GENOME

NEWSLETTER

Issue No. 2

July, 1995

Here is the summer version of the Poultry Genome Newsletter, Volume No. 2! I presume that all or almost all of you received Volume 1 in April, either in print or electronically. Just a reminder: the Newsletter is available in several formats: it is posted on the U.S. Poultry Gene Mapping Homepage (http://poultry.mph.msu.edu/) and on angenmap, the generic animal genome mappers newsletter angenmap@iastate.edu, (if you're not a member and want to join, just send an email to this address with your name and email address). The Newsletter is also sent to addresses on our mailing list as hard copy.

DON'T MISS THIS YEAR'S COMBINED NC-168, NAGRP (NRSP-8) MEETING IN COLLEGE PARK, MARYLAND. The meeting will be held October 25-27 at the U. of Maryland Continuing Education Center. Poultry gets a head start, as NC-168 will begin the afternoon of Wednesday, Oct. 25. The Swine (and NC-210) and Cattle (NC-209 meets separately this year) Species Subcommittees will join us beginning the morning of Thursday, Oct. 26. On Friday, the whole Animal Genome Technical Committee will meet together, and we'll hear from two keynote lecturers, along with representatives of the Washington funding scene. This may be an ideal time to learn the latest about the volatile climate inside the Beltway and put in a plug for continued support for animal genetics research.

Those of you who are participants in NC-168, expect a mailing in the not-too-distant future on the meeting from our Chairperson, Ed Smith. If you're not a member, but still want to get the meeting information, email Ed at edsmith@acd.tusk.edu. Non-poultry types (why are you reading this?) can get information from your Technical Committee Officers or by email from Joan Lunney at jlunney@asrr.arsusda.gov.

While Sue Lamont and Brian Kirkpatrick have been working on the meeting program, Joan Lunney has generously agreed to act as local host and has reserved the facilities at College Park. Many of us got a taste of Joan's gracious hospitality at the recent BARC Symposium XX (see below), so we know that a good time will be had by all in October. As an extra added attraction, Gail Juvik of the National Agriculture Library will demonstrate the latest developments in the animal genome databases at NAL. We should have a fully functional node of the Chickgbase database installed at Beltsville by then.

If you are not a member of the NC-168 or NRSP-8 technical committees or if you cannot get local Station support for your travel, there will likely be a limited amount of travel support available from the Poultry Coordination Budget. (Only for legitimate poultry types, though!) If you need travel support, please let me (22314jbd@msu.edu) know no later than October 1 (the sooner the better) so we can distribute the available funds appropriately.

Where in the world is Genome San Diego?: At the BARC XX Symposium, Coordinators and Technical Committee representatives discussed and gave tentative approval to a plan to have future NAGRP meetings (after the October meeting in Maryland) jointly with the plant gene mappers in an expanded and retitled version of their annual Plant Genome meetings held each January in San Diego, CA. Plant Genome III was held this January in San Diego and Plant Genome IV will be held in January of 1996. NAGRP will send representatives to the meeting next January and Margaret Dentine and Max Rothschild will attempt to work out an appropriate arrangement for the first joint meeting in January 1997. As recommended at the last NAGRP meeting in Minneapolis, this joint meeting would provide a widely advertised forum that should attract major scientists and administrators from the Federal government, industry and around the world. An update on these efforts will be provided at this Fall's NAGRP meeting.

Upcoming meetings:

4th Int. Veterinary Immunology Symposium, Davis, CA, July 16-21, 1995; contact: ljgershwin@ucdavis.edu

9th Colloquium on Cytogenetics, College Station,TX, July 17-19, 1995; contact: JWOMACK@vetmed.tamu.edu

American Society of Animal Science, Tampa, FL July 25-29,1995

Poultry Science Association, Edmonton, Alberta, August 14-18, 1995; contact: Poultry Science Association, 309 West Clark St., Chicago, IL 61820

Swine Chromosome 7 Workshop (and several related presentations), Minnesuing Acres Conf. Center (near Minneapolis, MN), September 21-24, 1995; contact Craig Beattie, beattie@map.marc.usda.gov

NC-168 and NRSP-8 (National Animal Genome Research Program), College Park, MD, Oct. 26-27, 1995; contact: JLUNNEY@asrr.arsusda.gov

XXV International Conference on Animal Genetics, International Society of Animal Genetics, Vinci Congress Centre, Tours, France, 22-26 July, 1996: contact: guerin@biotec.jouy.inra.fr for conference program details or jlamont@iastate.edu for ISAG membership details.

Meeting Reports. Knights of the Roundtable: Hans Cheng and Ron Okimoto attended the recent Poultry Breeders Roundtable in St. Louis. Hans presented an update on the gene mapping efforts to the breeders to keep them informed about the rapid progress in this area.

A BARC that's better than a bite: The Beltsville Agricultural Research Center (BARC) held its twentieth Symposium on "Biotechnology's Role in the Genetic Improvement of Farm Animals" on May 14-17. A wide array of talks were presented, along with two excellent poster sessions. Coverage extended from genetic diversity, gene mapping and applications and embryo/gamete technology to regulatory and social acceptance issues. On the mapping side, Craig Beattie updated the audience on the excellent progress by MARC (Clay Center, NE) on cattle and swine microsatellite maps, along with talks by Joan Lunney, Juan Medrano, Jim Womack and Harris Lewin. Of particular relevance to poultry, Sue Lamont gave an excellent overview of progress in chicken gene mapping, Bernie Wentworth reviewed transgenic poultry efforts using primordial germ cells, and Wayne Fairfull discussed the use of markers for poultry breeding. BARC scientists and staff did an excellent job of organizing and hosting the meeting, as well.

Reminder: We have developed a poultry "majordomo" mailing list service as described last time. To subscribe, send an email to: majordomo@poultry.mph.msu.edu. The body of the text should be: subscribe genomemap. Once subscribed, you can send text to all list participants via email to: genomemap@poultry.mph.msu.edu . We're not seeing a lot of traffic yet, but join now and be patient for the mail to come. Until then, there's always angenmap (see above).

Chickens are the Trend: "Chicken genome mapping: a new era in avian genetics" by Dave Burt, Nat Bumstead, Jim Bitgood, Abel Ponce de Leon and Lyman Crittenden was the feature article in the May issue of Trends in Genetics (11: 190-194; look for the chicken etching on the cover). In addition, a summary of nomenclature guidelines by Crittenden, Bitgood and Burt was published in a supplementary issue of Trends in Genetics on genetic nomenclature (pp. 33-34).

Surf City! Last issue, I introduced you to the U.S. Poultry Gene Mapping homepage on the World Wide Web (WWW) at the URL (universal resource locator) of http://poultry.mph.msu.edu/ . If you forget or lose our URL, you can probably find the Michigan State University homepage fairly easily and, again, just click on our listing, or enter from the Pig Genome Homepage (at http://www.public.iastate.edu/~pigmap). FYI there is also The ChickMap Homepage at the Roslin Institute developed by Andy Law and Dave Burt at Roslin. Their URL is http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html but the Roslin Homepage and the U.S. Homepages are linked such that anytime you are in one, you can just click on the appropriate heading for the other to be transferred there via the Web.. To access WWW, you will need browser software. Browsers are under continuous development and refinement, so you should upgrade your version as time goes by. Widely used browsers are Mosaic and Netscape (see your local computer expert to obtain these, if necessary.) Browsers vary widely in speed and presentation, so we can't always be sure you'll see exactly what we see, but we'll do the best we can. Also, our homepage is under continuous refinement, so don't forget to reload items every once in awhile (or your browser will keep giving you the old version out of its cache). We still have a lot to do to improve our homepage, but we believe the best way to do this is to get it out there for your advice. OUR HOMEPAGE IS REALLY YOUR HOMEPAGE. PLEASE MAKE SUGGESTIONS. THERE IS A HANDY ELECTRONIC SIGN-UP AND COMMENT SHEET AT THE BOTTOM WHICH MAKES IN VERY EASY FOR YOU TO TELL US WHAT YOU WANT. Note: this feature can also be used to add, correct or update your information in our address list. Please do so, if necessary.

More tricks to negotiating our homepage: You will initially see some general information (nomenclature rules, glossary, etc.), "Poultry Gene Mapping Activities", and "The ChickMap Home Page at the Roslin Institute". Most of these are self-explanatory. As noted above, you can click on the Roslin Home Page to see what they're up to in Europe (you may find electronic communications to Europe a little slower than to us). Our homepage also has a "Miscellaneous" section which includes information collected from a variety of sources, the latest monthly Crittenden bibliographies, and the signup and comment boxes. We will soon have a search option that will allow you to search all past Crittenden bibliographies, as well. (Reminder from last issue: hard copy mailings of the bibliographies will soon cease unless specifically requested. You can download what you need from the homepage or our majordomo maillist). You can also connect through the Genome Launching Pad to a variety of public database and search engines (still in development phase). Finally, there is the "See Also" section which can send you to the Pig Homepage, and a growing list of other relevant locations.

Click on "Poultry Gene Mapping Activities" to get to a menu of coordination information including our address list of interested participants, copies of newsletters, updated meetings list, etc. You can search the address list by Country or State or by Regional Committee membership. You can also get to the Roslin Institute Home Page (home of Chickgbase, the chicken genetic database under active development) or to angenmap, the Gene Mapping Discussion Group mentioned in the first paragraph.

New or soon to come under "Poultry Gene Mapping Activities". Hans Cheng and others have made great progress in the development of chicken microsatellite primer pairs (as will be described in a paper in press in Poultry Science). A table which summarizes these and all previously published microsatellites that are polymorphic on either the East Lansing or Compton reference families is provided under "Microsatellites and Probes" (what else!). Primer sequences, PCR conditions (where provided) and other details are given in the list. With the gracious permission of Poultry Science, we will soon also provide Hans' microsatellite genetic linkage map of the East Lansing reference population, so you will be able to scan the linkage groups, identify markers of interest, and click on the marker to get referred to the appropriate entry in the Table (ain't science wonderful?). With the assistance of K. Ladjadi, M. Tixier-Boichard, J. Bitgood, and F. A. Ponce de Leon, Poultry Gene Mapping Activities also shows the latest consensus karyotype map for chromosomes 1 to 8, Z and W.

Free Microsatellite Primers: As already mentioned, several labs worldwide are developing poultry microsatellite markers. The combined efforts and funds of Hans Cheng in East Lansing and Ilan Levin and Jossi Hillel in Israel have enabled the synthesis of a preliminary kit of fluorescent primers for several of these markers. However, new ones are coming in all the time, so coordination funds are being used to synthesize improved marker kits. We have already ordered and will very soon be able to distribute our Population Tester Kit. This will contain 9 primer pairs which define microsatellites with high polymorphic information content (numerous alleles widely distributed in several populations). For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. This kit will be available free of charge to those who wish to test just a few loci to characterize a strain or genetically fingerprint chickens (will chickens sue for loss of privacy?). Once we receive them, these primer sets will be available from the coordinators at no charge to academic laboratories doing large scale genome mapping and/or QTL identification. The relevant sequences will be listed on our WWW homepage and further information will be provided at that time.

A larger microsatellite kit containing primer pairs that define markers covering most of the chicken genome will be ordered shortly. This will be available to all public scientists who are involved in major mapping efforts. It should be ready at least by the next Poultry Genome Newsletter (Oct. 1) if not sooner. Email me 22314jbd@msu.edu or Hans Cheng hcheng@msu.edu if you are interested. We welcome information from everyone on useful microsatellite (or other) primers for posting on the WWW and for inclusion in free primer packages for distribution (send the info to 22314jbd@msu.edu). To be widely useful, primer sets to be synthesized should be demonstrated to be polymorphic on one or both of the international reference populations and/or in important resource populations.

The whole is greater than the sum of its parts: As advertised previously, Lyman Crittenden has been hard at work (despite his hypothetical "retirement") with Nat Bumstead in generating a consensus genetic map that combines data from both the East Lansing and Compton reference populations. This allows one to fuse some linkage groups that are separate in one or the other population and to derive broader linkage relationships. Nat is reviewing and adding to the consensus map at the moment. As soon as possible, we will attempt to add it to the microsatellite map (see above) soon to appear on the homepage (http://poultry.mph.msu.edu/ ).

A library of libraries: This summer we plan to install a list of available poultry genomic and cDNA libraries on the homepage. If you have one or more such libraries that you would be willing to provide to interested colleagues, please contact me at 22314jbd@msu.edu. The plan is simply to list existing libraries with an email and/or snailmail address of whom to contact. I don't expect that the volume of requests should present a problem for anyone (I've been sending out our original chicken lambda library for nearly 18 years now and only receive a couple requests per year these days.). However, if you prefer, we could probably house a sample of any library here in East Lansing and handle the distribution ourselves. In either case, please contact me so that I can let people know what's out there. In the interim, if you need a specific type of genomic or cDNA library, send your request to our poultry majordomo maillist and/or to angenmap (above).

Addresses:

Jerry Dodgson, Coord.
Dept. of Microbiology
Giltner Hall
Michigan State University
East Lansing, MI 48824
email: 22314jbd@msu.edu

Lyman Crittenden, Co-Coord.
same MSU address as above
email: slcritte@facstaff.wisc.edu

Hans Cheng, Co-Coord.
ADOL
USDA-ARS
3606 E. Mt. Hope Ave.
East Lansing, MI 48824
email: hcheng@msu.edu

Scott Eisensmith, Database Analyst
same MSU address as above
email: eisensmi@poultry.mph.msu.edu

Supported by Regional Research Funds, Hatch Act, to the National Research Service Program: NRSP-8.

National Animal Genome Research Program, Richard Frahm, Director, CSREES

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