GENOME

NEWSLETTER

Issue No. 1

January, 1996

HAPPY NEW YEAR TO ALL READERS OF THIS NEWSLETTER! May all your genes be tightly linked to existing clones and your QTL be significant and reproducible.

SAVE THE CHICKENS: A primary topic of discussion at last October's NAGRP and NC-168 meeting was the impending loss of a variety of valuable poultry germplasm. Jim Bitgood reported on the meeting held on this topic at UC Davis and the efforts of Jacqueline Pisenti to catalog available stocks. Roger Gerrits reported on on-going USDA-ARS efforts in this area which appear to be stalled, to some extent, by lack of recurring funding. At this point it appears the future of most chicken lines or stocks is simply a matter of local financial constraints and priorities. Several efforts (including Jim's work on the latest revision of the International Registry of Genetic Stocks, which we hope to eventually have on-line) are being made to assess the status of these birds. We were asked to use the Poultry Gene Mapping WWW Homepage to aid in (but not unneccesarily duplicate) these efforts. Thus we are coordinating with the UC Davis effort.

If you are maintaining poultry stocks at your location that you believe have value to other researchers and have not yet provided a description of these stocks to Dr. Pisenti at UC Davis, please take a few minutes to connect to the WWW Homepage (http://poultry.mph.msu.edu) and fill out the electronic survey under "Save our Chicken Stocks". (Other poultry are also welcome.) The entry form is set up so that you can submit information for one stock, send it, and then alter only those entries that vary for each subsequent stock you wish to submit. (Be sure to click "Submit Survey" for each entry.) All information will be sent to Dr. Pisenti (her email connection is also provided on the form).

ONLY 343 WRITING DAYS LEFT UNTIL THE NC-168 RENEWAL IS DUE: Yes, it's that time again; the next NC-168 project renewal will be due (with all relevant sign-offs, etc.) on Dec. 9, 1996. At our Fall Meeting, Sue Lamont agreed to organize the project (i.e., kick butt), Ed Smith agreed to be in charge of writing up the review of the previous project accomplishments, and the "Objective Chairperson" duties were "given" to Jerry Dodgson (Obj. 1), Doug Foster (Obj. 2) and Bill Muir/Mike Grossman (Obj. 3). The rest of you will be hearing from us. An added complication this round is that NC-168 will not meet again until after the deadline date, so we will need you all to provide requested input electronically or by mail.

NC-168 OBJECTIVE 1: a first draft. Given the Washington funding climate, this may be the most challenging program renewal effort ever. We were encouraged to "fit" our objectives to those of the NC Region (particularly, "Genetic Resource Development and Management/Biodiversity). As chairperson for Objective 1, I forward a first draft of an updated objective 1 below. Please note that this is an off-the-cuff first draft more to elicit commentary than anything else. Email me at 22314jbd@msu.edu with suggestions.

Existing Objective 1, NC-168: Identify, characterize and map poultry genes by molecular and classical methods. Draft "new" Objective 1, NC-168: Utilize modern molecular and breeding technologies to identify, locate, isolate and characterize poultry genes of economic importance.

WHILE WE'RE ON THE TOPIC OF REPORTS AND OBJECTIVES: The NRSP-8 National Animal Genome Research Program renewal application will be due in late 1997. However, it is already time to think about what we intend to do for at least three major reasons: first, many of the related NC committees, like NC-168, will submit renewals late in 1996 and what they choose as objectives may constrain NRSP-8, second, as we will have accomplished much of what we proposed in the original NRSP-8, a major "rethink" of "What's Next" is appropriate, and third, a very persuasive proposal will have to be made to retain any continued funding for animal gene mapping coordination. At our October meeting, the Cattle Species Subcommittee proposed the following objectives for a renewed NRSP-8:

Develop high resolution comparative maps integrated across species.

Identify QTL.

Develop strategies for economically viable implementation of genome technologies.

These are certainly worthwhile and pertinent objectives. Some concern has been expressed as to the extent they might overlap with already stated objectives of NC committees and therefore be seen as redundant. Other possible objectives that could be considered for NRSP-8 include:

Provide centralized resources and information for map development and dissemination.

Directed map development to improve density and coverage of markers (i.e., fill the gaps)

Objectives like these probably track what funds are used for more closely, but may be less dramatic and therefore less likely to be successful in a renewal. There is also some question as to how NRSP-8 might better assist in collateral Germplasm efforts under the coordination of ARS. In any case, the Species Coordinators have been asked to collect ideas and begin to formulate a strategy for an NRSP-8 renewal. Please email your comments and suggestions to me or to the other Species Coordinators.

MEETING NEWS

NAGRP (Third Annual) and NC-168, October, 1995. College Park, Maryland.

The combined NC-168 (and NC-210) and NAGRP meetings this October were a great success, especially for the poultry group, which had one of the largest and most diverse group of attendees ever. Excellent scientific progress was reported on all the NC-168 objectives, far too much to summarize here, other than a few general developments. One important trend is that objectives 1 and 3 (gene mapping and quantitative methods) are becoming more and more interdependent, as mappers begin to look for QTLs and quantitative geneticists have tools to examine questions of interest to them. This trend will surely continue, and it confirms the wisdom of including both objectives in our Project. Another highlight of the meeting were the excellent reports from numerous guests (including Drs. Gibbins, Kapur, Miller, Wong, Kühnlein, and Kuenzel). It is hoped that several of these guests will pursue a more formal association with NC-168. One problem has been that some of our potential colleagues (and some of our existing members) don't have access to travel support from their Stations (if any). However, travel funding for NC-168/NAGRP meetings has been provided to several attendees by the Coordinator, and this support will continue to be available at least for the duration of NRSP-8. The sad note of the meeting was the recognition of the end of poultry genetics at CFAR in Ottawa, which left us missing the input of past participants, Drs. Fairfull, Gavora and Benkel.

Highlights of the Business Meetings: Congratulations to the new Chairpersons and Secretaries/Chairpersons-Elect: Doug Foster and Mike Grossman, respectively, for NC-168 and Jim Bitgood and Abel Ponce de Leon, respectively, for NAGRP/Poultry Subcommittee. Discussions of germplasm preservation and the NC-168 project revision have been mentioned above. NC-168 agreed that our next annual meeting would be held in January, 1997, in San Diego, CA. This meeting will be in conjunction with the NAGRP meetings that will be held jointly with Plant Genome (below).

WELCOME INDUSTRIAL COLLEAGUES: It was agreed to make it more widely known that industrial colleagues are welcome at the joint NC-168/NAGRP-Poultry Meetings. We appreciate the continued advice and support of Alan Emsley as the industrial liason to NAGRP-Poultry, but other industrial colleagues are equally welcome to attend. (e.g., Come back Wayne Fairfull!)

The overall NAGRP meeting was highlighted by the National Scientific Agency Workshop at which Drs. Brayton (CSREES), Gerrits (ARS), Guyer (NIHGR), Nasser (NSF) and Ms. Wilson (NRC) described funding opportunities for animal geneticists. Other highlights were the Keynote speakers, Drs. Lyons (NCI) and Hennighausen (NIH) who discussed aspects of comparative gene mapping and the use of transgenic animals that were of general relevance to NAGRP scientists. There were also updates on genetic database development efforts from Gary McCone of the National Agriculture Library and Alan Hillyard of Jackson Labs. Margaret Dentine is the new Chairperson of the overall NAGRP (NRSP-8) Technical Committee and Hans Cheng is Secretary/Chairperson-Elect. Reports were made summarizing progress in each species (highlighted by the participation of Dylan Cockett, youngest gene mapper at the meeting.)

"A horse is a horse, of course, of course": Earnie Bailey (KY) reported on efforts to coordinate genome research in the horse, and it was agreed that the horse group could apply to join NAGRP as an addendum to NRSP-8 or, more likely, should be invited to participate in the NRSP-8 renewal process. Although there was no "official" representative from aquaculture, there was considerable enthusiasm for adding aquaculture as an additional species group in NRSP-8 (especially from Neal Jorgenson with particular emphasis on giant transgenics to be planted in his own favorite fishing spots).

As noted above, it was agreed that the next NAGRP meeting will be held in January, 1997 in San Diego as a coalition with the on-going Plant Genome meetings traditionally held at that time and place. A mixture of joint and concurrent sessions is anticipated, with time for NC-168 and other Regional Committees to have their regular Station reports, etc. Stock up now on your tanning lotion and cocoa butter. What about syntenic groups in those killer whales at Sea World?

Special thanks go to Joan Lunney (local host), Sue Lamont (Scientific Agency Workshop and outgoing [in both senses] NAGRP Chair), Gretel Dentine (overall coordination) and Brian Kirkpatrick (Keynote Speakers) for their efforts in putting together this very successful meeting.

MORE MEETING NEWS

The HUGO Comparative Genome Workshop was held on December 3-6 on Frasier Island, Australia. A detailed report is available in the latest Pig Genome Update available on the Pig Genome Homepage (at http://www.public.iastate.edu/~pigmap). Jim Bitgood represented the Poultry Species Subcommittee. Jim presented our widespread concerns about the loss of poultry genetic stocks that could eventually provide genes of interest for comparative mapping purposes (see p. 1 above). Jim's report will be posted on the Homepage. Another such meeting will be held in 2 years, possibly in conjunction with the 1998 ISAG.

Upcoming meetings of interest:

Plant Genome IV, San Diego, CA, January 14-18, 1996; contact: scherago@biotechnet.com

Genome Mapping and Sequencing, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, May 8-12, 1996; contact meetings@cshl.org or http://www.cshl.org/meetings/

Poultry Science Association, Galt House, Louisville, Kentucky, July 7-11, 1996; contact: Poultry Science Association, 1111 North Dunlap Avenue, Savoy, IL 61874 or http://gallus.tamu.edu/psa/psa.html/

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.

XX World's Poultry Congress and International Poultry Exhibition, New Delhi, India, September 2-5, 1996 (abstracts due Jan. 31, 1996). Contact: Dr. B.S. Sathe, Secretary, World's Poultry Science Assoc. (India Branch), Janaki, 189 Bhandarkar Institute Road, Pune - 411 004, India. Fax: 91-212-361729.

5th International Symposium on Marek's Disease, East Lansing, Michigan, September 7-11, 1996. Contact: Dr. R.L. Witter, USDA Avian Disease and Oncology Laboratory, phone: (517) 337-6828, Fax: (517) 337-6776.

Allerton II, Genetic Analysis of Economically Important Traits in Livestock, Allerton Park, Illinois, Nov. 6-9 (tentative), 1996; contact H. Lewin at blood@vmd.cso.uiuc.edu

HEY! PRIMERS! GET YOUR FREE PRIMERS!: Just a reminder of the free primer kits described in the previous edition of this Newsletter. The primer sequences and relevant collateral information are also provided on our Homepage (see below). If you are interested in one or both kits, contact Jerry Dodgson (22314jbd@msu.edu) or Hans Cheng (hcheng@msu.edu). 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. As more data become available, we plan to synthesize further primer kits containing additional informative loci.

POULTRY HOMEPAGE ON WWW

We have added several new items to the U.S. Poultry Gene Mapping homepage on the World Wide Web (WWW). Remember, our Web address is http://poultry.mph.msu.edu/. 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. (Want us to add pointers to your local homepage of interest? Just send the appropriate URL to Scott or Jerry (our addresses at end of Newsletter).

Now on the Homepage menu (items added since the last Newsletter are preceded by an *):

What's New

*Chicken Mapper's Message Board (post a message and see if you get answers)

*Sign our Guestbook (can also leave a message here; alternatively register for Poultry Newsgroup below)

About the poultry genome mapping project (*recently added to this is the Poultry Species Coordinator's Report for 1995 for your reference and suggestions)

Members of International Poultry Gene Mapping Community - Searchable Mail List (Check your address. Let us know of errors or if you've moved.)

Poultry Genetic Maps

Microsatellite Marker Information and Available Primer Kits (see above)

CHICKGBASE (connects to version at National Ag Library, Beltsville)

Poultry Genome and NAGRP Newsletters

Crittenden Reference Database (Searchable)

Genome Launching Pad (Genome Related Sites)

Inventory of cDNA and Genomic Clone Libraries (not yet active; please send info on libraries you would be willing to share)

See Also: other animal sites and discussion groups (e.g., signup for animal gene discussion group, angenmap)

*Community of Science Databases (includes CRIS, NSF, and other scientific database links for searching)

Places to Visit (Other miscellaneous WWW Sites, e.g., hardware and software companies)

Miscellaneous Poultry Information with Art & Sounds

*Save our Chicken Stocks (germplasm inventory, see Page 1 of this Newsletter)

*ChickMap Proposals (Andy Law's suggestions about future of CHICKGBASE, your comments to Jerry or Andy will be welcomed)

Upcoming Meetings (*includes Jim Bitgood's report on HUGO meeting described above)

U.S. PIG GENE MAPPING (Max Rothschild's Homepage at Iowa State)

ChickMap at the Roslin Institute, Scotland (Dave Burt and Andy Law, originators of CHICKGBASE)

National Agriculture Library Genome WWW Server (more than just CHICKGBASE node)

Poultry Newsgroup Registration

*Jobs (Message board where you can post a job opening or your interest in a new position. GIVE IT A TRY! What could it hurt?)

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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