UNIVERSITY OF NEBRASKA - Daniel Pomp
Annual (2002-2003) Report to NRSP-8
PROJECT NRSP-8: National Animal Genome Research Program (NAGRP)
COOPERATING AGENCIES and PRINCIPAL LEADERS
- Nebraska Agriculture Experiment Station and Department of Animal Science, UN-L.
- P.I. Daniel Pomp
- Collaborators: Max Rothschild, Chris Tuggle - Iowa; Randy Prather, Missouri; Rodger Johnson, Dale Van Vleck – Nebraska; Joe Ford – USDA-MARC; Alex Caetano – Embrapa (Brazil)
PROGRESS OF THE WORK and PRINCIPAL ACCOMPLISHMENTS
Objective 1: Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes.
Objective 2: Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes.
Maps (SSCP, RH) of ESTs from tissues relevant to pig reproduction are being produced. Homologies will be established between pig and human/mouse. Over 700 genes have been mapped to date. Objective 3: Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.
- Normalized libraries have been developed for tissues relevant to reproduction in pigs (Pig Reproduction EST Consortium; http://maize.math.iastate.edu/jmsgp/homepage.html). Libraries, sequences and mapping data will be shared.
- We created an ovarian follicle normalized library using tissue from the UN-L reproduction selection lines. Sequences for 7,000 clones were obtained, and ~4,000 clones representing unique clusters were spotted onto 120 glass slide arrays. All arrays were hybridized with follicle and/or ovary RNA from the high Index and Control selection lines; data analysis is nearing completion. Organized and annotated clones are available for collaborative mapping and expression studies.
USEFULNESS OF FINDINGS
Objective 1: Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes.
Objective 2: Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes.
- Denser maps and enhanced alignment with human/mouse maps will facilitate both the identification of chromosomal regions harboring QTL as well as the eventual cloning of the QTL themselves.
- The Pig Reproduction EST Consortium project has greatly increased the density of Type I markers on the pig physical map, focusing on genes relevant to economically important traits. This project also significantly enhanced the comparative maps between pig and human/mouse.
- The UN-L follicle library is being used to uncover the nature of response to selection for litter size, and better understand the complex genetic control of reproduction and the relationship between predisposition and physiology. Several relevant discoveries have been made that indicate how polygenic selection has changed ovarian physiology to impact ovulation rate.
Objective 3: Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.
- The Pig Reproduction EST Consortium project has yielded multiple resources that can be used by others for gene mapping and expression studies. The large numbers of mapped (and unmapped) ESTs developed in this project will greatly facilitate resources for microarray evaluation of gene expression in pigs and other species.
- The UNL follicle library, annotated clone database and ordered arrays are freely available for collaborative research. Clones have been shared with four other research groups.
WORK PLANNED FOR NEXT YEAR
Objective 1: Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes.
Objective 2: Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes.
Continued SSCP/RH mapping of reproduction ESTs in pigs. Focus will shift to mapping of specific genes exhibiting differential expression. The goal is to create a map of the "differentially expressed porcine ovarian transcriptome". Continued comparative mapping of ESTs. Objective 3: Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.
- Continued sharing of resources from The Pig Reproduction EST Consortium project.
- Continued sharing of resources (cDNA library, sequences, microarray) from the UNL pig ovarian follicle project.
RELEVANT PUBLICATIONS (2002)
Refereed Journal Articles Submitted:
Tuggle C, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares MB, Tack D, Robinson N, O'Leary B, Scheetz T, Casavant T, Pomp D, Edeal JB, Zhang Y, Rothschild MF, Garwood K, Beavis W. EST-Based Gene Discovery in Pig: Virtual Expression Patterns and Comparative Mapping to Human. Mammalian Genome (Submitted).
Wesolowski S, Allan MF, Nielsen MK, Pomp D. Evaluation of hypothalamic gene expression in mice selected for heat loss. Physiological Genomics (Submitted).
Refereed Journal Articles Published (or in press):
Bertani G, Johnson RK, Pomp D (2003) Mapping of porcine ESTs putatively differentially expressed in anterior pituitary. Animal Genetics (In Press)..
Caetano A, RK Johnson, D Pomp (2003) Generation and Sequence Characterization of a Normalized cDNA Library from Swine Ovarian Follicles. Mammalian Genome (In Press).
Childs KD, DW Goad, MF Allan, D Pomp, C Krehbiel, RD Geisert, JB Morgan, JR Malayer (2002) Expression of the NAT1 translational repressor in intramuscular adipocytes of Angus X Hereford steers. Physiological Genomics 10:49-56.
Leamy L, Pomp D, Eisen EJ, Cheverud J (2002) Pleiotropy of quantitative trait loci for organ weights and limb bone lengths in mice. Physiol. Genomics 10:21-29.
Risatti GR, D Pomp, RO Donis (2003) Patterns of cellular gene expression in cells infected with cytopathic or non- cytopathic bovine diarrhea virus. Animal Biotechnology (In Press).
Book Chapters
Pomp D, Caetano AR, Bertani GR, Gladney CD, Johnson RK (2001) Applying Functional Genomics Research to the
Study of Pig Reproduction. Reproduction Suppl 58:277-92
Rocha J, Pomp D, Van Vleck D (2002) QTL Analysis in Livestock. In: Quantitative Trait Loci: Methods and
Protocols. Methods in Molecular Biology Vol 195. Eds; NJ Camp, A Cox. Humana Press, New Jersey.
Chapter 12 (pp 311-346).
Papers in Proceedings
Bertani GR, C.D. Gladney, R.K. Johnson and D. Pomp. Gene expression analysis in anterior pituitary and EST mapping to investigate genetics of swine fertility. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France.
Caetano AR, R.K. Johnson and D. Pomp. RNA expression profiling of ovarian follicle development in swine lines selected for increased ovulation rate. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France.
Pomp D. DNA-Assisted Selection: A realistic Perspective (2002) Range Cow Symposium, Laramie WY.
Pomp D, N Jerez, M.F. Allan and E.J. Eisen. Integrated genomic, proteomic and metabolomic dissection of polygenic selection response for murine growth and fatness. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France.
Rocha JL, F. Siewerdt, L.D. Van Vleck, E.J. Eisen and D. Pomp (2002) Lessons regarding the genetic nature of continuous variation. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France.
Abstracts
Allan MF, G.R.Bertani, E.J. Eisen and D. Pomp (2003) Integration of genomic, proteomic and metabolomic analyses towards polygene discovery for energy balance in mice. Plant and Animal Genome, San Diego.
Caetano AR, RK Johnson and D Pomp (2003) Using cDNA microarrays to study ovarian follicle development in pigs selected for increased ovulation rate. Plant and Animal Genome, San Diego
Elo K, Merlyn Nielsen, Dale Van Vleck & Daniel Pomp (2002) Fine mapping of genes regulating heat loss in mice. ISAG, Germany.
Jerez-Timaure N, Daniel Pomp, Eugene J. Eisen (2003) Fine-mapping of a QTL region with large effect on body weight and fatness on mouse chromosome 2. Plant and Animal Genome, San Diego.Jerez-Timaure N, Pomp D, Eisen E. (2002) Confirmation of quantitative trait loci (QTL) affecting body weight
and fatness in a congenic line of mice. ASAS/ADSA Midwest.
Milan, D, Schiex T, Yerle M, Rink A, Beattie C, Alexander L, Hawken R, Schook L, Yasue H, Pomp D, Fredholm M, Rohrer G (2002) Integration of Genetic and Radiation Hybrid maps of the pig : The second generation IMpRH maps. ISAG, Germany.
Pomp D (2003) Functional genomics as a tool for integrated polygene discovery for complex traits. ASAS/ADSA Midwest.
Pomp D (2002) Integrated Polygene Discovery with Long-Term Selection Lines. Complex Trait Consortium Meeting, Memphis.
Pomp D (2002) Polygene Discovery for Body Weight Regulation in Animal Models and Relationship to Human Gene Discovery. Australian Genetics Society, Sydney.
Tuggle, C. K. J. A. Green, C. Fitzsimmons, R. Woods, R. S. Prather, S. Malchenko, M. B. Soares, C. A. Roberts, K. Pedretti, T. Casavant, D. Pomp, A.R. Caetano, J.B. Edeal, S. Olberding, Y. D. Zhang, M.F. Rothschild, K. Garwood, W. Beavis. (2002) Pig Reproduction ESTS: Development of sequence data and map locations for female reproductive genes. ASAS/ADSA Midwest.
Tuggle, C. K. J. A. Green, C. Fitzsimmons, R. Woods, R. S. Prather, S. Malchenko, M. B. Soares, C. A. Roberts, K. Pedretti, T. Casavant, D. Pomp, A.R. Caetano, J.B. Edeal, S. Olberding, Y. D. Zhang, M. F. Rothschild, K. Garwood, W. Beavis. (2002) A Pig Reproduction EST Project: Development of EST sequence data and map locations for genes expressed in major female reproductive tissues. Plant Animal Genome, San Diego.
Wesolowski S., Allan MF, Nielsen MK, Pomp D. (2002) Control of hypothalamic gene expression in heat loss mice. Plant Animal Genome, San Diego.
Wesolowski SR, K.T. Elo, M.K. Nielsen and D. Pomp (2002) Identification of loci controlling hypothalamic gene expression and phenotypic traits related to energy balance. IMGC, San Antonio.