Progress 01/01/10 to 12/31/13
Outputs
Target Audience: Graduate students in Animal Breeding, Statistics, Bioinformatics, and Genetics. Changes/Problems: One fellow terminated his program in the middle of year 3 for personal reason. Another fellow made a switch in major professor during year 2 because of differences in research interests but this was accommodated within the training group and he is now progressing well on his PhD program. The fellows will complete their PhD with funding from other research grants. What opportunities for training and professional development has the project provided? The project has provided funding for the recruitment and training of three graduate students.Professional development opportunities were provided through attendance and participation in scientific and industry conferences, short courses, and involvement in student associations. How have the results been disseminated to communities of interest? Fellows have presented results of their research to their peers within Iowa State University through research presentations and seminars, to collaborators, and to the industry and scientific community through presentations at scientific meetings and co-authorship on scientific manuscripts. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Three quality graduate students were recruited to our program. The presence of these Fellows and associated funding has fostered additional collaborations within the training group of faculty, including collaborations involving molecular genetics, genomics, quantitative genetics, and statistics. Interactions and collaborations of the Fellows with industry have enhanced the group's exposure and interactions with industry. Recruitment of these three students has also enhanced the critical mass of graduate students in statistics, animal breeding, bioinformatics and genetics, and enabled us to successfully apply for two additional National Needs Training grants. Research conducted by the Fellows as part of their research rotations and PhD research has resulted in their author- or co-authorship on several scientific manuscripts and scientific abstracts that were presented at research conferences and additional contributions are under development. One Fellow was invited to give a late-breaking abstract at the 2012 Joint Animal and Dairy Science meeting and gave an invited talk at the Plant and Animal Genome meeting in January 2013 in San Diego, giving great exposure to her research and the training program. The research of this Fellow has also resulted in the establishment of collaborations with other faculty within and outside Iowa State University on the use of the pig as a biomedical model for humans. During the three years of the fellowship, the Fellows have made good progress on their PhD programs with their respective major advisors. One Fellow unfortunately had to drop out of the program during year 3 for personal reasons. Another Fellow made a switch in major professor during year two of the fellowship because of differences in research interests but this was accommodated within the training group and he is now progressing well on his PhD program, focusing on statistical and bioinformatic analyses of gene expression data obtained by sequencing to understand the genetic basis of host response to PRRS, the most costly viral disease in pigs. Both Fellows are now funded from other research grants held by their major advisors to enable them to complete their PhD research programs. The Fellows have participated and continue to participate in weekly or biweekly meetings that exist for their respective research areas. One Fellow completed a paid internship with the information technology and data analysis group of Dow Agrosciences in the summer of 2012, gaining valuable experience in developing software for parallel calculations of network inference for high-throughput genomic datasets. Another Fellow spent time with a major breeding company in pigs, working with their geneticists on collaborative research. For their professional development, Fellows also have attended and presented several major scientific meetings, which has given them important exposure to the scientific community in their field. Fellows are also actively involved in their respective research groups, assisting other graduate and undergraduate students with their projects and training. Fellows are also active in the Animal Breeding and Genetics Graduate Student Organization and have been involved in recruiting candidates for the new training grants that members of our training group have received.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Lunney JK, Choi I, Souza CJ, Araujo KPC, Abrams S, Steibel JP, Arceo M, Ernst CW, Reecy J, Fritz E, Dekkers JCM, Boddicker N, Waide EH, Zhao X, Rothschild M, Plastow GS, Guan L, Bao H, Stothard P, Kemp RA, Kerrigan M, Trible B, Rowland RRR. 2013. Genetics of host resistance to PRRSV infection: Progress of the PRRS Host Genetics Consortium, 2013 International PRRS Symposium, Beijing, China, May 20-22, 2013.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
J. K. Lunney, I. Choi, C. J. Souza, K. P. C. Araujo, S. M. Abrams, J. P. Steibel, M. Arceo, C. W. Ernst, J. M. Reecy, E. Fritz, J. C. M. Dekkers, N. J. Boddicker, E. H. Waide, X, Zhao, M. F. Rothschild, G. S. Plastow, R. A. Kemp, J. C. S. Harding, M. Kerrigan, B. Trible, R. R. R. Rowland. Genetic control of swine responses to PRRSV infection: Progress of the PRRS Host Genetics Consortium. Plant and Animal Genome XXI, Abstract, January 2013.
- Type:
Other
Status:
Published
Year Published:
2014
Citation:
Eisley, C., E. Fritz-Waters, I. Choi, J. Koltes, N. Boddicker, J. Reecy, J. Lunney, S. Carpenter, C. Tuggle, P. Liu, J. Dekkers. 2014. Analysis of Gene Expression in a Region Associated with Host Response to Porcine Reproductive and Respiratory Syndrome Virus Challenge. Animal Science Industry Report, AS-Leaflet-R2919, Iowa State University.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Eisley, C., E. Fritz-Waters, I. Choi, J.E. Koltes, N. Boddicker, J. Reecy, J.K. Lunney, S. Carpenter, C.K. Tuggle, P. Liu, J.C.M. Dekkers. 2013. Analysis of gene expression in a region associated with host response to porcine reproductive and respiratory syndrome virus challenge. 2014 Plant and Animal Genome meeting.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
M. Schroyen, M.S. Herrmann, E.J. Powell, E.H. Waide, J.C.M. Dekkers, C.K. Tuggle. 2014. Can Quantification of sjTRECs be Used to Distinguish Between SCID and Non-SCID Piglets? P606, Plant and Animal Genome 22.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Waide, E., C.K. Tuggle, J. Ross, M. Ellinwood, J. Dekkers 2014. Not All SCID Pigs Are Created Equally: Two Natural Mutations Cause Severe Combined Immunodeficiency (SCID) in Pigs. P598, Plant and Animal Genome 22.
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Each fellow is progressing on schedule with regard to completion of the course requirements for their respective programs, with GPAs of 3.61, 3.22, and 3.56. Each fellow has been working within the research group of their chosen major professor. One fellow has recently made a switch in major professor because of differences in research interests and this has been accommodated within the training group. Each fellow has formed a program of study committee and a program of study and defined the major thrust and objectives of their respective PhD research programs. Fellows participate in weekly or biweekly meetings that exist for their respective research areas. One Fellow completed a paid internship with the information technology and data analysis group of Dow Agrosciences in the in the summer of 2012, gaining valuable experience in developing software for parallel calculations of network inference for high-throughput genomic datasets. Another Fellow has spent several days at a major breeding company in pigs, working with their geneticists on collaborative research. For their professional development, Fellows have attended major scientific meetings, which have given them important exposure to the scientific community in their field. Fellows are also actively involved in their respective research groups, assisting other graduate and undergraduate students with their projects and training. Fellows are also active in the Animal Breeding and Genetics Graduate Student Organization and have been involved in recruiting candidates for a new training grant that members of our training group received. PARTICIPANTS: Fellows: PhD students Chris Eisley, Nathan Bowerman, Emily Waide. Major (co-)advisors: Karin Dorman, Dorian Garrick, Chris Tuggle, Jack Dekkers. Co-PIs: Susan Lamont, Peng Liu. Other faculty involved in collaborative research with Fellows: Peng Liu, Alicia Carriquiry, Rohan Fernando, Susan Carpenter, Matthew Ellinwood, Jason Ross. Professional development opportunities were provided through attendance and participation in scientific and industry conferences, short courses, and involvement in student associations. TARGET AUDIENCES: Target audience for this training grant consists of the three Fellows, along with their peers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Availability of the training grant has allowed us to attract three high quality students into our graduate programs. This has fostered additional collaborations within the training group of faculty, including collaborations involving molecular genetics, genomics, quantitative genetics, and statistics. Interactions and collaborations of the Fellows with industry has enhanced the group's exposure and interactions with industry. Recruitment of these three students has also enhanced the critical mass of graduate students in statistics, animal breeding, and genetics, and enabled us to successfully apply for another new National Needs Training grant. Research conducted by the fellows as part of their research rotations and PhD research has resulted in their author- or co-authorship on several scientific manuscripts and scientific abstracts for presentation at research conferences. One Fellow was invited to give a late breaking abstract at the 2012 Joint Animal and Dairy Science meeting and gave an invited talk at the Plant and Animal Genome meeting in January 2013 in San Diego, giving great exposure to her research and the training program. The research of this Fellow has also resulted in the establishment of collaborations with other faculty within and outside Iowa State University on the use of the pig as a biomedical model for humans.
Publications
- Lunney J.K., I. Choi, C.J. Souza, K.P.C. Araujo, S. Abrams, J.P. Steibel, M. Arceo, C. Ernst, J.M. Reecy, E. Fritz, J.C.M. Dekkers, N.J. Boddicker, E. Waide, X. Zhao, M. Rothschild, G. Plastow, R.A. Kemp, J.C.S. Harding, M. Kerrigan, B. Trible, R.R.R. Rowland. 2012. Genetic control of swine responses to PRRSV infection: Progress of the PRRS Host Genetics Consortium. Abstract for the 33rd Conference of the International Society of Animal Genetics, Cairns, Australia on July 15-20th, 2012
- Seumois G, Vijayanand P, Eisley CJ, Omran N, Kalinke L, North M, Ganesan AP, Simpson LJ, Hunkapiller N, Moltzahn F, Woodruff PG, Fahy JV, Erle DJ, Djukanovic R, Blelloch R, Ansel KM. 2012. An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol. 1(2):70-89.
- Waide, E., C. Tuggle, M. Ellinwood, J. Ross, N. Boddicker, D. Thekkoot, J. Young, E. Snella, S. Ho, R. Rowland, C. Wyatt, H. He, J. Dekkers. 2012. Discovery and Use of a Natural Mutation that Results in Severe Combined Immuno Deficiency in Pigs. Iowa State University Animal Industry Report AS Leaflet-R2755
- Waide, E.H., C.K. Tuggle, D.M. Thekkoot, N. Boddicker, R.R.R. Rowland, C.R. Wyatt,and J.C.M. Dekkers. 2012. Identification of a genomic region associated with severe combined immunodeficiency in pigs. Joint Animal and Dairy Science Annual Meeting. Late breaking abstract LB1. http://www.jtmtg.org/2012/abstracts/i.pdf
- Waide, E.H., C.K. Tuggle, N.M. Ellinwood, J.W. Ross, N. Boddicker, D.M. Thekkoot, J.M. Young, E. Snella, C.-S. Ho, R.R.R. Rowland, C.R. Wyatt, H. He, J.C.M. Dekkers. 2012. Bone marrow allotransplantation rescues severe combined immunodeficiency phenotype in pigs. Abstract #59, p.77. 2012 International PRRS Symposium/NSIF conference. http://www.prrssymposium.org/Documents/Proceedings/PrrsSymposiumProce edings2012.PDF
- Waide, E.H., N. Boddicker, Z. Jiang, J.J. Michal, R. Rowland, J.K. Lunney, and J.C.M. Dekkers. 2012. Analysis of candidate gene SNP on piglet response to experimental infection with PRRSv. Midwest Animal Science, abstract # 65. http://adsa.asas.org/midwest/2012/MW2012Abstracts.pdf
- Dekkers, J.C.M., N. Boddicker, E. Waide, J. Lunney, R.R.R. Rowland, J. Garrick, J. Reecy. 2012. The genetic basis of host response to experimental infection with the PRRS virus in pigs. ADSA/ASAS annual meeting, Phoenix, AZ.
- Dekkers, J.C.M., N. Boddicker, E. Waide, J. Lunney, R.R.R. Rowland, J. Garrick, J. Reecy. 2012. Genome-wide Association Study of Host Response to Experimental Infection with the PRRS Virus in Pigs. Plant and Animal Genome XX. W156. http://pag.confex.com/pag/xx/webprogram/Paper1677.html 115# 275943
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: The three fellows have each completed at least three research rotations and have made their decision on the research group and major professor they are joining for their PhD study. Each fellow completed a rotation in at least one group that is oriented to molecular genetics and at least one quantitatively oriented group. These rotations have already resulted in several research publications and abstracts submitted for presentation at scientific meetings. Each fellow is progressing on schedule with regard to completion of the course requirements for their respective programs, with GPAs of 3.66, 3.54, and 3.77. Following their rotations and choosing a major professor, each fellow has been in the process of forming a program of study committee, developing a program of study and defining the major thrust and objectives of their respective PhD research programs. They have or are well on their way to completing the first parts of their research programs. Nathan Bowerman joined the group of Dr. Dorian Garrick in the Department of Animal Science, with a research focus on genome-wide association analysis using high-density SNP and imputed mutations from next-generation sequencing analysis. Chris Eisley joined the group of Dr. Karin Dorman in the Department of Statistics, with a research focus on statistical analysis of genomics data. Emily Waide joined the group of Dr. Jack Dekkers in the Department of Animal Science, with Dr. Chris Tuggle as co-advisor. Emily has a research focus on immunogenetics and genomics in pigs. For their professional development, Fellows have attended major scientific meetings, which have given them important exposure to the scientific community in their field. Each fellow is also actively involved in his/her respective research group, assisting other graduate and undergraduate students with their projects and training. Fellows are also active in the Animal Breeding and Genetics Graduate Student Organization and have been involved in recruiting candidates for a new training grant that members of our training group received. PARTICIPANTS: Fellows: PhD students Chris Eisley, Nathan Bowerman, Emily Waide. Major (co-)advisors: Karin Dorman, Dorian Garrick, Chris Tuggle, Jack Dekkers. Co-PIs: Susan Lamont, Peng Liu. Professional development opportunities were provided through attendance and participation in scientific and industry conferences, short courses, and involvement in student associations. TARGET AUDIENCES: Target audience for this training grant consists of the three Fellows, along with their peers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Availability of the training grant has allowed us to attract three high quality students into our graduate programs. This has fostered additional collaborations within the training group of faculty, including collaborations involving molecular genetics, genomics, quantitative genetics, and statistics. Recruitment of these three students has also enhanced the critical mass of graduate students in statistics, animal breeding, and genetics, and enabled us to successfully apply for a new National Needs Training grant. Research conducted by the fellows as part of their research rotations and PhD research has already resulted in their authorship or co-authorship on several scientific manuscripts and submitted scientific abstracts for presentation at research conferences.
Publications
- Bowerman, N., Habier D., Wolc A., Arango J., Settar P., Fulton J.E., OSulllivan N.P., Preisinger R., Dekkers J.C.M. 2011. Linkage maps using high-density SNP data. XIX International Plant and Animal Genome Conference. http://www.intl-pag.org/19/abstracts/P05m_PAGXIX_574.html
- Boddicker, N., Waide E.H., Rowland, R.R., Lunney J.K., Garrick D.J., Reecy J.M., and Dekkers, J.C.M. 2011. Evidence for a major QTL associated with host response to PPRS virus challenge. J. Anim Sci, Dec 28 [Epub ahead of print].
- Wolc A., Habier D., Bowerman N., Arango J., Settar P., Fulton J.E., OSullivan N.P., Preisinger R., Dekkers J.C.M. 2011. Efficiency of an evenly spaced low density SNP panel for predicting genomic breeding values in laying hens. XIX International Plant and Animal Genome Conference. 15-19.01.2011 - San Diego. USA. p.566.
- Sandford EE, Orr M, Balfanz E, Bowerman N, Li X, Zhou H, Johnson TJ, Kariyawasam S, Liu P, Nolan LK, Lamont SJ. Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC Genomics. 2011 Sep 27;12:469.
- Waide, E.H., N. Boddicker, B. Rowland, J.K. Lunney, and J.C.M. Dekkers. 2011. Analysis of two genomic regions shown to be associated with response to experimental infection with PRRS virus in piglets. Abstract #20 in Proc. 2011 International PRRS Symposium, Chicago, IL. http://www.prrssymposium.org/Documents/Proceedings/PrrsSymposiumProce edings2011.PDF
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Progress 01/01/10 to 12/31/10
Outputs
Advertising and recruiting of fellows was initiated the end of 2009 and resulted in eight strong candidates to be interviewed through the Interdepartmental Genetics and the Bioinformatics and Computational Biology graduate programs. Three outstanding candidates were made offers to and all three accepted: Chris Eisley (BSc University of California, Berkley), Nathan Bowerman (BSc Hope College), and Emily Wade (BSc Auburn Univ). Nathan and Emily will pursue a PhD in the Interdepartmental Genetics program and Chris will co-major in Bioinformatics and Statistics. The first two Fellows started their PhD programs in the fall of 2010 with course work and laboratory research rotations and will make their choice on major professor before April 30, 2011. With a heavy course load, GPA's over the first semester were very good: 3.58 and 4.0. Emily started in January of 2011 and will make a decision before August 31, 2011. The progress on recruitment, filling the three positions with excellent candidates, and initiation of course work and laboratory rotations is in right in line with the original time line. PRODUCTS: A brochure and a website on the program was developed and distributed for recruiting and advertising purposes. OUTCOMES: Enrollment of three students with interests in the integration of molecular and quantitative genetics for animal breeding into a PhD program that meets these interests. The strength of our research and graduate training in this area has also resulted our participation in a training grant entitled European Graduate School on Animal Breeding and Genomics (EGS-ABG) that was award by the European Community to a consortium of Universities in Europe. DISSEMINATION ACTIVITIES: None at this point. FUTURE INITIATIVES: Once fellows have chosen their major professor, plans will be developed for PhD research projects. Our participation in the European EGS-ABG program will involve hosting students from the European program, which will complement our training activities in this area well and will allow our Fellows to interact with these international PhD students.
Impacts
Availability of these fellowships has increased the interest of potential graduate students in animal breeding and genetics and allowed us to establish important collaborative graduate training initiatives with European Universities.
Publications
- No publications reported this period
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