Source: UNIVERSITY OF ILLINOIS submitted to
HIGH-RESOLUTION PHYSICAL MAPPING OF THE PORCINE GENOME BY BAC FINGERPRINTING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0187223
Grant No.
2001-35205-09965
Project No.
ILLU-538-562
Proposal No.
2004-05737
Multistate No.
(N/A)
Program Code
43.1
Project Start Date
Dec 1, 2000
Project End Date
Nov 30, 2005
Grant Year
2005
Project Director
Beever, J. E.
Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801
Performing Department
ANIMAL SCIENCES
Non Technical Summary
The identification of genes that influence economically important traits has been the driving force for the development of genome maps of agricultural species. To this end, the genome map of the pig contains sufficient genetic markers to conduct genome scans for these genes. As a result of these studies, there is an increasing need to fine-map regions of the genome for the eventual identification of the underlying gene or polymorphism causing the effect. This project fulfills a need for development of physical mapping resources that will allow for the efficient identification of these economically important genes.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3043599104050%
3043599108050%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3599 - Swine, general/other;

Field Of Science
1080 - Genetics; 1040 - Molecular biology;
Goals / Objectives
Construction of a high-resolution physical map of the porcine genome will be required for eventual identification of many economically important genes or ETL. To contribute to the success of positional cloning of these genes in the pig, the following objectives are proposed: (1) construct a genome-wide framework for a high-resolution physical map of the swine genome; (2) create a panel of DNA pools that can be used for PCR-based screening of 12X coverage of the swine genome; and (3) anchor the BAC-fingerprinted contigs to the current genetic and physical marker maps. Thus, an integrated high-resolution physical map will be produced for the swine genome. The integration of previously mapped genetic markers to the framework of BACs produced will provide immediate access and usability of the map to the swine genome community.
Project Methods
High-throughput large insert fingerprinting is becoming a commonly used method for the rapid development of genome-wide high-resolution physical maps of both human and model organisms. The available physical mapping resources will be used to implement this strategy in the pig. Large-insert porcine libraries will be obtained and a "whole-clone" fingerprinting strategy implemented to construct an initial clone-based physical map of the swine genome. An 8-dimensional pooling, single-tier screening strategy that was recently developed at Los Alamos National Laboratory (LANL) will be used to make 376 PCR-screenable pools that can be used to identify BAC clones based on STS content. Library segments used for fingerprint analysis will be given first priority for pooling. Aliquots of DNA pools will be available to the swine genome mapping community. Approximately 750 markers that have been previously mapped by genetic or physical methods will be selected for PCR-based screening of the library pools. This will generate map integration points across the genome at a density of approximately 1 every 4 Mb, with each point potentially represented by 10-12 individual BAC clones. Concurrently, the genetic and physical maps will be integrated with some of the small fingerprinted contigs developed. Approximately twice the number of BACs will be scored for STS content than where used in the fingerprint analysis providing a database of clone addresses for future studies targeted at specific regions of the genome.

Progress 12/01/00 to 11/30/05

Outputs
All data generated by this project has been submitted to a publicly accessible database that contains the results of joint analyses from collaboration of four contributing international laboratories (http://www.sanger.ac.uk/Projects/S_scrofa/mapping.shtml). The completed physical map of the porcine genome is represented by 176 large-insert clone contigs that represent >98% of the genome. Currently, this map is the most contiguous (i.e., least number of contigs) of any unsequenced mammalian genome. Additionally, the contiguity of the map has allowed for the selection of ~21,000 large-insert clones that represent the porcine genome. These clones are the minimum set of clones that could be sequenced to generate a complete DNA sequence of the pig genome.

Impacts
The physical map of the porcine genome, that was completed in part by this project, provides a resource for the entire swine genomics community to interogate specific genomic regions of interest. These include regions that contain individual genes influencing traits of economic importance to animal agriculture, as well as biomedical research and human health. Furthermore, this physical map is the underlying basis for the initiation of a complete porcine genome sequencing project.

Publications

  • Meyers, S.N., Rogatcheva, M.B., Yerle, M., Milan, D., Hawken, R.J., Schook, L.B. and Beever, J.E. 2005. A high-resolution, physically-anchored, human-pig comparative map of the porcine autosomes. Plant and Animal Genome XIII, San Diego, CA.
  • Humphray, S.J., Clark, R.C., Beever, J.E., Scott, C.E., Plumb, B., Chardon, P., Mila, D., Archibald, A., Schook, L.B. and Rogers, J. 2005. An integrated physical map of the porcine genome. Plant and Animal Genome XIII, San Diego, CA.
  • Larkin, D.M., Murphy, W., Everts-van der Wind, A., Auvil, L., Beever, J.E., Bourque, G., Chowdhary, B., Galibert, F., Gatzke, L., Hitte, C., Menotti-Raymond, M., Meyers, S.N., Ostrander, E.A., Pape, G., Parker, H.G., Pevzner, P.A., Raudsepp, T., Rogatcheva, M.B., Schook, L.B., Skow, L., Tessler, G., Welge, M., Womack, J.E., O'Brien, S.J. and Lewin, H.A. 2005. Multi-species comparative mapping of mammalian genomes: Identification of lineage-specific and reuse breakpoints in chromosomes. Plant and Animal Genome XIII, San Diego, CA.
  • Meyers, S.N., Rogatcheva, M.B., Yerle, M., Milan, D., Hawken, R.J., Schook, L.B. and Beever, J.E.. 2005. Piggy-BACing the human genome: II. A high-resolution, physically-anchored, comparative map of the porcine autosomes. Genomics, 86:739-752.
  • Meyers, S.N., Rogatcheva, M.B., Yerle, M., Milan, D., Schook, L.B. and Beever, J.E. 2005. A high-resolution, physically-anchored, human-pig comparative map of the porcine autosomes. Swine in Biomedical Research Conference 2005, Chicago , IL.
  • Murphy, W.J., Larkin, D.M., Everts-van der Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S.N., Ostrander, E.A., Pape, G., Parker, H.G., Raudsepp, T., Rogatcheva, M.B., Schook, L.B., Skow, L.C., Welge, M., Womack, J.E., O'Brien, S.J., Pevzner, P.A. and Lewin, H.A. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617.
  • Rogatcheva, M.B., Meyers, S.N., Larkin, D.M., Marron, B.M., He, W.-S., Schook, L.B. and Beever, J.E. 2005. Piggy-BACing the Human Genome: I. Constructing a porcine physical map through comparative genomics. Anim. Genet. (Submitted).
  • Rogers, J. and Members of the Swine Genome Sequencing Consortium. 2005. The swine genome sequencing project. Swine in Biomedical Research Conference 2005, Chicago , IL.
  • Schook, L.B., Beever, J.E., Rogers, J., Humphray, S., Archibald, A., Chardon, P., Milan, D., Rohrer, G. and Eversole, K. 2005. Swine Genome Sequencing Consortium (SGSC): A strategic roadmap for sequencing the pig genome. Comp. Funct. Genom. 6:251-255.


Progress 12/01/00 to 11/30/03

Outputs
Approximately 5.3 X genome coverage of BAC clones (n = 101,376 clones) from the RPCI-44 (segment 2, plates 241-528) and CHORI-242 (segment 1, plates 1-20) library have been fingerpinted representing completion of Objective 1 of the modified objectives. Additionally, 591 STS have been used to anchor clones to the physical map (i.e., radiation hybrid map) falling short of the 750 proposed STS to be mapped. However, this effort continues and is being coordinated with complementary projects at The Wellcome Trust Sanger Institute (Cambridge, United Kingdom) and INRA (Dr. P. Chardon, Jouey-en-Josas, France) that have fingerprinted 150,000 and 100,000 additional clones, respectively. Integration efforts are planned for early 2004 via the Swine Genome Sequencing Consortium formed in September 2003. Additional funding through USDA-ARS has allowed end-sequencing of approximately 60,000 of the fingerprinted BACs. These sequences are being used to anchor assembled contigs to the human-pig compartive map.

Impacts
This work establishes the first whole genome-based physical map of the pig genome. Following integration with of the two other major international efforts, a minimal set of clones can be selected to initiate sequencing efforts for the genome.

Publications

  • Marron, B.M., Ehrhardt, M.J., Rogatcheva, M., Meyers, S.N., DeYoung, B., Keil, J.A., Tao, N., Wang, Q., Byatt, J.C., de Jong, P.J., Schook, L.B., and Beever, J.E. 2004. A high resolution physical map of Chromosome 11. International Plant and Animal Genome XII Conference. January 11-14. San Diego, CA.


Progress 01/01/02 to 12/31/02

Outputs
The modified objectives of the project were 2-fold including 1) whole-clone fingerprinting of approximately 100,000 BAC clones (5 genome equivalents) and assembly of clones into contigs; and 2) STS content mapping of 750 loci for integration of the BAC physical map with existing genetic and physical maps. Currently, 70,000 BAC clones have been fingerprinted representing 70% of the proposed 5X genome coverage. Additionally, 150 loci have been mapped to their respective BAC clones by hybridization (20%% of the proposed 750 loci). Each locus/BAC assignment is confirmed by rescreening of positive hybridizing clones. All STS correspond to loci mapped by radiation hybrid analysis.

Impacts
The physical map constructed upon completetion of this project will provide the swine genomics community with a valuable resource for fine-mapping of genes influencing economically important traits. Furthermore, this detailed physical map will serve as the basis for sequencing the swine genome.

Publications

  • Marron, B.M., Erhhardt, M.J. and Beever, J.E. 2002. Construction of a physical map of the procine genome by BAC fingerprinting. 28th Congress of the International Society of Animal Genetics, August 11-15, Gottingen, Germany.
  • Marron, B.M., Tao, N., Erhardt, M.J., Wang, Q., Schook, L.B., Byatt, J.C. and Beever, J.E. 2003. Construction of a physical map of the porcine genome. International Plant and Animal Genome XI Conference. January 11-15. San Diego, CA.


Progress 01/01/01 to 12/31/01

Outputs
The identification specific genes that influence economically important genes will require the construction of detailed physical maps for positional cloning. An effort to construct a high-resolution physical map using large-insert BAC clones was initiated. Currently, 7,000 clones of the RPCI-44 BAC library have been fingerprinted and 2,880 additional clones are being completed each week. An initial assembly of the fingerprint information will be conducted at 1X genome coverage (19,000 clones), estimated March 15, 2002. Additional assemblies will be conducted in 1X genome equivalent segments or an estimated every 7 weeks. Approximately 5X genome coverage should be completed by late 2002. This effort is also being coordinated with complementary projects being initiated by The Wellcome Trust Sanger Institute (Cambridge, United Kingdom) and INRA (Dr. P. Chardon, Jouey-en-Josas, France). The combined effort is aimed at the construction of a 15X coverage physical map of the porcine genome by January 2003, in preparation for a draft genome sequencing effort within the next 5 years.

Impacts
The physical map constructed upon completetion of this project will provide the swine genomics community with a valuable resource for fine-mapping of genes influencing economically important traits. Furthermore, this detailed physical map will serve as the basis for sequencing the swine genome.

Publications

  • No publications reported this period