Pig Genome Update No. 25

July 1, 1997

New pig genome database goes live. The new generic single species database (Arkdb) developed by the Bioinformatics group at the Roslin Institute (Archibald et al., 1996. Animal Genetics 27, Suppl 2. 55) has been implemented for pig genome mapping data (and chickens and sheep). At present the Arkdb version of PiGBASE is only mounted on the Roslin Institute genome server [URL = http://www.ri.bbsrc.ac.uk/pigmap/pigbase/pigbase.html] or [URL = http://www.ri.bbsrc.ac.uk/cgi-bin/arkdb/browsers/browser.sh?species=pig]. It is planned that a mirror copy of the database will be mounted at one or more sites in North America - beginning with Iowa State. Meanwhile, there are of course links to PiGBASE from the US pig genome coordinator's page [URL = http://www.genome.iastate.edu]. Editorial responsibility for the new pig genome database will continue to be shared by Alan Archibald (Roslin Institute) and Max Rothschild (Iowa State University). The hard work of data entry and curation is undertaken by Alison Brown (Roslin) and Lizhen Wang (Iowa). There is no requirement to download additional software in order to view the maps associated with the database. All you need for access is a WWW browser. As we are developing new features with Java, it is worth using the latest versions of the browsers that can handle Java. Some brief hints on using the new database have been posted on the Angenmap news group. There is also on-line help, especially for the Anubis map viewer software (Mungall, C. 1996. Visualisation tools for genome mapping - the Anubis map manager. Animal Genetics 27, Suppl. 2. 56; URL = http://www.ri.bbsrc.ac.uk/anubis/). The loading of the new data types is progressing well. For example, details of primer sequences, PCR conditions, sources of probes and libraries have been entered for all the papers currently recorded in the database. Links have been established to the DNA sequence databases where appropriate. It is anticipated that further links from within PiGBASE to other databases will be added. The most recent comprehensive linkage maps from the USDA-MARC group and the Nordic collaboration have been entered. (Kindly provided on behalf of the Roslin Institute's animal genome database group by Alan Archibald).

Several of the genome coordinators met recently with advisors Dick Frahm and Colin Scanes in Madison, Wisconsin. Issues discussed included the development and upgrading of sites for nodes for the genome databases and plans for the NRSP-8 renewal. Progress on the NRSP-8 renewal continues to be made. Several writing committees have completed their portion of the new draft. The renewal will now include Pigs, Cattle, Sheep, Poultry and Horses. The renewal rewrite efforts are headed by Jerry Dodgson. The coordinators also attended the retirement celebration for Neal Jorgensen. Neal was extremely involved in the development of NRSP-8 and played a significant role in getting it funded. The coordinators, on behalf of the U.S. Animal Genome Community, presented Neal with a plaque honoring his involvement. Plans to honor Neal at PAG VI are being made (see travel to PAGVI).

The National Animal Genome Research Program was recently recognized by receiving a USDA Honor Award. This is a significant award and the team of Dick Frahm and the genome coordinators were recognized under the group category for "Personal and Professional Excellence". The citation read "for development and implementation of the first structured National Animal Genome Research Program in the United States." The award was presented by USDA Secretary Dan Glickman to team leader Dick Frahm and recognized also at a separate ceremony held by CSREES. The team especially thanks all the scientists in NRSP-8 for their efforts and cooperation.

PAG VI is shaping up nicely and it's not too early to start planning for the PAGVI meeting in San Diego. The Plant and Animal Genome VI will be January 18-22, 1998 and again will be in San Diego. The organizing committee is already well along in planning next year's PAGVI. Ideas for workshops and speakers can be directed to any of the planning committee (Daniel Pomp, Jay Hetzel, Hans Cheng and Max Rothschild). Next year's meeting will run in similar fashion with the probable addition of new species groups and a meeting with industry representatives as a mechanism to obtain more input and advice from them. Hotel accomodations for PAG-VI next January will be limited by the Superbowl following us into San Diego on the weekend after the meeting. Those who wish to attend PAGVI will need to get their application forms in promptly. These will be distributed later in the year. Travel assistance from Pig Genome Coordination funds will again be available to help those individuals who need it. There will be a Neal Jorgensen Animal Genome Travel Award for a Pig Genome graduate student to attend the meeting. If you missed PAGV, you can find the abstracts and other information at: http://probe.nalusda.gov:8000/otherdocs/pg/pg5/allabstracts.html.

The Fifth International Congress on Pig Reproduction met in Rolduc, the Netherlands. This meeting is every 4 years and features advances in male and female pig reproduction. Over 180 scientists attended the 3 day meeting. A total of 22 talks were given and over 70 posters dealing with regulation of reproductive efficiency, factors affecting breeding efficiency, embryonic and fetal development, boar fertility and semen preservation, advances in biotechnology in pig reproduction including gene mapping and aspects of oocyte and embryonic development were presented. The proceedings will be published in book form later this year by the Journal of Reproduction and Fertility.

The International Conference on Animal Biotechnology held in Beijing, China, June 10-14, 1997 was particularly interesting from a pork industry perspective since China produces 425 million of the world's 900 million head of swine produced annually. Since 1987, China has mounted a concerted effort to catch up to the West in biotechnology with projects including transgenic pigs, recombinant vaccines, transgenic fish, and others. Still, China's investment in biotechnology is low compared to other countries. Access to livestock at the China Agricultural University in Beijing is limited and laboratory facilities are outdated and crowded. Considering these conditions and level of investment, the faculty and students of animal biotechnology (totaling approximately 500 people at several locations) in China are impressive. China also started an effort in researching the human genome in 1994 with its 56 nationalities totaling 22 percent of the world's population. Here again, funding is lower than in Europe, Japan, and the U. S., but information from this work will significantly enhance efforts in livestock research. This conference was attended by more than 150 scientists from some 20 countries and brought together some of the top researchers from the two major fields of animal biotechnology, gene mapping and transgenics. It featured a presentation by Keith Campbell of Edinburgh on the cloning of the first adult mammal (Dolly the sheep) and a presentation by Emanuele Cozzi from England on genetic engineering of pigs to provide organs for human transplantation. There were a number of presentations of information significant for the pig industry among the 46 papers presented. David Meeker of the U. S. spoke on the practical implications of biotechnology for the commercial pork industry. Ariel Darvasi of Israel (now of Jackson Labs in Maine) presented information on the use of selective genotyping and selective phenotyping for QTL mapping which could be particularly helpful to pig gene mapping efforts with smaller budgets. Patrick Chardon of France spoke on the swine SLA Class I region. Hein van der Steen of PIC in the UK spoke on a new genetic marker for litter size in Meishan pigs. Ning Li of China spoke on a candidate gene approach for the identification of genetic loci controlling litter size in pigs. Craig Beattie of the U. S. presented information on the human genome project and its implications for livestock biotechnology and health. Michele Mouricout of France presented an research approach to developing genetic disease resistance in pigs. Torsten Hardge of Germany spoke on the use of association analysis of candidate genes for economically important traits in extreme phenotypes of commercial pig breeds. Robert Wall of the U. S. gave a keynote presentation of the progress and future prospects for transgenic livestock. (Kindly provided by David L. Meeker)

It is not too late to plan to go to Armidale. The 6th World Congress on Quantitative Genetics Applied to Livestock meets January 10-16 in Armidale, Australia. Gene mapping and QTL sessions are planned. Abstracts are due July 11, 1997.

Differential Display PCR (dd-PCR) is a powerful method for elucidating differences and/or changes in gene expression between animals with divergent phenotypes. This primer set consists of 10 oligo-dT anchor antisense primers with different 2-base extensions on the 3' end, and 20 arbitrary 10-mer sense primers (5'), yielding a total of 200 primer combinations for screening cDNA populations. Each anchor primer has T7 sequence on the 5' end, while each arbitrary primer has M13 sequence on the 5' end. These extensions allow for simplified reamplification, sequencing, and expression studies of bands of interest. The set was put together by Daniel Pomp and are available for distribution. Given the more limited production of these primers, priority for distribution will be NC-210 members and pig gene researchers. If interested, please request primers from the Pig Genome Coordinator at mfrothsc@iastate.edu.

A third set of fluorescently labeled primers for pig microsatellites is now being compiled. Funds for these materials are provided by the USDA-CSREES Pig Genome Coordination Project. Suggestions to produce additional primer pairs are still welcome.

Upcoming meetings:

Transgenic Animals in Agriculture, Granlibakken Conference Center, Tahoe City, CA, August 24-27, 1997; see http://pubweb.ucdavis.edu/Documents/BIOTECH/biotech1.htm.

International Course in QTL Detection and Marker-Assisted Selection, Mitzpa Rachel Convention Center, Jerusalem, Israel, August 24-Sept. 4, 1997 (dates tentative). Contact: Joel Weller at weller@agri.huji.ac.il.

6th World Congress on Genetics Applied to Livestock Production, Armidale, New South Wales, Australia, January 12-16, 1998. Contact: Dr. Laurie Piper at 61 67 73-3609, Fax: 61 67 73-3611, email: 6wcgalp@mendel.une.edu.au.

PAGVI, January 18-22, San Diego CA.

Contributions to Pig Genome Update 26 including short meeting announcements are always welcome. Please send by August 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

cc: Dick Frahm, CSREES and Roger Gerrits, ARS

Paid for by funds from the NRSP-8 USDA/CSREES sponsored Pig Genome Coordination Program
Mailing list: angenmap@iastate.edu

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