Pig Genome Update No. 29

angenmap@iastate.edu
March 1, 1998 
 1. Help Promote Animal Genome Research ................................ 21
 2. The Food Genome Program is Moving Ahead ............................ 20
 3. Set IV of Fluroescent Primers are to be Ready ......................  6
 4. The Annual Species Genome Meetings were Held ....................... 10
 5. Highlights of
     the 6th World Congress on Genetics Applied to Livestock Production.  8
 6. Highlights of PAGVI, Jan. 1998, San Diego .......................... 72
 7. Highlights of American Association for the Advancement of Science .. 21
 8. First International Workshop on Pig Chromosome 13 planned........... 52
 9. Meeting Updates .................................................... 37

Please get involved and help promote animal genome work. The recent meetings of the species committees from NRSP8 at PAGVI were excellent examples of the progress we as animal genome scientists are making. It also served as a time to get together and discuss how we need to help get the NRSP-8 renewal approved and how we can inform the researchers, administrators and the public we work with of the importance of genome research involving farm animals and aquaculture. Our department heads already have the message. At a recent Animal Science Heads meeting they overwhelmingly supported the NRSP-8 renewal and had a motion to support new money for animal genome research. What can you do to help? You can visit with your experiment station director and outline the progress made, the need for cooperation and the need to approve the NRSP-8 renewal. In addition, you can visit with those people in industry including producers, company people and commodity organizations and outline the importance of the work we do. As part of this effort, David Meeker and I recently met with the CEO of the National Pork Producers Council to seek their support. Mr. Al Tank was extremely interested and was pleased to hear of our progress and said NPPC would be supportive. Please take a few minutes and call or visit with the people you know. The directors from each region will be meeting soon and their support is crucial!

The Food Genome Program is moving ahead. A very significant bright spot in President Clinton's budget proposal is for a Food Genome Project in the USDA CSREES budget, funded in year 1 at $16 million. This will, if Congress accepts the recommendation, markedly increase competitive grants for genome research in plants and livestock. The USDA Food Genome initiative follows a meeting at the National Academy of Science and major thrusts by commodity groups. There is concern that U.S. research may start to fall behind if problems of inadequate funding are not resolved. The competitiveness of U.S. agriculture depends on strong research. Moreover, international collaboration is facilitated when the funding "playing field is more level." For Congress to appropriate the requested $16 million (or more) for the Food Genome Initiative, a united front supporting this is essential. This should encompass scientists and commodity groups as well as include agricultural businesses, food and feed processors, environmentalists, and consumers concerned with the safety of food. A web site ( http://www.genome.iastate.edu/community/proposal98.html) contains the description of the Food Genome Project. For further information, contact Assoc. Dean Colin Scanes at cscanes@iastate.edu. (kindly provided by Colin Scanes).

Primers, primers, primers. The next set of 53 pairs of fluorescent primers are now being made and should be ready for shipping by March 20. As before, please request these only if you plan to use the entire set and you will acknowledge that these were a part of the USDA/CSREES sponsored pig genome coordination program. To request them, please email the pig genome coordinator at mfrothsc@iastate.edu.

The species committee meetings for NAGRP were recently in San Diego. As part of PAGVI, the annual species meetings were held as workshops the first day of PAGVI. All the species’ committee meetings featured some great talks and some are highlighted on later pages. At the business meeting Daniel Pomp was elected chair and Sue DeNise was elected secretary. A resolution encouraging support of the Food Genome Project initiative was also passed and the future ISAG meeting in Minnesota was discussed. At the swine business meeting officers for the Swine Species committee and the NC210 committee were elected and they will be Chair Sara Sunden, Texas and Secretary Deryl Troyer, Kansas.

Meetings, meeting, meetings! The 6th World Congress on Genetics Applied to Livestock Production met in Armidale in early January. The meeting included some excellent papers that included updates on recent research on QTL mapping, statistical procedures to detect QTL s and some of the latest research findings of candidate genes and QTLs in pigs and the other livestock species. Proceedings (6kg worth!) or a CD with all the papers from the event are still available from Dr. Laurie Piper at fax: 61 67 73-3611 or email: 6wcgalp@mendel.une.edu.au.

PAG VI highlighted advances in animal and plant genomics. PAG VI marked the second year of the animal insertion with our fellow plant genomics colleagues. And this year showed more than ever that besides techniques, there is much in common between the plant and animal kingdoms. At the Animal QTL Session Reudi Fries (Technical University of Munich, Germany) started the session by describing the difficulties in trying to positionally clone a gene for a complex trait, especially in livestock species where it may be difficult to control environmental effects and incomplete penetrance and epistasis play a role. Nat Bumstead (Compton, UK) gave a very nice example of how genomics might impact food safety. Employing a combination of genome-wide screens and representational difference analysis (RDA) on three resource families, a major QTL for salmonella resistance was located on Ch. 5. Efforts are underway to produce a YAC contig map of this region. A major advantage of the Plant and Animal Genome (PAG) meeting is the large number and breadth of workshops. These workshops enable attendees to participate in a more intimate dissemination and discussion of selected topics. The National Animal Genome Research Program (NAGRP) has also elected to hold its annual workshops for cattle, horse, poultry, sheep, swine, and aquaculture in conjunction with PAG. In a relatively short period, all the major livestock and aquaculture species have generated the fundamental tools of genomics. Most of the species have genetic maps that contain 1,000+ markers, and where more than one map is available, consensus maps have been generated. Physical maps which provide landmarks for the assignment and orientation of linkage groups to specific chromosomes are available for many species. There are numerous large-insert libraries and radiation hybrid panels to integrate maps and fine-map markers. These resources and others not mentioned are continuously being improved through the efforts of numerous groups.

Armed with these resources, several success stories were presented on the identification and cloning of genes of interest, especially those involved in complex and economically-important traits. Tim Smith (USDA-ARS) answered the question of "Where's the beef?" by describing mutations in the bovine myostatin gene that result in the double muscling trait found in cattle. Jon Beever (U. of Illinois) identified the fibroblast growth factor receptor 3 (FGFR3) as the likely responsible gene for hereditary chondrodysplasia commonly known as Spider Lamb Syndrome. In swine Max Rothschild presented good evidence of a new candidate gene, the prolactin receptor, for litter size. Lee Alexander presented evidence of a QTL in swine, Chris Tuggle of advances in the porcine comparative map, David Meeker discussed industry issues related to genome mapping, Joan Lunney discussed her work on disease resistance and Graham Plastow showed how the industry was using genome results to improve pigs commercially.

Finally, the "Grand Unification of Biology" was a recurrent theme at PAGVI as data presented from the genomes of model organisms indicates significant commonality. It was evident at the Animal Comparative Mapping Workshops that rapid progress supporting this idea is being made with livestock species. Pat Venta (Michigan State University) described how to create universal mammalian STS for comparative mapping. Following a set of rules, PCR primers are developed that can amplify the same gene in any mammalian species and preliminary data by others suggest that this will be the case 50 to 80% of the time. Dave Burt (Roslin Institute, Scotland) showed that the avian genome has been relatively stable over time. So despite the fact the last common ancest or between mammals and avians was over 300 million years ago, there is a surprisingly high amount of conserved synteny. This has a great practical application as it appears that positional candidate genes can be identified through the chicken-human comparative map. Joel Gellin (INRA, Toulouse, France) presented an approach of using human ESTs to improve the comparative map in the pig and other species including dogs and cattle. To date this approach has been useful in putting many genes on the comparative map and offers the hope of revealing new chromosomal arrangement. So like the weather in San Diego, the future of animal genomics appears very bright. And given the rapid pace of developments, next year promises to be even better. Plans are already under way for the next meeting so if you have suggestions please contact committee members, Daniel Pomp, Sue Denise, Leif Andersson or Max Rothschild (kindly provided in great part by Hans Cheng).

The American Association for the Advancement of Science met in Philadelphia in February. The meeting featured a speech by President Bill Clinton in which he discussed increased funding for science. Unfortunately funding for USDA and agriculture will benefit less than some other agencies. Of interest also was an excellent discussion at the Fellows Forum in which the honorable Mike McCormick, a member of the House, and the AAAS Congressional Fellow, Dr. Sharon Hays, discussed the need to improve science education in this country and the goal to set new science policy. This is another example of how much we need to get involved in improving the public’s understanding of science. Relative to helping to design a new science policy is a site for scientists to offer comments. The address is http://www.house.gov/science/science_policy_study.html. Of special interest also was the Genome Seminar: Countdown to 2000-Medicine. Sponsored by The Institute for Genomic Research (TIGR) and AAAS. The seminar featured several talks including those by Craig Venter on the Current Status of Human Genome Research, Roger Bent on Functional Genomics, Dean Hamer on Behavior Genomics, Jeffery Friedman on the Genetics of Obesity, John Hardy on the Genetics of Neurodegenerative Diseases, Anne Spense on the Genetic Architecture of Complex Diseases and Stephan Fodor on Genes, Chips and the Human Genome.

A First International Workshop on Pig Chromosome 13 will be held on Sunday August 9, 1998 in conjunction with the International Society of Animal Genetics (ISAG) meeting in Auckland, New Zealand. You are invited to attend. The Workshop will be held near the ISAG conference center and will last one day. Registration will be 30 New Zealand dollars (about 20 USD), which includes a lunch and coffee breaks. This represents participants paying only half of these costs; the remaining funds has been generously donated by the US National Pig Genome Coordination program, one of the sponsors of this Workshop. PIC USA has also generously donated funds to help cover costs of speakers for this workshop.

Four sessions are planned, covering a) integration of the linkage and cytogenetic maps for Chromosome 13, including a presentation on the integrated AFLP, PiGMaP and MARC linkage maps, b) comparative mapping, c) QTL/ETL projects, and d) future plans for cooperation and collaboration. Speakers will cover new technologies for gene discovery and detailed mapping strategies, including a Plenary Talk by Dr. Denis Milan on the current status of the RN gene mapping project. Other planned speakers include A. Archibald, L. Alexander, D.Troyer, B. Choudhary, M. Yerle, C. Tuggle, L. Peelman, J. Gellin and M. Rothschild. All sessions will be informal, and questions and discussion regarding these works in progress will be encouraged. Talks are scheduled for 20-25 minutes, except for the Plenary Lecture and Linkage integration lecture, which will be 45 minutes. The philosophy is to encourage an informal atmosphere, so speakers will be lecturing for a limited time, allowing for discussion. The final session, following directly after the Plenary lecture, is intended to broaden the scope of the discussion to explore development of additional collaboration on major projects. It is expected that this Workshop will be an important and useful meeting for pig geneticists interested in chromosome 13, as well as those geneticists interested in an informal discussion of current research problems and technologies being used to solve genetic questions in the pig. As such, the Organizing committee has arranged the Workshop to make participation as convenient as possible, and specifically encourages students and post-docs to consider attending. Please circulate this information to all appropriate individuals. To register, please provide the following information: 

 Name:          ____________________
 Organization:  ____________________
 Email:         ____________________
 Address:       ____________________
and send to ashuey@iastate.edu with the subject line: "ISAGWorkshop". Alternatively, you can FAX to Chris Tuggle, Chair, Organizing Committee Pig Chromosome 13 Workshop, at 515-294-2401. All respondents will be included in future email announcements regarding this Workshop. Although all pig geneticists and other interested parties are encouraged to attend, space may be limited and preference will be given to pig geneticists currently working in genome mapping projects.

Meeting Updates:

Contributions to Pig Genome Update 30, including short meeting announcements, are always welcome. Please send by April 10. 

                    Max Rothschild
                    U.S. Pig Genome Coordinator
                    225 Kildee Hall, Department of Animal Science
                    Iowa State University
                    Ames, Iowa 50011
                    Phone: 515-294-6202, Fax: 515-294-2401
                    mfrothsc@iastate.edu

cc: Dick Frahm, CSREES and Roger Gerrits, ARS

U.S. PIG GENOME COORDINATION PROJECT
Paid for by funds from the NRSP-8 USDA/CSREES sponsored Pig Genome Coordination Program
http://www.genome.iastate.edu
Mailing list: angenmap@iastate.edu

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