Pig Genome Update No. 16angenmap@db.genome.iastate.eduJanuary 1, 1996 |
Several meetings have been recently held which offer new insights for livestock gene mappers. Below are summaries of some of them attended by of our colleagues.
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The HUGO Comparative Genome Workshop was held on December 3-6 on Frasier Island, Australia. This meeting was the first such workshop held to solely consider topics associated with comparative gene mapping. It was attended by 60 individuals representing mice, rats, cats, dogs, marsupials, deer, cattle, pigs, birds, fish, Drosophila, and informatics. The goals of the workshop included updating the existing maps, comparing similarity among species, coordinating databases and improving efforts to support comparative mapping. The sessions included small presentations on the comparative maps, vertebrate genomic evolution, phenotypes, diseases and QTL, and informatics. The meeting was attended by several pig gene mappers from the PiGMaP consortium, members of the NAGRP and by the U.S. Genome Coordinators for pigs and cattle. Data for the mouse and rat were clearly the most extensive with over 1,500 genes mapped in the mouse. In the pig, there are now over 210 mapped genes in PiGBASE, and perhaps 30 more in press and 30 in the research databases. It is likely that an additional 1000 ESTs exist. The average size of conserved segments between the pig and human is about 37cM. Data for cattle, sheep and birds was also presented which showed a smaller number of genes mapped. Drs. Leslie Lyons and Steve O'Brien discussed plans to share information on PCR primers on a set of over 300 anchor loci for all species. These were chosen such that they had excellent coverage in the human and the mouse and would provide a framework in other species. A presentation of The Comparative Animal Genome database (TCAGdb) was made by Dr. Alan Hillyard. One special part of the meeting was devoted to correct use of nomenclature. Conserved synteny was defined as the association of two or more genes on the same chromosome in two species. A conserved segment was defined as a continuous segment of genes linked together in two species and conserved order was defined as the same linkage order in two species. The naming of new genes was also discussed and sharing names with the human gene nomenclature committee prior to publication was encouraged. The workshop closed with a final session devoted to plans for the future. This included writing of a workshop report which Mammalian Genome will publish in 1996. The report will include information on the value of the comparative maps, mapping strategies, status of species maps and a fold-out comparative map. It is hoped that this report will be useful in generating more support for comparative gene mapping. Future meeting plans were also discussed. The organizers of the meeting, Drs. Steve Brown, Jenny Graves, and Jay Hetzel did a superb job in organizing this important meeting. Those wishing copies of the pig abstracts can e-mail me at mfrothsc@iastate.edu .
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A Livestock QTL Workshop was held on December 7 in Brisbane and hosted by Jay Hetzel. The purpose of this workshop was to present information in QTL results in cattle, pigs, sheep and deer. Several interesting results were presented which included studies and apparent QTL for growth, meat quality, excess sheath skin and double muscling in beef cattle, milk and fat traits in dairy cattle, and growth, backfat and litter size in pigs. Plans for several new QTL experiments were also discussed. Of particular interest was the open discussion at the end of the meeting in which concerns were raised on analysis of QTL data, funding opportunities and the need to pass useful results on to the livestock industry. The meeting was attended by 30 individuals from Europe, the U.S., Australia and New Zealand.
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The Sixth Australasian Gene Mapping Workshop and New Zealand Genetical Society Conference was held in conjunction with a Mammalian Interspecies Hybrid Workshop in Dunedin, November 27-December 1. The meetings consisted of 62 oral presentations and 40 poster presentations on plant and animal genetics and new technologies with a heavy emphasis on markers and complex traits. The mammalian interspecies hybrid workshop focused on the biology of interspecific hybrids and their value in the study of genomic imprinting and in constructing linkage maps. Maps under construction using the interspecific hybrid approach were presented for cats (Lyons), deer (Tate), mice (Copeland), pigs (Andersson), cattle (Womack), and marsupials (Cooper) (kindly provided by James Womack).
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The ISAG Pig Workshop in Ghent was held on November 15-17 and was attended by about 40 people from a number of different laboratories. The reports included information on blood groups and biochemical polymorphisms, immunoglobulin markers, gene mapping and reports on QTL for litter size, disease resistance and neuromuscular disease in pigs. Overall physical and linkage maps in the pig were discussed as was an updated map with over 35 genes of the SLA region in the pig. Considerable progress has been made in France and in Germany with development of YAC libraries and their use in identifying and mapping genes was discussed at length. Further information will be published from this meeting in the form of abstracts and activity reports and will be made available probably in January. Those interested in details about the meeting or abstracts can contact me at mfrothsc@iastate.edu .
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The International Symposium on Swine in Biomedical Research was held at the University of Maryland at College Park on October 22-25, 1995. The first session on basic physiology emphasized the importance of the pig for cardiovascular and pulmonary studies, and as a model for endotoxemia and intestinal pathobiology. Later sessions emphasized use of pigs for pharmacology and toxicology research. The pig has increasingly become an important model for studies of neonatal metabolism, of total parenteral nutrition, and of hormonal influences on metabolism. Improved swine management procedures will enable scientists to use the pig more effectively for basic research as well as for behavioral studies and analyses of stress effects. Several speakers documented the current availability worldwide of numerous lines of miniature swine and their genetic interrelationships. The second session focused on the use of pigs as a model for transplantation. Within species (allotransplantation) studies have enabled scientists to analyze the allograft rejection process and possibilities of retroviral vector systems for inducing alloantigen tolerance. Xenotransplantation (between species transplantation) using the pig as the organ or tissue source has recently become a major focus of research. Several companies have produced transgenic pigs expressing different human complement inhibitors as they try to overcome the hyperacute rejection response. Several scientists emphasized the importance of engineering transgenes for appropriate levels and tissue specificity of expression and of producing swine embryonic stem cells for broader studies of genome modification. The development of a detailed swine genome map has meant that analyses of the genetic control of disease responses can be investigated. Studies on the spontaneous regression of melanoma have indicated that a major gene regulates inheritance of melanoma. Despite the inverted structure of its lymph nodes the overall physiology of the pig immune system is quite similar to humans. Cellular and soluble immune regulatory functions are quite analogous although the pig is notable for the presence of high numbers of peripheral CD4/CD8 double positive T cells and for the limited number of variable immunoglobulin (Ig) genes, a single joining (J) segment and no IgD. Effector mechanisms against infectious diseases are quite similar to humans with the emerging importance of certain infections being attributed to major changes in management procedures. Overall, this symposium was an effective means of documenting the importance and applicability of swine for current biomedical research. The meeting was organized by Drs. Mike Tumbleson, Univ. Illinois-Urbana, and Larry Schook, Univ. Minnesota, St. Paul and proceedings will be published by Plenum Press (kindly provided by Joan Lunney).
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The 9th International Mouse Genome Conference took place in Ann Arbor, Michigan from November 12-16, 1995, and was attended by over 300 scientists from around the world. Sessions included Mutation Identification, Comparative Mapping, Informatics, Complex Traits, Mutagenesis, Gene Identification, New Technology, and Genetic and Physical Mapping. The mouse genetic linkage map now has over 6,500 markers, and most efforts are shifting towards development of physical and transcriptional maps. Each chromosome is represented by committees that maintain and organize the mapping efforts for that chromosome. Many mutations, disease genes, and other single-locus phenotypes have already been positionally cloned, and dozens of other genes are close to being identified and cloned. In addition, several efforts in mouse QTL identification are in progress, and a few QTL should be positionally cloned within the next few years. QTL efforts focus on obesity, disease susceptibility and behavior. Many of the new technologies and mapping reagents that are being developed for mouse genome mapping will have direct relevance for livestock genome mapping efforts (kindly provided by Daniel Pomp).
Several of the meetings reported in Pig Genome Update including the Swine in Biomedical Research and the HUGO Comparative Genome Workshop received some funding from the U.S. Swine Genome Coordination effort. If you have a worthwhile meeting and would like support please visit with the Coordinator concerning your request.
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As previously reported a new set of 25 primer pairs has been produced and is available. This brings the total to 294 pairs of primers that have been shipped to gene mappers and QTL researchers in over 26 labs in 10 countries. Please request a set if you want the latest addition to the previous set of primers.
Ideas from pig gene mappers are always appreciated. A list of microsatellite primers that could be used in automated genotyping projects is being compiled by a committee of D. Pomp, B. Kirkpatrick and C. Tuggle thanks primarily to the help of Martien Groenen and Denis Milan. If you have experience in this area and want to help please contact one of the committee members or me. Once a list is complete, we will consider making fluorescent markers for some or all of these primers. Other ideas of services that can be provided as part of the coordination effort are under consideration. Your thoughts would be appreciated.
Pig Genome Home Page grows. We continue to update the home page for pig gene mapping. It serves as a gateway for other databases, information on gene mapping, newsletters, meeting updates and much much more. This is your home page so please give us your ideas to include.
Confused by all databases and how to use them? Pig Genome Update 15 had directions to help you out. Just go back to our WWW home page and look at the Update 15. If you have any questions and problems, just let us know. We expect several new database developments. We will be developing in conjunction with Alan Hillyard and PiGMaP a new pig database containing more detailed experimental information. In addition, a new database, named TCAGdb for The Comparative Animal Genome database, is planned that will pull together the data from the single species databases for cross-species comparisons.
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Upcoming meetings:
Plant Genome IV, San Diego, CA January 14-18, 1996
Midwest ASAS/ADSA meetings, March 18-20, 1996, Des Moines, IA
Genetic Susceptibility & Complex Traits, Vancouver, Canada, April 17-19,
phone: 212-726-9281
XXV International Conference on Animal Genetics, International Society
of Animal Genetics, Vinci Congress Centre, Tours, France, July 22-26,
1996, contact guerin@biotech.jouy.inra.fr
for details
Allerton II, Genetic Analysis of Economically Important Traits in
Livestock, Allerton Park, Illinois, November 1996, contact
h-lewin@ux1.cso.uiuc.edu
for details
Contributions to Pig Genome Update 17 including short meeting announcements are always welcome. Please send by the 10th of February.
Holiday greetings to you, your families and friends. May this new year be filled with good health, happiness and success.
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Max Rothschild
U.S. Pig Genome Coordinator
2255 Kildee Hall, Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202, Fax: 515-294-2401
mfrothsc@iastate.edu
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