. SPECIFIC OBJECTIVES MET: These experiments conclude 3 of 3 goals of the project. SIGNIFICANT RESULTS ACHIEVED: We now have genomic data including CNVs and single nucleotide variants associated with Campylobacter jejuni colonization from specific genetic lines and commercial broilers. OUTCOMES: The PD has been able to map regions along chicken chromosomes in genetic lines with differences in their response to Campylobacter jejuni colonization in the chicken. Based on this information, the PD created a custom array platform. Based on this custom array, we were able to produce a fine-map of these chromosomal regions. We then created a genetic map with candidate regions that might affect Campylobacter resistance in chickens. We further defined a bioinformatic pipeline for analysis of the chromosomal regions identified to generate high-confidence copy number variants. Lastly, we created a high-throughput sequencing library and sequenced commercial broilers with varying campylobacter colonization. The information we have found benefits the scientific community by providing coordinates along regions of chicken chromosomes that may impact genes affecting bacterial colonization and infection. The information and custom platform can be used for related experiments in an attempt to identify causal chromosomal aberrations. We will directly use the information learned to further create additional experimentation.
Publications
- Type:
Journal Articles
Status:
Other
Year Published:
2013
Citation:
J. Abernathy, X. Li, X. Jia, S.J. Lamont, R. Crooijmans and H. Zhou. Fine-mapping of chicken genomic aberrations by identifying copy number variants associated with Campylobacter jejuni colonization
- Type:
Journal Articles
Status:
Under Review
Year Published:
2013
Citation:
Copy number variation in Fayoumi and Leghorn chickens analyzed by array comparative genomic hybridization
- Type:
Other
Status:
Published
Year Published:
2013
Citation:
H. Zhou. Fine-mapping of chicken CNVs associated with Campylobacter jejuni in the chicken. 21st Annual International Plant and Animal Genome Conference (abstract). San Diego, CA. Invited Oral Presentation.
- Type:
Other
Status:
Published
Year Published:
2012
Citation:
J. Abernathy. Genetic association between Copy Number Variation (CNV) and resistance to Campylobacter jejuni colonization in the chicken. AFRI NIFA Fellowships Project Directors Meeting (abstract). Washington, D.C. Poster Presentation.
- Type:
Other
Status:
Published
Year Published:
2012
Citation:
J. Abernathy, X. Li, X. Jia, and H. Zhou. Fine-mapping of chicken genomic aberrations by identifying copy number variants associated with Campylobacter jejuni colonization. 33rd Conference of the International Society of Animal Genetics (abstract). Cairns, Australia. Invited Oral and Poster Presentation.
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: The following outcomes have been reached since the beginning of this project. ACTIVITIES: A candidate pool of Copy Number Variants (CNVs) in four genetic lines (two inbred and two broiler lines) has been identified through the use of the Agilent chicken 244K array Comparative Genomic Hybridization (aCGH). We took those candidate CNVs and built a custom Agilent aCGH platform to saturate the identified CNVs with probes in order to reduce the spacing, referred to here as fine-mapping, of the chromosomal aberrant regions closer to the Quantitative Trait Loci (QTL) affecting genetic resistance to Campylobacter colonization. The original line A and line B broiler samples were then analyzed by the custom Agilent aCGH. We now have a list of candidate CNVs that have been fine-mapped from the original 244K platform. We have since aligned this data with existing data (including but not limited to gene expression information, gene ontologies, QTL databases) and created a genetic map in which these regions might be associated with Campylobacter colonization resistance. We have further validated a selected number of these identified CNV regions using alternative experimental approaches including quantitative and digital PCR. These experiments conclude 2 of 3 goals of the project. EVENTS: We have presented this data at the 21st Annual International Plant and Animal Genome Conference in San Diego, California and the 33rd International Society of Animal Genetics Conference in Cairns, Australia. PRODUCTS: We created a custom Agilent 4x44K chicken aCGH array for fine-mapping chromosomal aberrations. We have also created a genetic map with candidate regions that might affect Campylobacter jejuni colonization resistance in the chicken. This information has been disseminated as both oral and poster presentations at several major conferences. Information will further be disseminated by publication in peer-reviewed journals; the preparation of manuscripts for publication is underway. Genetic maps and custom array platforms will be released to the public upon publication. PARTICIPANTS: INDIVIDUALS: The PD, Jason Abernathy, was the main participant of this project as this was his postdoctoral fellowship. Jason performed the necessary laboratory experiments and data analyses to meet the goals specified in the grant proposal. Throughout the duration of the project, the mentor, Huaijun Zhou, provided guidance where needed and allowed the PD the use of all general laboratory supplies and equipment. PARTNER ORGANIZATIONS: The USDA-ARS in College Station, Texas allowed the use of facilities and equipment as specified in the proposal. COLLABORATORS: Our collaborator at the USDA-ARS in College Station, Michael Kogut, provided use of the facilities, equipment, and chicken samples to our laboratory. He also provided skilled scientific expertise. TRAINING AND PROFESSIONAL DEVELOPMENT: The PD has been afforded many opportunities for training and professional development after being awarded this postdoctoral fellowship. The PD has presented this work at major scientific conferences and is preparing for publications. As the PD, and with the support of the mentor, Jason has been allowed to lead a team of undergraduate students, graduate students, and a postdoc in the execution of major parts of the project, such as field work with chickens and large-scale genomic data analyses. Jason attended his first PD meeting in Washington D.C., and as such was able to learn more about the USDA grant process and provide feedback on the fellowships program. Additionally through the use of travel funds from this grant, the PD was able to network with fellow scientists, sharpen presentation skills, and establish potential collaborations. The PD also had informal bioinformatic training from the mentor and other institute members in order to meet the established goals. TARGET AUDIENCES: TARGET AUDIENCE: The target audience is the poultry / genetic scientific community as well as the general public with an interest. EFFORTS: Partial information has been provided at scientific conferences; complete information will be provided at completion of all goals and publication of the work. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
CHANGE IN KNOWLEDGE AND ACTIONS: To date, the PD has been able to map regions along the chicken chromosome in genetic lines with differences in their response to Campylobacter jejuni colonization in the chicken. Based on this information, the PD was able to create a custom array platform. Based on this custom array, we were able to produce a fine-map of these chromosomal regions. We then created a genetic map with candidate regions that might affect Campylobacter resistance in chickens. We further defined a bioinformatic pipeline for analysis of the chromosomal regions identified to generate high-confidence copy number variants. The information we have found so far will benefit the scientific community by providing coordinates along regions of chicken chromosomes that may impact genes affecting bacterial colonization and infection. The information and custom platform can be used for related experiments in an attempt to identify causal chromosomal aberrations. We will directly use the information learned to further the goals of this project and create additional experimentation.
Publications
- J. Abernathy. (2012) Genetic association between Copy Number Variation (CNV) and resistance to Campylobacter jejuni colonization in the chicken. AFRI NIFA Fellowships Project Directors Meeting (abstract). Washington, D.C. Poster Presentation.
- J. Abernathy, X. Li, X. Jia, H. Zhou. (2012) Fine-mapping of chicken genomic aberrations by identifying copy number variants associated with Campylobacter jejuni colonization. 33rd Conference of the International Society of Animal Genetics (abstract). Cairns, Australia. Invited Oral and Poster Presentation.
- H. Zhou. (2013) Fine-mapping of chicken CNVs associated with Campylobacter jejuni in the chicken. 21st Annual International Plant and Animal Genome Conference (abstract). San Diego, CA. Invited Oral Presentation.
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