Genome Newsletters

POULTRY GENOME NEWSLETTER Issue No. 2, April, 1999

PLANT & ANIMAL GENOME VII (PAG-VII) & NAGRP/NC-168 REPORT

There again was a large and enthusiastic turn-out in San Diego this past January for the NC-168 meeting, held jointly with the NAGRP and PAG-VII. Participants have already received Station Report summaries and the Annual Report, so I won't go into further detail here. An extra added attraction this year was Bob Ivarie's guest presentation on transgenic poultry research going on at his company, Avigenics, Inc. Thanks to Bob for making time out of his busy schedule to participate. Several other industry scientists attended, as well. It was also a treat to catch up with special guest Lyman Crittenden and get his unique insight and historical perspective on research projects, many of which he was involved with on the ground floor. Most NC- 168 scientists were able to stay around for most, if not all, of the PAG-VII and NAGRP sessions. The workshop sessions were particularly busy this year, leaving many of us trying to sneak in and out of one or another room to catch relevant talks on grant funding, large insert libraries, computer analysis, etc. We're trying to schedule the workshops a little better next year to cut down on the overlap (see below). Several nice talks were also presented in the plenary sessions. Of particular note were those on linkage disequilibrium mapping by D. Cohen and a whirlwind update of genome sequencing at TIGR and Celera by A. Kerlavage. As a reminder, all abstracts from past PAG meetings can be found (in searchable format) at the PAG Website: http://www.intl-pag.org. Overall, nearly 300 animal scientists were represented among over 1,350 participants at PAG VII. See below for more information about next year.

"RUST NEVER SLEEPS": 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). As usual, NC-168 gets an early start (we have more to do than most) on Saturday, January 8 around 7:00 p.m. NOTE THAT WE'RE STARTING ABOUT A WEEK EARLIER NEXT YEAR! You'll arrive fresh from your New Millenium Parties and Y2K- induced chaos! 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 inbetween 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; there won't be Thursday morning sessions. (However, for those interested, PAG-VIII will be followed directly by the first Ag Microbial Genome meeting; see the Upcoming Meetings list below.) Speakers for morning talks at PAG-VIII are being chosen and contacted. Thanks to all who have already provided suggestions and comments.

WASHINGTON UPDATE: FUNDING FOR AGRICULTURAL GENOMICS

Our last two issues discussed the 1999 USDA National Research Inititiative- Competitive Grants Program (NRI) and its Animal Genome and Genetic Mechanisms Program whose application deadline was Feb. 15, 1999. Funding for the 1999 NRI increased substantially, from $97.2 million to $119.3 million, with the four different Programs in Animal Systems going from $24 million to $29 million. As most readers are aware, just after our last issue went out, a Supplement to the NRI Program Description was announced and circulated, including a program to generate "Animal Genome Basic Reagents and Tools". I am told that it is likely (but, of course, not certain) that this supplemental program request will also appear in next year's NRI grant program. (See http://www.reeusda.gov/crgam/nri/programs/suppl/angenmec.htm.) Rather than distributing all of this year's increase evenly among existing Programs, NRI hopes to promote rapid progress in a few selected new areas, including animal genome reagents, to make a case to Congress in support of sustaining and enhancing NRI funding. The President's proposed USDA budget for next year includes another large increase for NRI Grants, but one must remember that Congress historically has reduced the President's NRI request in the final USDA Appropriations Bill. So don't get your hopes too high. Meanwhile, the National Institutes of Health (NIH) held a "Non-Mammalian Models Workshop" in Bethesda, MD on Feb. 16-17. A variety of non- mammalian model species were represented, including S. cerevisiae, nematode, fruit fly, Xenopus, zebrafish (the "five major organisms", sort of the Security Council of non-mammalian genomics), along with Chlamydomonas, Tetrahymena, Dictyostelium, S. pombe, Neurospora, Aplysia (marine snail), sea urchin, pufferfish, and, last but not least, CHICKEN (the Third World of genomics). A small number of NIH grantees using these latter species were invited to participate. Chicken was represented by Dr. Paul Goetinck of the Mass. General Hospital and Harvard Med. School (pgoetinck@cbrc.mgh.harvard.edu), who presented a 10 min. summary based on email contacts with several relevant investigators. Richard Frahm and Peter Brayton represented CSREES at the meeting. Both indicated that discussion of chicken and other "Third World" species was brief. The outcome of the Workshop remains uncertain, but (as reported by the NIH representative at PAG VII) NIH is in process of considering what other genomes should be completely sequenced in support of progress in biomedical research. Hopefully, the chicken genome will be on that list, but there is no indication at the moment. (Recall, however, that NIH Director, Harold Varmus, received the Nobel Prize for research done primarily in the chicken.) Thanks to Mary Delany for providing much of the info. summarized above.

TOOL KIT FOR CHICKEN GENOMICS

The paragraphs below include updates on some of the new experimental resources for poultry genomics that we and others have been developing. A more complete list, generated mainly by Christoph Knorr and at the Poultry Genome Workshop discussion at last year's ISAG meeting, is available at our Web Site (http://poultry.mph.msu.edu). Click on "Maps and Tables", then on "Partial List of Useful Resources . . ." If you have a poultry genome resource you'd like to share and add to this list, please email me (dodgson@pilot.msu.edu).

CHICKEN GENE PRIMERS AND MICROSATELLITE KITS

GENE PRIMERS: As noted previously, PCR primer pairs complementary to 200 chicken genes of known sequence are now available. In each case, a likely primer pair for PCR was derived using primer optimization software based on Genbank sequences. A Table entitled "Chicken Gene Primers #1"is available on our Web Page which provides the gene name and Genbank ID number for each primer pair, along with the predicted product size, if the primers are used in RT-PCR (http://poultry.mph.msu.edu, click the "Maps and Tables" button, then "Microsatellite Marker Information and Available Primer Kits", and then scroll down). None of these primers are fluorescently labeled. Due to the high cost of synthesis, we are not able to provide the whole set of 200 primer pairs on request. However, requests for primer pairs for one or several specific genes (up to 20 pairs at a time) will be filled as long as the primers remain. Requests should be forwarded to J. Dodgson (dodgson@pilot.msu.edu) or H. Cheng (hcheng@pilot.msu.edu). A second kit of 100 more primer pairs, "Chicken Gene Primers #2", has been ordered and will soon be available. Keep an eye on our Web Site for relevant information, soon. (Thanks to Steven Suchyta for help in primer design).

MICROSATELLITE PRIMERS: A new kit (kit #5) of 37 more microsatellite primer pairs based on information provided by Dave Burt of the Roslin Institute and Abel Ponce de Leon of the U. of Minnesota is available, bringing the total number of microsatellite primer pairs to 612. Information can be found and requests can be made as in the previous paragraph. PLEASE NOTE: We are very low on primer pairs in kit #1, and their dye labels are probably starting to degrade with age, anyway. At this point, we don't intend to re-synthesize Kit #1 until and unless demand increases. If you have a particular need for this kit, please let us know asap.

CHICKEN BAC LIBRARY IS AVAILABLE!! Coordination funds have supported the construction of a chicken BAC library by Hong-bin Zhang of the Texas A&M BAC Center, which is now available. This second BAC library used the UCD 001 Jungle Fowl line as its DNA source, one of the two lines used in the East Lansing reference map backcross. As of now, the library consists of about 30,000 clones with average insert size of about 150 kb (approximately 4X coverage). Inserts are into the BamHI site of the pBeloBAC11 vector. A limited number of robot- spotted filter sets have been ordered and will be available free upon request to the Coordinators, once we get them. Alternatively, filter sets can be obtained directly from the Texas A&M BAC Center (http://hbz/tamu.edu) at the cost of preparing and sending them(about $400 per filter set with two spots of each clone per set; half this for one spot/clone). Once your clone of interest is identified by hybridization, individual clones can be obtained at cost from the BAC Center. If you'd like a complete replica of the library for pooling or other purposes, this can also be ordered from the BAC Center at a cost of about $4000 ($50 per 384 well plate, 80 plates in all) in the U.S. (about twice this outside the U.S.) Again, contact Dr. Zhang if interested at http://hbz/tamu.edu.

As noted previously, Martien Groenen's lab also constructed a BAC library in collaboration with the Texas A&M BAC Center . This BAC library consists of nearly 50,000 clones with average inserts of about 130 kb (about 5X coverage) in the HindIII site of pECBAC1. (Different enzymes were used for clone inserts to enhance the likelihood that any given gene will be found in at least one of the two libraries.) For more info on this library, see the Groenen homepage at http://www.zod.wau.nl/vf/research/chicken/frame_chicken.html. If you wish to screen the Wageningen BAC library, contact R. Crooijmans at richard.crooijmans@alg.vf.wau.nl.

CHICKEN AFLP MAPPING 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). It also can be used to generate a resource family map that can be linked to the framework map (see Knorr et al., Animal Genetics 30:28-35, 1999, for more information on chicken AFLP). Unfortunately, existing commercial kits (fluorescent primers available through PE AgGen and primers for radioactive labelling through Life Technologies, Inc.) are designed for plant genomes and don't work well with chicken 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 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; give them to a friend doing plant AFLP.] 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 4000 possible primer combinations, often 2-20 markers per primer combination) without making your own primers (or sharing with friends).

REMINDER: CHANGES IN ACCESSING THE POULTRY DATABASE

Iowa State is now home to the U.S. nodes for both the swine and poultry genome mapping databases, just as the Roslin Institute remains home to the European versions. Choose whichever site works fastest and easiest for you. When using the U.S. site, go to http://www.genome.iastate.edu/. If you then click on the poultry icon, you will get a local ISU version of our East Lansing homepage (http://poultry.mph.msu.edu). Clicking the "Database" image on the left will get you into the Iowa State node of the same database that's at Roslin (choose either CHICKGBASE or CHICK MAP). (If you still wish to access to the Roslin site for whatever reason, connect to it through the East Lansing homepage or go directly to http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html). Thanks to Max Rothschild and Zhiliang Hu for their assistance in putting up the Iowa State nodes.

JOIN THE ANIMAL GENE MAPPING COMMUNITY DIRECTORY

Please also take a minute to enter your name into the Animal Gene Mapping Community Directory at Iowa State. Go to http://www.genome.iastate.edu/community/join.html.

GREAT--EST POULTRY WEBSITES

U. OF DELAWARE: Joan Burnside and colleagues have developed the University of Delaware Chick EST Project Web Site at http://udgenome.ags.udel.edu/chickest/chick.htm. This site includes information on their activated chicken T cell EST database, search options for genes or sequences of interest, methods for using microarrays, and other interesting items. Lots of things are cooking at Delaware, so look for additional EST data and other information to be added. This is a good site to add to your bookmarks. Thanks to Joan Burnside for making all this available to the public.

DT40: As a reminder from last issue, Jean-Marie Buerstedde has also developed a web site dedicated to the chicken transformed B cell line, DT40. Among many other things, this site provides access to the ESTs that Jean- Marie has obtained from DT40 cell mRNA. The URL is http://www.uke.uni- hamburg.de/Institutes/HPI/div3/dt40.htm.

WAU: Although it doesn't yet have any EST data included, it's worth noting that the Chicken Genome Mapping Site of Wageningen Agricultural University, coordinated by Martien Groenen, has changed its URL to the one listed above with regard to Martien's BAC library: http://www.zod.wau.nl/vf/research/chicken/frame_chicken.html. Keep an eye on this site for future developments, including the 2nd edition of the Consensus Genetic Linkage Map of the Chicken, which Martien has almost completed.

ADOL: Most readers are familiar with the many critical contributions made through the years at the USDA-ARS Avian Disease and Oncology Lab (ADOL, formerly the Regional Poultry Research Lab) in East Lansing. Find their Web Site at http://www.msu.edu/~arsadol/.

While we're on the subject, congratulations and best wishes to Dr. Aly Fadly, who has recently assumed the position of Research Leader at ADOL and is faced with the task of filling the large shoes of former ADOL Director, Dick Witter.

ON THE ROAD AGAIN. UPCOMING MEETINGS:

From Jay Lush to Genomics: Visions for Animal Breeding and Genetics, May 16-18, 1999, Iowa State U., Ames, IA. Info at: http://www.public.iastate.edu/~ans/graduate/visions.html

Genome Sequencing and Biology, May 19-23, 1999, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. Contact: http://www.cshl.org/meetings

1999 Summer Institute in Statistical Genetics, May 26-June 11, 1999, North Carolina State U., Raleigh, NC. Contact http://www.stat.ncsu.edu

Symposium on Genome Diversity and Evolution in conjunction with the Annual Meeting of the American Genetic Association, June 12-13, 1999, Penn State U., University Park, PA..

11th North American Colloquium on Domestic Animal Cytogenetics and Gene Mapping, June 14-18, 1999, U. of Minnesota Twin Cities Campus, Minneapolis/St. Paul, MN. See http://www.extension.umn.edu/Courses/cytogene.htm

Molecular Biology Techniques Workshop, June 14-24, 1999, U. of Minnesota, St. Paul, MN. Sponsored by the Food Animal Biotechnology Ctr. See: http://fabctr.umn.edu/mbtw/1999.htm

Agricultural Genomics: New Technologies, Functions, and Advances, June 23-25, 1999, Sheraton San Diego Hotel and Marina, San Diego, CA. See http://www.iir-ny.com.

Techniques in Bioinformatics and Comparative Genomics, June 27-July 2, 1999, Madison Wisconsin. Five day computer laboratory course offered by the Biopharmaceutical Technology Center Institute. See: http://www.btci.org/courses/TBCG99.htm

Poultry Science Association Annual Meeting, August 8-11, 1999, Springdale, Arkansas (hosted by the U. of Arkansas). Info at: http://www.psa.uiuc.edu/

Transgenic Animal Research Conference, August 14-19, 1999, Granlibakken Conference Center, Tahoe City, CA. Sponsored by the U.C. Davis Biotechnology Program. Contact info.: mmmcgloughlin@ucdavis.edu

50th Annual Meeting of the European Association for Animal Production, August 22-26, 1999, Zurich, Switzerland. Contact: http://eaap-1999- zurich.ethz.ch.

Candidate Genes for Animal Health (sponsored by the Research Institute for the Biology of Farm Animals), August 25-27, 1999, Rostock, Germany. Contact: http://www.fbn-dummerstorf.de/fb3/Symp99.htm

The Microarray Meeting, Sept. 22-25, 1999, Phoenix, Arizona. Hosted by Nature Genetics. More information to follow or see http://genetics.nature.com/

Cold Spring Harbor Fall Courses: Genome Informatics; Positional Cloning: Contig to Candidate Gene; Computational Genomics, application deadline, July 15, 1999. Contact: http://www.cshl.org/meetings/

Plant and Animal Genome VIII, joint with NC-168 and NAGRP annual meetings, Jan. 8-13, 2000, Town & Country Convention Center, San Diego, CA. More information on page 1 of newsletter and/or see http://www.intl- pag.org. Followed immediately by Ag Microbial Genome I, Jan. 13-14, same location. See http://www.ag-microbial.org/agm/

Addresses: Jerry Dodgson, Poultry Coordinator Dept. of Microbiology Giltner Hall Michigan State University East Lansing, MI 48824 email: dodgson@pilot.msu.edu Hans Cheng, Co-Coord. USDA-ARS ADOL 3606 E. Mt. Hope Ave. East Lansing, MI 48823 email: hcheng@msu.edu Supported by Multi-State Research Funds, Hatch Act, to the National Research Service Program: NRSP-8. National Animal Genome Research Program, Richard Frahm, Director, CSREES