Progress 12/06/13 to 09/30/18
Outputs
Target Audience:Basic research scientists, agricultural scientists, poultry molecular biologists and geneticists, graduate students. The public and government agencies and those interested in knowledge and utilization of genomics to improve animal and human health. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two female graduate students were trained for their PhD programs of study in Genetics. One graduated and is a post doc at Stanford University and the other is set to graduate spring 2019. How have the results been disseminated to communities of interest?Result were disseminated through conference presentations by myself and my students at national and international meetings as well as through peer-reviewed research publications in journals. What do you plan to do during the next reporting period to accomplish the goals?This is the final report for the NRSP-8 2013-18 5-yr project.
Impacts
What was accomplished under these goals?
Discovery and analysis of the genomic, genetic, molecular and cellular basis underlying inherited mutations in chicken: talpid-2 and wingless-2. Improved poultry genome annotation and understanding of sequence elements and their roles and in common-vertebrate aspects through the FAANG project (functional annotation of animal genomes). Improved understanding of the biology of Marek's disease herpesvirus integration into the chicken genome through the use of genomics tools.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Kern, C., Y. Wang, J. Chitwood, Korf, I., Delany, M., H. Chen, J.F. Medrano, A.L. Van Eenennaam, C. Ernst, P. Ross, and H. Zhou. Genome-wide Identification of Tissue-Specific Long Non-Coding RNA in Three Farm Animal Species. BMC Genomics 19:684
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Webb, A., Youngworth, I., M. Kaya, C.L. Gitter, E.A. O'Hare, B.P. May, H.H. Cheng, and M.E. Delany. 2018. The wingless-2 mutation maps to a 227 kb region on chicken chromosome 12. Poultry Science 97:1872-1880.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Target audience includes poultry and animal genomics scientists and students-in-training, breeders and molecular geneticists employed by commercial poultry companies, industries that support creation and utilization of genomics tools, at the state, national and international scales. The public is also a target audience to improve understanding of 'genomics' and how such analyses contribute to animal agriculture and to human health. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One female Ph.D. student was mentored and trained. Collaboration is ongoing with a former graduate student as we work to finalize her manuscripts from her dissertation. How have the results been disseminated to communities of interest?We have several peer-reviewed research publications in various stages of preparation, submission or revision. My student and I have presented research presentations at conferences (Poultry Science Association 2017, Plant and Animal Genome Meeting 2017, Society for Developmental Biology 2017) and I have held one-on-one conversations with research staff in poultry breeding companies about our work. What do you plan to do during the next reporting period to accomplish the goals?We will emphasize the finalization of several manuscripts in the upcoming year which is the final year of this project. We are continuing to refine the candidate region by fine mapping (SNP variant analysis with breeding) for cleft-primary palate. We will continue to contribute to poultry FAANG efforts to better annotate the chicken genome.
Impacts
What was accomplished under these goals?
The poultry FAANG group has worked together toward functional annotation of the chicken genome and has continued to provide high quality content to the research community (one manuscript submitted). My student was a recipient of a Student Presentation Excellence Award - Genomics, Molecular and Cellular Biology Section for her presentation at the 2017 Poultry Science Association Annual Meeting. We continue to advance the chicken model as a useful and highly relevant system for analysis of congenital malformations found in humans to understand the pathways involved (one manuscript revised and resubmitted).
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Youngworth, I., and M. E. Delany. 2017. Capture array genomic analysis of the causative region for wingless-2,a developmental syndrome in the chicken. Poultry Science Association 106th Annual Meeting, July. Orlando FL (oral presentation abstract #169).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Youngworth, I., and M.E. Delany. 2017. Sequence analysis of the causative region for wingless-2, a developmental syndrome in the chicken model. Society for Developmental Biology 11th Structural Birth Defects Meeting. FASEB Beaumont Campus, Bethesda, MD.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
McPherson, M.C., Smith, J.M. Cheng, H.H., and M.E. Delany, M.E. Host chromosome integration profiles of Marek's disease (MD) virus and vaccine strains differ between MD resistant and susceptible lines. International Plant and Animal Genomes XXV, January 14-18, 2017 San Diego CA (Poultry Workshop, oral).
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Target audience includes poultry and animal genomics scientists and students in training, breeders and molecular biologists at commercial poultry companies, industries that support genomics tools, at the state, national and international scales. The public is also a target audience. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two female Ph.D. students were mentored and trained; one student completed her Ph.D. How have the results been disseminated to communities of interest?Through publications, research presentations at conferences, and news released by UC Davis. What do you plan to do during the next reporting period to accomplish the goals?We are developing a new methodology for further analysis of candidate regions to find the causative sequences for the wingless-2 developmental mutation (a capture array). We are collecting data and analyzing resistant and susceptible lines (to Marek's disease) for host, virus and vaccine genome interactions. We will continue to refine the candidate region by fine mapping (SNP variant analysis with breeding) for cleft-primary palate. We will contribute to FAANG efforts to better annotate the chicken genome.
Impacts
What was accomplished under these goals?
The development of the FAANG group to advance functional annotation of livestock animal genomes. Advancing the chicken model as useful and highly relevant for analysis of congenital malformations found in humans. Providing evidence the chicken herpesvirus disease vaccines are capable of integrating into the host chicken genome. Refining the germplasm and breeding populations of chickens used to study developmental mutations.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
McPherson, M.C., H.H Cheng, and M.E. Delany. 2016. Marek's disease herpesvirus vaccines integrate into chicken host chromosomes yet lack a virus-host phenotype associated with oncogenic transformation. Vaccine 34:5554-5561
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Tuggle, C.K. E. Giuffra, S. N. White, L Clarke, H. Zhou, P. J. Ross, H. Acloque, J. M. Reecy, A. Archibald, 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 47(5):528-533
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
McPherson, M.C., and M.E. Delany. 2016. Virus and host genomic, molecular and cellular interactions during Marek's disease pathogenesis and oncogenesis. Poultry Science 95:412-429.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Schock, E.N., C.-F. Chang, I. Youngworth, M. Davey, M.E. Delany, and S.A. Brugmann. 2016. Utilizing the chicken as an animal model for human craniofacial ciliopathies. Developmental Biology 45(2):326-337
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Scientists at academic and government institutions, nationally and internationally working in the area of poultry breeding, genetics, genomics. Industry scientists and breeders working in the area of poultry breeding, genetics and genomics. Undergraduate and graduate students in a variety of academic programs. Training two female PhD students in Genetics. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One student passed her oral qualifying exam presenting her dissertation research project on poultry developmental genetics. The topic of developmental mutations involving the limb and craniofacial defects is the focus of her dissertation work. How have the results been disseminated to communities of interest?Through annual meetings of the International Plant and Animal Genome meeting. What do you plan to do during the next reporting period to accomplish the goals?Genome sequencing and RNAseq experiments will be conducted for wingless-2 and cleft primary palate mutations to further define the candidate region and determine candidate genes for further study.
Impacts
What was accomplished under these goals?
Research was finalized and two publications resulted describing the the underlying genetic mutation for the talpid-2 limb and craniofacial malformations in chicken and describing the importance of the chicken model for research in developmental biology and human congenital malformations. This is a major accomplishment and supports the original goal for the sequencing of the chicken genome for its importance as a vertebrate model.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Schock, E.N., C.-F. Chang, I. Youngworth, M. Davey, M.E. Delany, and S.A. Brugmann. In Press. Utilizing the chicken as an animal model for human craniofacial ciliopathies. Developmental Biology http://dx.doi.org/10.1016/j.ydbio.2015.10.024
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Schock, E.N., C.-F. Chang, J. N. Struve, J. Chang, M. E. Delany and S.A. Brugmann. 2015. Using the avian mutant talpid2 as a disease model for understanding the oral-facial phenotypes of oral-facial-digital syndrome. Disease Models & Mechanisms 8:855-866. http://dmm.biologists.org/content/8/8/855.full.pdf+html
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Progress 12/06/13 to 09/30/14
Outputs
Target Audience: Poultry scientists in the U.S. and internationally. U.S. government researchers and administrators (USDA, NIH). Poultry industry breeding companies. Graduate students studying poultry genomics. Animal genomics researchers and students. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The research included training and mentoring of one female PhD student who is now a post doctoral scholar at the University of Maryland School of Medicine. A new female PhD student was incorporated into the lab to continue the work on our poultry developmental mutations project and began her initial studies. How have the results been disseminated to communities of interest? The laboratory provides research updates annually for the NRSP-8 project at the Poultry Workshop of the International Plant and Animal Genome meeting whose audience includes close to 100 scientists and poultry industry representatives, as well as graduate students and post doctoral scholars and other animal genomicists. Also the developmental mutation work was highlighted by the Faculty of 1000 (http://f1000.com/prime/718507249, F1000Prime Recommendations, Dissents and Comments for [Chang CF et al., Development 2014, 141(15):3003-12]. In F1000Prime, 12 Aug 2014; F1000Prime.com/718507249 ) What do you plan to do during the next reporting period to accomplish the goals? Work will continue as planned, projected on the objectives of the project.
Impacts
What was accomplished under these goals?
Key accomplishment includes the discovery of the genetic, molecular and cellular basis for the talpid-2 mutation; a feat involving an interdisciplinary team of geneticists, genomicists/bioinformaticists, developmental and poultry biologists working together at the molecular, cellular and organismal biology levels. This is an important work that improves our understanding of craniofacial development and defects important to human and animal biology.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Chang, C-F.; Schock, E.N.; O'Hare (formerly Robb), E.A., Dodgson, J.B., Cheng, H.H., Muir, W.M., Edelman, R.E., Delany, M.E., and S.A. Brugmann. 2014. The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant, talpid2. Development 141:3003-12.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Miller, M.M., C.M. Robinson, J. Abernathy, R.M. Goto, M. Hamilton, H. Zhou, and M.E. Delany. 2014. Mapping of genes for olfactory receptors, cysteine-rich-domain containing scavenger receptors and other proteins to GGA 16, the chicken MHC microchromosome. J Heredity. 105:203-215.
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