GENOME

NEWSLETTER

Issue No. 3

July, 1996

SORRY, WE'RE LATE

This issue of the Poultry Genome Newsletter is running a little late. The charitable interpretation is that I chose to wait to include reports from the just-completed Poultry Science Association meeting, but a more cynical view would be that I fell behind working on my talk and paper for PSA and didn't get this done.

POULTRY SCIENCE ASSOCIATION MEETING REPORT: LETTER FROM LOUISVILLE

What?--Me, Ancillary??: The PSA meeting got off to a fast start for geneticists with the Ancillary Scientists Symposium on "Genetic Selection - Strategies for the Future", beginning Sunday night, July 7. Bill Rishel of Arbor Acres gave the keynote address in which he provided a historical context for the rest of the Symposium. Monday morning began with Paul Siegel, who discussed the limits to (artificial) selection that are the inherent result of the millions of years of natural selection that produced todays birds. Bill Muir discussed computer modeling and played the Jeremiah role in stating that existing selection strategies are flawed because they generate too much inbreeding, and that they should be abandoned in favor of low selection pressure used solely via mass selection. Graham Bulfield then gave a necessarily brief overview of the excellent work going on at the Roslin Institute, which also provided a fine introduction to later talks. Among the highlights were his emphasis on the importance of bioinformatics in the new era of biology, and the discussion of his own mouse QTL experiments which identified 11 highly significant growth QTL, all of which were of rather small effect, in themselves. Graham also pointed out that the Roslin Institute has become an independent entity, with private funding approaching nearly half of its total, and it has also recently moved to set up its own separate genotyping entity that will serve industry and other researchers on a contract basis. Being able to access the demonstrated expertise of the Roslin on a private basis should be very attractive to those who don't have the capital or the desire to set up their own high throughput genotyping labs. The next session of the Symposium focused on transgenic technologies, with Jim Petitte giving an excellent talk focused on primordial germ cells (PGCs), Ken Simkiss providing provocative insights into the potential for developing new transgenic techniques for birds, and Rob Etches discussing the success that he and Ann Gibbins have had in using embryonic blastodermal cells to produce germline chimeras. It was generally agreed that both PGCs and blastodermal cells are at a stage where germline chimeras can be made with routine success, at least by experienced investigators, and that the key for the future is improving methods by which these cells can be kept in long term culture for the selection of the desired DNA-transfectants. The afternoon session began with my survey of DNA-based marker technology, followed by Hans Cheng, who discussed the present state of the chicken genome map (617 markers now on the East Lansing reference map, with 340 of them being microsatellites). Hans also discussed his own Marek's Disease resistance QTL studies, which provided a good segue into Jossi Hillel's talk on QTL hunts. Jossi pointed out that the population one chooses or develops are the most important factor in any QTL search, and he discussed the relative likelihood of false positives and false negatives in various populations, along with mechanisms by which valid QTLs might be sorted out. The final section of the Symposium involved talks from industry geneticists, Derek Emmerson, Larry Vint, Alan Emsley, and David Pollack. A variety of interesting views and results were presented. Perhaps a useful summation of the Symposium would be Alan Emsley's comment that poultry geneticists were willing and able to use the new molecular data now being generated, once mechanisms by which that data can be productively applied are more fully worked out. Thanks to Murray Bakst, Colin Baxter-Jones, and Ed Smith for organizing this interesting Symposium.

MORE FROM PSA:

PSA Genetics Session: There were also several talks later in the week of interest to the genome mapping community, principally in the Genetics and the Immunology sessions and the Posters. One highlight was Morris Soller's discussion of his on-going 20+ year selection experiments on photoperiodic drive, which concluded with the observation that it may be possible to use selection for photoperiodic drive in males to improve overall layer performance (see July issue of Poultry Science). In addition, Tom Savage described his Web site which includes descriptions and pictures of single gene mutations of turkeys at http://www.orst.edu:80/dept/animal-sciences/poultry/tc.html (we will also provide a link to this site on our Poultry Gene Mapping Homepage at http://poultry.mph.msu.edu/.

Germplasm Preservation: There was also time for a discussion of the present state of poultry germplasm preservation during the Genetics Session at the PSA on Wednesday. The bad news is well known, i.e., that due to financial pressures and retirements, many poultry lines and stocks developed over years and years of breeding are being eliminated. Such decisions are sometimes made summarily, and obviously they are irreparable. Some good news was reported by Mary Delany of UC Davis, who indicated that USDA-ARS plans to hire personnel to staff their cryogenic facilities in Beltsville, which should be able to store sperm and, eventually, PGCs or embryonic blastodermal cells of valued lines. Furthermore, she had recently been informed that a small amount of funding was being made available to the Davis-based effort to catalog and maintain key poultry lines. As a reminder, 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. Jacqueline Pisenti at UC Davis, please either contact her at jmpisenti@ucdavis.edu or 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.

ONLY 142 WRITING DAYS LEFT UNTIL THE NC-168 RENEWAL IS DUE: As noted in the last newsletter, the next NC-168 project renewal will be due (with all relevant sign-offs, etc.) on Dec. 9, 1996. Sue Lamont has developed a detailed timeline that will allow us to meet this goal, but, of course, we're already behind. Ed Smith is in charge of writing up the review of the previous project accomplishments, and the "Objective Chairpersons" are: Jerry Dodgson (Obj. 1), Doug Foster (Obj. 2) and Bill Muir (Obj. 3). Available participants met briefly at PSA. Those involved in Objective 1 include Cheng, G. Smith, Okimoto, M. Miller, Emara, Lamont, Ponce de Leon, Dodgson, Foster, Ed Smith, Bitgood and Gibbins (still working on Bob Taylor and Eric Wong as possibles). Objective 1 is to: Utilize modern molecular and breeding technologies to identify, locate, isolate and characterize poultry genes of economic importance. Present members of Objective 2 are Foster, Salter, Dodgson, Kuenzel, Okimoto, and Petitte. Those in Objective 3 include Muir, Cheng, Grossman, Lamont, Nestor and Velleman. If your name isn't listed but you still are interested, please contact Sue Lamont or one of the Objective coordinators asap.

1996 NATIONAL BREEDERS ROUNDTABLE: MEET ME IN ST. LOUIE, LOUIE.

This year's Breeders Roundtable (May 2-3) was organized by Jim Arthur, who did a fine job of assembling speakers and running the meeting. Talks that were of particular interest to geneticists included an analysis of the role of new mutations in selection by William Hill, a discussion of genetic evaluation in crossbred animals by Rohan Fernando, and a talk on heat stress vs. growth rate for different lines in various environments by Avigdor Cahaner. Jim Petitte gave an overview of transgenic technologies and Henry Hunt did likewise for genes in the major histocompatability complex (B complex). Yours truly gave a brief annual update of the poultry genome mapping project.

ALLERTON II: Genetic Analysis of Economically Important Traits in Livestock

This meeting will be held November 6-9, 1996 at the Allerton Conference Center near Champaign-Urbana, Illinois. Registration is limited and is on a first come, first serve basis. Information and on-line registration can be accessed at http://c3po.ceps.uiuc.edu/allertonII/.

PLANT AND ANIMAL GENOME V (PAG-V)/NAGRP/NC-168; January12-16, 1997, San Diego, CA.

As noted previously, the next NAGRP meeting will be held January 12-16, 1997 at the Town & Country Hotel (1-800-772-8527) in San Diego as part of the Plant and Animal Genome V (PAG-V) meeting. It is anticipated that the NC-168 Station Reports and Business Meeting (and the Poultry Subcommittee of NRSP-8) will occur on Sunday, January 12. (Fly in Saturday for low rates.) PAG-V will include Plenary Sessions in areas such as New Technologies, QTLs, Gene Discovery and Characterization, Comparative Map Based Analysis, Gene and Chromosome Organization, and Genome Diversity. Poster Sessions and the combined NRSP-8 (NAGRP) Business Meeting will also be included. Advance registration will be $325 ($100 for predoctoral students), and the hotel room rate will be $75.00 plus tax (single or double occupancy). All administrative questions should be directed to Scherago International, Inc.; 212-643-1750; email pag5@scherago.com. Abstract submission deadline is Nov. 4, 1996. Abstracts from previous Plant Genome meetings can be viewed at http://probe/nalusda.gov:8000.

Mark your calendars now. Note: It is expected that some Poultry Coordination funds will be available to assist with travel costs to PAG-V, especially for those NAGRP or NC-168 Technical Committee members who don't have or can't access Experiment Station travel support.

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-ARS-ADOL, phone: (517) 337-6828, Fax: (517) 337-6776.

Tuskegee Genome Conference, September 26-28, 1996, Tuskegee University, Tuskegee, Alabama. Contact: Dr. Ed Smith at edsmith@acd.tusk.edu or phone (334) 727-8961.

Poultry Science Association, University of Georgia, Athens, GA, August 4-8, 1997; contact: Poultry Science Association, 1111 North Dunlap Avenue, Savoy, IL 61874 or http://gallus.tamu.edu/psa/psa.html/

COORDINATION CHANGES: CRITT HEADS FOR DAIRY STATE; SCOTT GOES PART-TIME.

As reported last time, Lyman and Margaret Crittenden are moving to the Madison, Wisconsin area to be closer to family and, especially, the grandchildren, and they are heading out virtually as I write this. Until the new house in the country is finished, Critt's address will be 634 Emerson St., Madison, WI 53715-1716 and his email will be slcritte@facstaff.wisc.edu. Although we'll miss them a lot, we wish them the very best, and will be filling up Critt's daughter's email regularly with our messages to him.

Scott Eisensmith, the Poultry Genome Homepage computer expert and Webmaster has recently taken a full-time job in the private sector. Happily for us, he has agreed to maintain and update our Website (http://poultry.msu.edu) on a part-time, contractual basis. This should allow us to keep serving the poultry gene mapping community, while the NAGRP pursues more centralized database management.

NAGRP PLANNING FOR THE FUTURE OF ANIMAL GENETICS BIOINFORMATICS

Due to the departure of Gail Juvik from the National Agricultural Library (NAL) as detailed in our last issue, and several other developments, the NAGRP Coordinators (Max Rothschild, Noelle Cockett, Jim Womack and myself) are trying to work out a mechanism by which we can divert some of our funding to hire a centralized Animal Genome Database Manager, who would probably be located at NAL, and who would work to maintain all the animal database nodes at NAL and also to coordinate with similar efforts at the Roslin Institute (chickens and swine), INRA in France (cattle), Ivermay in New Zealand (sheep), and with U.S. initiatives at MARC (see below) and elsewhere. It is our hope that this would provide the momentum necessary to generate permanent animal genome bioinformatics support at NAL. The mechanism for hiring and supervising such a person in collaboration with Gary McCone at NAL is still being determined, but we hope to identify and hire someone by around this October. Any suggestions of who should be hired and/or how this arrangement might best work to serve you would be appreciated.

BEEN GONE TO ARGONNE

Jim Womack, Dick Frahm and I visited Argonne National Labs on behalf of the NAGRP to discuss potential collaboration between the DOE National Labs and USDA in a variety of areas, including genome mapping. At Argonne, we saw some very interesting work on DNA chip technology and 2-D protein gel analysis. While we support DOE-USDA collaboration in principle, the problem seems to be that both agencies are presently resource-poor, at least in their research programs. The 3 NAGRP representatives agreed that, to be effective, such a collaboration in the genome mapping area would need to include Human Genome Program-DOE Lab researchers at Lawrence Livermore, Lawrence Berkeley and Los Alamos National Labs, and that these scientists would be welcome to attend PAG-V as a first step.

COORDINATORS, TECH. COMMITTEE REPRESENTATIVES, MARC TO MEET IN MADISON

At the request of Neal Jorgensen, Lead Administrative Advisor to NAGRP, Dick Frahm, the NAGRP Coordinators, several representatives from the NAGRP Technical Committee, and other administrators and scientists including some from the USDA-ARS Meat Animal Research Center (MARC), will meet on August 15 and 16 in Madison, WI to discuss future plans for the NAGRP and how to maintain momentum for animal agricultural genetics at USDA. Improved participation by MARC scientists is one priority.

DON'T HAVE A COW: MAP A COW!

BOVGBASE, an informational bovine genome database supported by the NAGRP is now available at http://bos.cvm.tamu.edu/bovgbase.html. Thanks go to Jim Womack who has directed much of this effort.

CHECK IT OUT: It's simply FABulous!!

The University of Minnesota has instituted a Food Animal Biotechnology (FAB) Center, directed by Larry Schook, for the purpose of applying new molecular technologies in support of food animal productivity. Check out the FAB programs at http://fabctr.umn.edu (link to be added to our homepage, also).

COMING SOON! THE SEQUEL! CHICKEN MICROSATELLITE PRIMER COMPREHENSIVE MAPPING KIT # 2: The second comprehensive mapping kit of fluorescently-labeled microsatellite primers will be ordered in just a couple of days and should be available by September. This will contain approximately another 120 microsatellite primer pairs (beyond the 120 pairs already in Kit #1) which have been located on the East Lansing reference map. These loci are primarily based on new microsatellites developed by Hans Cheng at ADOL and those recently published by Martien Groenen (Poultry Science 75:746-754, 1996). Information on this kit, along with updated microsatellite loci and map information will be posted under "Microsatellite Marker Information and Available Primer Kits" on our homepage at http://poultry.mph.msu.edu. Like Kit #1, this kit will be available free of charge to those involved in major mapping efforts. Email me (22314jbd@msu.edu) or Hans Cheng (hcheng@msu.edu) if you are interested. ONE CAVEAT: Those markers in this Kit developed by the Groenen lab (designated by "MCW") are the subject of patent applications by Euribred B.V. which financed the Groenen effort. Inquiries about the use of these primers should be directed to Euribred as noted in the reference cited above. The kit is offered with the understanding that appropriate use of potentially patented material is the responsibility of the user and not of the Poultry Coordinator (although it is our belief that non-commercial use of the primers is, at a minimum, unrestricted).

Addresses:

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

Lyman Crittenden, Co-Coord.
Dept. of Microbiology
634 Emerson St.
University of Wisconsin
Madison, WI 53715
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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