POULTRY GENOME NEWSLETTER 2001

ISSUE NO. 2, APRIL 2001

Better late than never!! Sorry for the delay in getting this issue out. As compensation for the delay, this issue is extra large!

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

PAG-IX was another big success this past January, with almost 1700 scientists in attendance from 47 States (where were you Alaska, Rhode Island and Wyoming?) and 47 foreign nations. As usual, the Poultry Workshop/NC-168 meeting got the whole affair off to a rousing start. Stations represented included Arkansas, California (and Beckman Research Inst.), Connecticut, Delaware, Indiana, Iowa, Michigan, Minnesota, North Carolina, Virginia, and USDA-ARS-ADOL. Of particular note, representatives from at least 7 different companies were in attendance. Excellent guest presentations were provided by Robin Morgan (DE), Hongbin Zhang (TX), Chris Ashwell (USDA Beltsville) and Michelle Tixier-Boichard (INRA). Marlene Emara (emara@UDel.Edu) and Jim Petitte (j_petitte@ncsu.edu) will again chair NC-168 and NRSP-8/poultry next year, as we move to two year administrative terms. It was agreed to request a one-year extension for NC-168, in part so that both NC-168 and NRSP-8 renewals will occur in the same year. The extension request should be submitted shortly.

PAG-IX was highlighted by a very active workshop schedule and an enormous poster session, not to mention a very active "vendor alley". Several interesting plenary talks were presented, highlighted by those of William Talbot, Harris Lewin, Terry Gaasterland, and Willem Stemmer in the Animal Genome section (several of our plant genome colleagues were noted in the audience). PAG-IX was followed directly by the Agricultural Microbes Genome conference again this year.

Planning is already well underway for PAG-X next year. See www.intl-pag.org/pag for more information. Francis Collins, "Czar" of the Human Genome Program at NIH, has agreed to give one of the plenary talks. Several changes are on tap for next year. PAG-X will again be at the Town & Country Convention Center in San Diego, CA, next year running from Sat., Jan. 12, through Wed., Jan. 16. Tentatively, the Poultry Workshop/NC-168 meeting will begin at 3:45 p.m. on Saturday next year, in order to provide more time for Station reports, guest speakers and discussing our renewals. PAG-X will include plant, animal and agricultural microbe genomics all in one meeting. Next year a weekend-only registration rate ($175) will be made available in addition to the usual student ($225), non-profit ($425 early/$525), and industry ($550 early/$650) full week registrations. Registration badges will be required to participate in any workshop. As usual, some support will be available from the Coordinators for member and student participation, including the Neal Jorgensen Travel Award for Poultry, awarded this past year to Wei Liu of Iowa State University.

WASHINGTON UPDATE: PRESIDENT'S USDA BUDGET FOR 2002

Unfortunately, the new administration has proposed to provide only $106M to the 2002 USDA NRI Competitive Grants Program. This amount is unchanged from this year's NRI budget, which was a reduction from $119M awarded in 2000. It's uncertain what Congress will do with the President's proposal, but this is a disturbing change from the long-standing tradition of administration proposals for large increases in NRI that were later reduced by Congress. The Bush budget also eliminates most "special grants" (aka, "pork") that are typically added back by Congress at the expense of NRI and other programs.

On a more optimistic note, the Bush budget recommends continued support for the Initiative for Future Agriculture and Food Systems (IFAFS) program at $120M/yr. During the last two years (this year's deadline was 4/23/01), the IFAFS program included an animal genome component, designed to fund consortium-based grants in the $0.5M to $2M range. $4.7M was awarded in 2000 in animal genomics, including funds for mapping growth genes in broiler chickens, marker-assisted improvement of pork, functional genomics of bovine T-cells, and genetic resistance to bovine paratuberculosis. More details on the year 2000 awards are at www.reeusda.gov/1700/programs/IFAFS/ifafsawards.htm. Past sentiment has been mixed in Congress for IFAFS, so there is no guarantee that 2002 funds will remain in the final budget. On the other hand (unfortunately in the mind of this author), it appears that State Experiment Station support for the IFAFS program considerably exceeds their support for the NRI program, on which more investigators depend. For more on IFAFS, see http://www.reeusda.gov/ifafs/. For a summary of the overall administration proposed 2002 USDA budget, see http://www.usda.gov/agency/obpa/Budget-Summary/2002/2002budsum.htm.

ADOL OF A JOB

USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory (ADOL), East Lansing, MI is seeking a permanent RESEARCH GENETICIST at the GS-12/13 level. The incumbent will contribute to a unit working on the biology and control of avian tumor viruses with an emphasis on the identification of genes and pathways associated with viral disease resistance in poultry. Preference will be given to individuals with skills in molecular quantitative genetics or bioinformatics. Ph.D. in genetics, molecular biology, animal science or related area is required. Salary range is $51,927 to $80,279 with full benefits. U.S. citizenship is required. For research program information, contact Hans Cheng; Tel: (517) 337-6758; hcheng@pilot.msu.edu. To address specific qualification requirements and application instructions, applicants must request a copy of Vacancy Announcement ARS-X1W-1295 by calling Tel: (517) 337-6825 or via the ARS website: www.ars.usda.gov. Applications must be postmarked by May 18, 2001. The USDA is an Equal Opportunity Provider and Employer. You must be a U.S. citizen to apply.

 

CONGRATULATIONS ELWOOD!!

The American Poultry Historical Society has elected Dr. Elwood Briles to the Poultry Hall of Fame. The Poultry Historical Society Hall of Fame "recognizes leadership in the poultry industry by electing individuals of exceptional character and integrity, who have rendered outstanding and unselfish service to the industry". This is the industry's most prestigious recognition. A maximum of 5 individuals are elected every three years. As most of you know, Elwood has been a pioneering spirit in studies of the chicken B-locus (major histocompatibility complex) for longer than most of us can remember. (From Bob Taylor via Mary Delany)

MOVE OVER NOAH!! DATABASE UPDATE: ANDY AND ALAN'S ARKdb.

Poultry geneticists, please take note of the following (abstracted from a recent Angenmap email notice, thanks to Andy Law and Alan Archibald of The Roslin Institute): The Roslin Institute Bioinformatics Group (http://bioinformatics.roslin.ac.uk) are pleased to announce that the ARKdb database system has moved to a new, easy-to-remember domain. The main site can now be found at http://www.thearkdb.org. The Roslin site is also accessible as http://roslin.thearkdb.org , while the mirror sites at Texas A&M and Iowa State can be accessed as http://texas.thearkdb.org and http://iowa.thearkdb.org. The full set of ArkDB genome databases covering pigs, chickens, sheep, cattle, horses, deer, cats, tilapia, salmonids and turkey can be found on the Roslin site. The Iowa mirror site carries chicken and pig databases while Texas houses cattle, horses and sheep. Comments and questions on ARKdb-related issues should be sent to mailto:info@thearkdb.org or mailto:feedback@thearkdb.org . If you need to cite data held within the ARKdb databases, please cite ARKdb-<species name> genome database, with URL http://www.thearkdb.org and refer to the published paper Hu et al., (2001). Nucleic Acids Research 29(1), 106-110, noting the date on which the data were retrieved/accessed.

IN THE NEWS: THE HUMAN GENOME AND THE CHICKEN GENOME

It's hard to imagine that anyone could have missed the recent publication of the human genome sequence (International Human Genome Sequencing Consortium, Nature 409:860-921; Venter, J.C., et al., Science 291:1304-1351). With this under their belts, we hope that the human genome sequencers may soon turn their ABIÔ machines towards the chicken genome.

Less heralded, perhaps, but of comparable size, is the recent publication: "First Report on Chicken Genes and Chromosomes", Cytogenetics and Cell Genetics 90:169-218 (2000). Authors are M. Schmid, I. Nanda, M. Guttenbach, C. Steinlein, H. Hoehn, M. Schartl, T. Haaf, S. Weigend, R. Fries, J-M. Buerstedde, K. Wimmers, D.W. Burt, J. Smith, S. A’Hara, A. Law, D.K. Griffin, N. Bumstead, J. Kaufman, P.A. Thomson, T.A. Burke, M.A.M. Groenen, R.P.M.A. Crooijmans, A. Vignal, V. Fillion, M. Morisson, F. Pitel, M. Tixier-Boichard, K. Ladjali-Mohammedi, J. Hillel, A. Mäki-Tanila, H.H. Cheng, M.E. Delany, J. Burnside, and S. Mizuno. Among its many highpoints are an updated version of the Consensus Linkage Map, a detailed listing of FISH-identified microchromosomal linkage groups, and thorough descriptions of avian sex chromosomes and avian telomere biology.

AND DON'T FORGET THE TURKEY GENOME

Kent Reed kindly has provided the following update: The University of Minnesota has established a program to create a comprehensive linkage map for the turkey genome with funding from the USDA-NRICGP. The long term goal of this project to create public resources that will be available to both the research community and poultry industry. This research will utilize marker-loci previously developed for turkey and chicken in addition to the development of new turkey loci. Initial efforts will focus on: (1) the development of new microsatellite loci; (2) determining marker heterozygosity in commercial lines; and (3) development of a linkage map of the turkey to support QTL mapping. Several F2 reference families, developed from commercial lines, have been created and are being provided to support public linkage map development. The industrial partner in this effort is Nicholas Turkey Breeding Farms. Additional collaborative partners are sought and are encouraged to participate in this project. As part of this collaborative effort, a manuscript detailing the turkey cDNA/RFLPs genome map(presented at PAG-IX) is in preparation and DNA sequences for the mapped markers will soon be available through GenBank. For further information or to forward comments, please contact: Dr. Kent M Reed, Leader, Turkey Genomics Program, 295 ASVM, 1988 Fitch Ave, Department of Veterinary PathoBiology, University of Minnesota, St. Paul, MN 55108. email: reedx054@tc.umn.edu .

ON THE ROAD AGAIN. UPCOMING MEETINGS:

12th North American Colloquium on Animal Cytogenetics and Gene Mapping, July 15-19, 2001, Davis, California. Abstracts for oral and poster presentations may be submitted to Abstract Selection Committee, Veterinary Genetics Laboratory, One Shields Avenue, Davis, CA 95616-8744, fax (530) 752-3556 or to animalcyto@vgl.ucdavis.edu by June 1, 2001. More information at www.vgl.ucdavis.edu/research/cytoconf (scroll down and right) or at the above email address.

6th International Veterinary Immunology Symposium, July 15-20, 2001, Uppsala, Sweden. To receive the final announcement and registration form email ivis@slu.se.

Poultry Science Association annual meeting, July 24-28, 2001, Indianapolis, Indiana, to be held as part of the International Animal Agriculture and Food Science Conference. See http://www.fass.org/fass01 or http://www.psa.uiuc.edu for more information. Register by May 15 to receive the early registration discount.

Plant and Animal and Agricultural Microbe Genome X, joint with NC-168 and NAGRP annual meetings, Jan. 12-16, 2002, Town & Country Convention Center, San Diego, CA. More information above and/or see www.intl-pag.org/pag/.

International Society of Animal Genetics, Göttingen, Germany, August 11-15, 2002. See http://www.gwdg.de/~bbrenig/ISAG2002.html for further information.

7th World Congress of Genetics Applied to Livestock Production, August 19-23, 2002, Montpellier, France. See http://www.wcgalp.org for more information.

11th European Poultry Conference, September 6-10, 2002, Bremen, Germany. See www.epc2002.de for further information.

CHICKEN GENE PRIMERS AND MICROSATELLITE KITS

Microsatellite primer kits: Information on microsatellite primer pairs can be found at http://poultry.mph.msu.edu/resources/microkits.htm. We now have a new streamlined replacement kit #1/2 that contains the most polymorphic and evenly distributed markers in kits #1 and #2 (including all of those that are anchor markers on the Groenen et al. Consensus Map, Genome Res. 10:137-147, 2000). Kits #4 to #6 and the Population Tester Kit (for line and/or parentage characterization or for testing the utility of chicken microsatellites in other avian species [not generally recommended]) remain available, although these kits are getting fairly old, and some problems, especially with the dye labels, may result. Contact: (dodgson@.msu.edu) or (hcheng@.msu.edu). New users are asked to request only one kit at a time. Thanks.

Please note: we're always anxious to obtain new chicken (or turkey) microsatellite sequence data and will consider purchasing new kits based on such sequences to make available to the poultry gene mapping community, pending available funding. Any suggestions are welcomed.

Gene primers: (Reminder) Two sets of PCR primer pairs complementary to chicken mRNAs are still available. In each case, a likely primer pair for PCR was derived based on DNA sequence data (mostly cDNA sequences, so they should be used for RT-PCR). See the Tables entitled "Chicken Gene Primers #1 and #2" under "Resources" (scroll down) at http://poultry.mph.msu.edu. Contact: (dodgson@.msu.edu) or (hcheng@.msu.edu). We'll send you up to 20 primer pairs of your choice. If you find them useful, let us know, and we will be happy to send more.

THE BAC PAGE!

A small supply has now been obtained of new robot-spotted filter sets of the chicken BAC library constructed at the Texas A&M BAC Center, using UCD 001 Jungle Fowl line as its DNA source. If interested, email me at dodgson@msu.edu. The new filter sets contain the full array of 39,400 BAC clones with BamHI-derived inserts. A requirement for receiving a free filter set is that the user agree to provide BAC clone locations and the name of the probe used at a later date, so that all users can benefit from what has been learned. 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. In either case, once your clone of interest is identified by hybridization, individual clones can be obtained at cost from the BAC Center. Another 80,000 chicken BACs have now been constructed using EcoRI and HindIII insert inserts (39,400 each into pECBAC1) to insure complete coverage of the genome. We are working on the purchase of filter sets containing BACs from all three sublibraries, that will then be distributed as above. In addition, for those wishing to use PCR rather than filter hybridization to screen for your gene(s) of interest, a copy of the first 30,000 BAC library (equivalent to the filter sets first distributed) has been sent to Research Genetics, who are constructing PCR-ready, superplate, column, and row pool DNAs. As soon as these DNA sets become available, we will add this new resource to our "Resources" section of our homepage (http://poultry.mph.msu.edu/resources/resources.htm). (Unfortunately, technical problems and staff changes at Research Genetics have delayed delivery of the PCR pools. We hope to receive these in the very near future.) As noted previously, Martien Groenen and Richard Crooijmans have also constructed a BAC library in collaboration with this the Texas A&M BAC Center (Crooijmans et al., Mammalian Genome 11: 360-363, 2000). This library consists of approximately 50,000 BACs (HindIII inserts, average: 130 kb). See http://www.zod.wau.nl/vf/research/chicken/frame_chicken.html for more information. If you wish to purchase or use the Groenen-Crooijmans library, either contact the Texas A&M BAC Center (http://hbz.tamu.edu), the Groenen site URL given above, or the UK Human Genome Mapping Project Resource Center at http://www.hgmp.mrc.ac.uk which sells filter sets of this library.

PUT YOUR ITEM OF INTEREST HERE

We're always happy to include items of general interest to the poultry genetics community in the Poultry Genome Newsletter. Please email your contributions to us at the addresses below. Please send any items by June 15 to be sure it gets into the next issue.

Addresses:

Jerry Dodgson, Poultry Coordinator

Dept. of Microbiology & Molecular Genetics

Giltner Hall

Michigan State University

East Lansing, MI 48824

email: dodgson@msu.edu

Hans Cheng, Co-Coord.

USDA-ARS ADOL

3606 E. Mt. Hope Ave.

East Lansing, MI 48823

email: hcheng@msu.edu