Pig Genome Update No. 36

May 1, 1999

 1. Set VIII Primers Are on Their Way
 2. Pig AFLP Primers
 3. The RH Panel for Swine Will Soon Be Available
 4. More New Tools -- A RPCI-44 Male Porcine BAC Library
 5. The Excellent Biannual Pig Breeders Roundtable Met in Wye, England
 6. Planning for the Future was the Purpose of FAIR
 7. Plans Already Underway for PAG-VIII.
 8. "Animal Gene Mapping Community Directory" Database
 9. Time to Regiser for From Jay Lush to Genomics Conference
10. Upcoming Meetings (16 Items)

Primers, primers, primers are on their way: A new set of 73 pairs of fluorescent primers (Set VIII; April 1999) are being made and will be available for distribution on about May 15. This brings the total number of fluorescent primer pairs distributed by the U.S. Pig Genome Coordinator to 377 pairs. Check our updated information on these primers at: http://www.genome.iastate.edu/resources/fprimerintr.html or you may browse down from our main page: http://www.genome.iastate.edu to "US Pig Gene Mapping Coordination Program Shared Resources" section) and then to "Fluorescent Primers". To order Set VIII fluorescent primers, please send your request, along with your detailed postal address and your daytime phone number (required), to mfrothsc@iastate.edu . Please continue to make use of them and also be sure to acknowledge their source as it helps to improve cooperation and coordination activities.

Pig AFLP primers: AFLP is a patented genome mapping technique that has particular value for rapid assembly of a full genome map in species for which microsatellites are not available (or are sparse) and is also of use to find markers related to certain traits. Unfortunately, existing commercial kits (fluorescent primers available through PE AgGen and primers for radioactive labeling through Life Technologies, Inc.) are designed generally for plant genomes and may not work as well with pig DNA (or most mammalian DNA). A further problem arises because Keygene n.v. (which holds the AFLP patent) has negotiated an exclusive agreement with these two distributors such that buying the plant kit is the only way one can officially be licensed to use AFLP. Extensive discussions have made it clear that PE AgGen has no large interest in marketing a kit for animal AFLP, and Keygene cannot do so without violating their previous agreement. Dian Pouwels of Keygene has now indicated that those animal scientists wishing to use AFLP should purchase the Perkin Elmer kit ( http://www2.perkin-elmer.com/ag/775601/775601.html) and then should contact Keygene (keygene@euronet.nl) which will provide you the additional primers needed for animal AFLP mapping for a nominal fee ($100 US). The PE kit provides you reagents, enzyme and EcoRI primers and adapters, and Keygene will provide the complementary TaqI primers and adapters needed for animal genomes. You will also get MseI primers and adapters in the PE kit which are useless to you. Alternatively, Keygene will do the whole AFLP analysis for you on a contract basis through their Molecular Marker Service (email to keygene@euronet.nl). Because of Keygene's concerns about protecting their license and because some kit reagents may not be easily stored and re-shipped by the Coordinators, we regret that we will not be able to provide these AFLP kits directly to you as we had previously hoped. Please also realize that the above arrangement limits you to 64 possible primer combinations in the kits (8 EcoRI primers and 8 TaqI). While this is more than enough to test the AFLP technique out and generate a low resolution map, one still cannot utilize the full range of available AFLP markers (over 4,000 possible primer combinations, often 2-20 markers per primer combination) without making your own primers or sharing with friends (kindly provided by Jerry Dodgson).

The RH panel for swine will soon be available. Developed at INRA in Toulouse and tested extensively by the University of Minnesota the panel is now ready for distribution. To obtain aliquots, please contact Larry Schook at schoo009@maroon.tc.umn.edu . Considerable funding will be provided by the US Pig Genome Coordinator to help support this distribution activity. Another RH panel is also now available through Research Genetics at: http://www.resgen.com .

More new tools! A RPCI-44 Male Porcine BAC Library has been constructed by the BACPAC Resource Center in the Department of Cancer Genetics at Roswell Park Cancer Institute in Buffalo, New York, USA. Library construction was supported by a contract from the United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE. Blood from four male pigs (breed: 37.5% Yorkshire, 37.5% Landrace, and 25% Meishan) was pooled and genomic DNA was isolated from the white blood cells. The DNA (partially EcoRI digested) was size selected and cloned into the EcoRI sites of the pTARBAC2 vector. The average insert size is 165 kb and there is 10X coverage. The library has been arrayed into 384-well microtiter dishes and also gridded onto 22x22cm high-density nylon hybridization filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct porcine BAC clones, stamped in duplicate. As part of the Pig Genome Coordination effort, up to $650 will be supplied to US laboratories interested in obtaining the filter sets. This will pay for approximately 50% of the filters. Prior to taking advantage of this offer, please contact me at mfrothsc@iastate.edu to confirm availability of funds.

The excellent biannual Pig Breeders Roundtable met in Wye, England in March. Nearly 120 researchers, students and industry people met to discuss new developments in the genetics of pigs. Topics included genetics of performance, reproduction, health and behavior. In terms of molecular genetics there were talks on Leptin in mice, QTLs and new candidate genes in pigs for health, growth, backfat and reproduction. As is traditional, the meeting tries to foster open exchanges among industry members and challenging discussion. We extend a special thanks to Dr. John King for organizing and hosting this interesting meeting.

Planning for the future was the purpose of FAIR (Food Animal Integrated Research) 2002 meeting sponsored by many animal groups. This meeting was held in mid April in Baltimore and brought 200 people from very diverse backgrounds to follow up on the previous FAIR 95. The FAIR 95 discussions had included enhancing responsiveness to consumer and societal concerns, increasing efficiency and competitiveness, developing integrated food animal management systems, enhancing environmental quality, improving food safety and quality and enhancing animal well being. Fair 2002 "Animal Products for the Next Millenium" followed up on these and had presentations and discussion sections on the world situation, enhanced public and animal health and well being, economic and environmental sustainability, and animal agricultural in society and a global marketplace. The extremely diverse group of participants included individuals from farms and ranches, the production and food industries, animal health, universities, government agencies and animal welfare groups. Discussions were extremely useful and recommendations have been put forth. Hopefully this meeting and the information coming from it will provide some direction to obtain more research funds and to move our industry along in the future. This will be reported in a document to be developed in the near future.

Plans already underway for PAG-VIII. Under the leadership of Steve Heller, planning for PAG-VIII was underway even before we left San Diego. A draft schedule of the meeting workshops, plenary sessions, and computer demos is nearly complete ( http://www.intl-pag.org/pag/pag8work.html). Please note that we're starting about a week earlier next year. Plant genomics and animal genomics sessions will run concurrently after an initial plenary talk to open the day on both Tuesday and Wednesday. In addition, next year's meeting will provide more time for dinner in between the afternoon and evening workshops, and all of Tuesday night will be free to heed the call of San Diego's (or Tijuana's) evening attractions. Finally, PAG-VIII will end with the banquet on Wednesday evening and there will be no Thursday morning sessions. However, for those interested, PAG-VIII will be followed directly by the first Ag Microbial Genome meeting. Speakers for morning talks at PAG-VIII are being chosen and contacted. Thanks to all who have already provided suggestions and comments (kindly provided by Jerry Dodgson).

We have developed an "Animal Gene Mapping Community Directory" database. This "Directory" will contain a name list of scientists/ researchers in the research areas including but not limited to animal gene mapping, molecular biology, genome analysis and related fields. The "Directory" will serve the community as a people/ address finder, and as a guide to the current studies in the community. Please go to http://www.genome.iastate.edu/community/join.html to add your own information. The database information is accessible to the ANGENMAP subscribers only.

It is not too late to register for a special conference: From Jay Lush to Genomics: Visions for Animal Breeding and Genetics which will be held May 16-18, 1999 at Iowa State University Ames, Iowa. This not-to-be-missed conference will bring together quantitative and molecular geneticists from industry, government, and academe to discuss the future of animal breeding and genetics in light of changes in the fields of molecular genetics and bioinformatics. The program will feature eleven plenary lectures by renowned international scientists and a poster session of current research by participants. The schedule is arranged to encourage participant interaction and discussion. Information on the program and speakers can be found at http://www.public.iastate.edu/~ans/graduate/visions.html .

Upcoming meetings:

Contributions to Pig Genome Update 37, including short meeting announcements, are always welcome. Please send by June 10.

                    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

cc: Dick Frahm, CSREES and Roger Gerrits, ARS

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