GENOME
NEWSLETTER
Issue No. 1
April, 1995
GREETINGS! Welcome to the Poultry Genome Newsletter, No. 1, and belated best wishes for 1995! This newsletter is an unabashed ripoff of Max Rothschild's Pig Genome Update, and I wish to credit him from the very beginning for developing this idea and the general format we'll use. At least for now, I plan to shoot for quarterly updates, but if you'll feed me enough news, we'll get out more newsletters. The Newsletter is available in several formats: it will be posted on the U.S. Poultry Gene Mapping Homepage (see below) 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 will also be sent to addresses on our mailing list as hardcopy. If you are reading this electronically, but want a hardcopy from us, email Scott Eisensmith at eisensmi@poultry.mph.msu.edu
Welcome to the Web. In response to the growing popularity of the World Wide Web (WWW) on Internet, we've established the U.S. Poultry Gene Mapping homepage 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 therein. Another route is 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 may want to upgrade your version as time goes by. Widely used browsers are Mosaic and Netscape (see your local computer expert to obtain these, if necessary.)
Mea culpa. If you have viewed our homepage or when you view our homepage, you will see that we are far from finished in its development. We decided it was better to get up and running and show you our dirty laundry for your input than waiting to clean everything up first (in this business, technology is always jumping back ahead of you anyway). That which is presently available owes much of its development to material imported as whole cloth from Max Rothschild's Pig Genome Homepage and/or from Dave Burt's Homepage at the Roslin Institute. You will see many things that are not yet available or still provide "Pig" information. Other responsibilities have slowed our progress, but, as can be seen by this Newsletter, at least we're on our way. OUR HOMEPAGE IS REALLY YOUR HOMEPAGE. PLEASE MAKE SUGGESTIONS. THERE IS A HANDY ELECTRONIC SIGNUP 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 correct or update your information in our address list. Please do so, if necessary.
Surf's Up!: A few 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". The first of these is self-explanatory. 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. We will be adding to and updating these features (for example, we eventually hope to enable you to click on anyone's name in the address list to get immediately to their email). 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 monthly Crittenden bibliographies (see below), and the signup and comment boxes. 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 few other relevant locations. Experiment ("surf") with these as you like. Because the homepage is getting so long, we'll soon be turning some sections into secondary pages.
Poultry chauvinism. Do you ever want to send information or questions to other poultry geneticists without all the swine, cattle and sheep people on angenmap seeing it? We have developed a poultry "majordomo" mailing list service just for those occasions. 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 just starting the mail list, so it will take a little while for enough subscribers to join to make it widely useful. Join now, but be patient for the mail to come. Until then, there's always angenmap (see above).
Visitor from the East: Nat Bumstead from the Institute for Animal Health in Compton, England visited East Lansing from March 14 to 19. The primary purpose for the visit was to confer with Lyman Crittenden on how we can fuse data from the two international reference mapping panels developed at Compton and East Lansing into one consensus map. Efforts have been on-going worldwide to map markers on both panels so that the maps can be fused. Given the size of the two populations, there clearly will be differences in genetic distances (furthermore, meioses in the Compton panel are in females and in males in the East Lansing panel, so there will likely be a sex bias in recombination frequencies), however the goal will be to agree on common linkage groups where possible and, eventually, on marker order for the common markers. Progress was made during the visit, and it is hoped that a common map can be published and distributed later this year.
"A rose is a rose . . . .": Since he stepped down (or up?) from Species Coordinator to Co-Coordinator as of last October, Critt has been concentrating on cleaning up the sticky business of genetic nomenclature for chicken gene mapping. This is crucial in order to make appropriate linkages in the databases, to compare animal genes to human genes, and to use characters that computers can utilize and print. A summary of nomenclature guidelines is available on the homepage and will be printed as a supplement to the March issue of Trends in Genetics, along with similar information for other animals and for plants.
Save the trees: Many of you now receive the montly bibliography searches done by Margaret Crittenden from the National Library of Medicine database in the areas of chicken genes and of mapping techniques. The latter search which is shorter and more generally interesting to all animal gene mappers is also sent via angenmap. As noted in the most recent listing, Critt will be gradually converting to sending this information solely by electronic means. This will be done through the WWW connection noted above and through the majordomo mail list group. If you cannot access either of these and still would like a hard copy version, you should write to Critt at the address given at the end of this newsletter.
Coming soon, Free Primers: Several labs worldwide are developing poultry microsatellite markers. Hans Cheng of the Avian Disease and Oncology Laboratory (ADOL) in East Lansing is preparing a publication which surveys the existing useful microsatellites determined by his lab. Using combined funds from the USDA-ARS and Jossi Hillel in Israel, fluorescent primer sets have been made and aliquotted for all of these markers. Once the publication is accepted, 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. The Coordination budget has an account with Operon, Inc. that will provide for the synthesis of several further primer sets developed by Hans and/or others later this year. 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.
Turkey mappers note: Ilan Levin and Jossi Hillel of Israel have tested microsatellite primers developed in collaboration with the East Lansing group at ADOL and MSU on turkeys and found that several chicken microsatellite primer sets amplify polymorphic bands in turkeys. These results will soon be published (in press, Animal Genetics). Therefore our chicken microsatellite primer sets should be of some use to turkey gene mappers as well.
Upcoming meetings:
5th Annual New England Animal Biotechnology Symposium, Storrs, Connecticut, April 19-20, 1995; contact: Center for Professional Development, 203-486-3231 or Dr. Steven Zinn, szinn@ansc1.cag.uconn.edu
European Technical Turkey Conference, Renfrew (near Glasgow) Scotland, April 20 and 21, 1995; contact: TURKEYS, Andover Road, Highclere, Newbury, Berkshire, RG15 9PH, England, UK. Tel: +44.(0)1635.253239. Fax: +44.(0)1635.254146. or cfisher@cix.compulink.cc.uk.
National Breeders Roundtable, St. Louis, Mo., May 4-5, 1995; contact: Poultry Breeders of America, 1530 Cooledge Road, Tucker, GA 30084; phone 404-493-9401.
Genome Mapping and Sequencing, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, May 10-14, 1995; contact: meetings@cshl.org or WWW to http://www.cshl.org/
Biotechnology's Role in the Genetic Improvement of Farm Animals, Beltsville, MD, May 14-17, 1995; contact: Virginia Hupfer, Symposium Secretary, USDA-ARS, 301-504-6108 or Fax: 301-504-8092
NABC-7 (National Ag Biotechnology Conference), Columbia, Mo., May 23-26
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
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 sjlamont@iastate.edu for ISAG membership details.
Further meeting news: If you have news about additional meetings or further information about meetings posted above, please send that to eisensmi@poultry.mph.msu.edu. A proposal has been made that in January of 1997, the animal gene mappers meet with the plant gene mappers in an expanded version of their annual Plant Genome meetings organized by Sherago International Inc. Plant Genome III was held this January in San Diego and Plant Genome IV will be held in January of 1996. These meetings, as you probably know, are widely advertised and attract major scientists and administrators from the Federal government, industry and around the world. This is still in a very tentative stage, but would be in line with recommendations made at the last National Animal Genome Research Program (NAGRP) meeting in Minneapolis. A combined meeting with plant gene mappers would probably (although not necessarily) serve as the annual NAGRP meeting, as well. There is concern as to how this would impact the present arrangment of NAGRP meeting jointly with Regional Research Committees such as NC-168. Questions of cost, timing, and location might require that Regional Research committees separate from the NAGRP meeting. Your responses and suggestions should be relayed to us at 22314jbd@msu.edu.
Hans Cheng will address the Poultry Breeders Roundtable in May (see information above) on the progress of chicken gene mapping and prospects for its application.
All of the Species Coordinators will probably meet in May directly after the Beltsville Symposium (May 14-17, see above) to discuss future coordination and database development efforts. Suggestions are welcomed for topics the Coordinators should consider; email us at 22314jbd@msu.edu.
PLAN NOW ON ATTENDING THIS YEAR'S COMBINED NC-168, NAGRP (NRSP-8) MEETING IN COLLEGE PARK, MARYLAND (see above). You may have read the worrisome news regarding future USDA research budgets, and this may be our best chance to put in a plug for continued support for animal genetics research. 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. (This was also available for last year's NAGRP meeting, but we only had one taker.) If you need travel support, please let us know no later than October 1 (the sooner the better) so we can distribute the available funds appropriately.
Coordination Budget. The FY 93-94 Species Coordinator's Budget Report and the planned 94-95 budget are available as hard copy on request. Funds have been or will be expended for database development and support, freely available microsatellite primer distribution, reference panel DNA distribution, and travel and conference support with matching contributions from MSU and ADOL. Suggestions about additional initiatives are welcomed. Remember that coordination funds cannot be spent for specific research projects but must be used for the general good of the mapping effort.
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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