**POULTRY GENOME NEWSLETTER** Issue No. 4, October, 1998
*PLANT AND ANIMAL GENOME VII and NAGRP/NC-168*
NC-168 will again meet jointly with the NAGRP and PAG-VII. NC-168 will begin Saturday, Jan. 16 (in the evening) and Jan. 17 and PAG-VII will go from Jan. 17 to 21. The pre-registration deadline for PAG-VII is Nov. 13, 1998 and the abstract deadline (on-line submission) is October 16. All the relevant information and abstracts from past meetings can be found at the new PAG Website: http://www.intl-pag.org.
As in the past, limited funding will be available to assist those who need it to attend NAGRP/NC-168/PAG. Priority will be given to active NAGRP members. If interested, please email me asap at dodgson@pilot.msu.edu. Grad students are encouraged to apply for a Neal A. Jorgensen Genome Travel Award (http://www.intl-pag.org/pag/grants.html).
*WASHINGTON UPDATE*
AGRICULTURAL GENOME INITIATIVE and RESEARCH FUNDING
The 1998 NRI Competitive Grant Program was described in our last issue, with emphasis on the Animal Genetic Mechanisms and Gene Mapping Program. The program announcement of the 1999 NRI-CGP has recently become available at http://www.reeusda.gov/nri. (The server is down at the moment, but the deadline for the Animal Genetic Mechanisms program should be Feb. 15, 1999.) Questions can be directed to the NRI at nricgp@reeusda.gov or (202) 401-5022. Poultry geneticists are strongly encouraged to submit proposals to the Animal Genetic Mechanisms and Gene Mapping Program or to other NRI Programs.
The transcript of the July 9, 1998, Public Meeting for the Solicitation of Input from Stakeholders Regarding the Initiative for Future Agriculture and Food Systems is available at http://www.reeusda.gov. A variety of lobbyists, scientists, and other representatives of agriculture testified as to the possible use of funding under this Initiative. It is clear that the Ag Genome Initiative is only one of many research efforts looking for these funds. At the moment the question is moot as, to the best of my knowledge, funding for the Initiative is still locked in Conference Committee with Senate support but House opposition.
On a separate note, Hans Cheng and Dave Burt will represent poultry at the Joint European Commission-United States Task Force on Biotechnology, Farm Animal Workshop to be held in Brussels, Belgium on Sept. 15-16, 1998. There will be brief presentations as to the state of the art in Europe and the U.S. followed by discussion of opportunities for continuing and new collaborative research (and hopefully for funding).
*ISAG & POULTRY GENOME MAPPING WORKSHOP*
The International Society for Animal Genetics meetings, along with the Poultry Genome Mapping Workshop, the latter coordinated by Martien Groenen and Hans Cheng, were held in Auckland, New Zealand on August 9-14, 1998. A brief summary of the Workshop is given below. Details will be published in a forthcoming Animal Genetics issue.
1. Integration of linkage maps and overview of all linkage data. Martien Groenen presented a preliminary integrated linkage map based on the East Lansing, Compton and Wageningen mapping families that now has 1364 loci and will be extended to about 1900. Martien displayed the integrated map in both framework (based on a skeleton of most reliable markers) and comprehensive (all markers placed in the most likely position, based on available data) versions. It is hoped that the integrated map will be completed shortly and submitted for publication. It will also be made available at http://www.zod.wau.nl:80/vf, the Wageningen web site. Hans Cheng summarized the status of the East Lansing map, which now contains about 1000 markers, 969 of which define 42 linkage groups covering over 3,400 cM.
2. Physical mapping data. Cytogenetic maps have been aligned with linkage maps for chromosomes 1-8 and Z, and work from A. Vignal enables identification of 17 microchromosomes with linkage groups. Efforts continue by Vignal, R. Crooijmans and others to complete the alignment of FISH and linkage maps. In addition, a submitted manuscript describes the standardized banded chicken chromosome karyotype (contact F.A. Ponce de Leon for details).
3. Comparative map. Dave Burt has made a comparative map of the chicken genome with those of human and mouse, soon to be available on the Roslin web site: http://www.ri.bbsrc.ac.uk.
4. Resources in genome mapping. Available libraries, mapping panels, etc. were discussed. A summary has been prepared by C. Knorr and will soon be put on our web site: http://poultry.mph.msu.edu. (More information also provided below).
A. Vignal was elected as chair of the Poultry Gene Mapping Standing Committee, which will meet again at the 2000 ISAG in Minneapolis.
The ISAG meeting itself involved numerous other workshops, along with Plenary Sessions on Diversity, Expression, Trait Analysis, and Marker-assisted Selection. Considerable progress was reported on the isolation and characterization of several QTLs. For example, Mariani, Barrow, Bumstead, Cheng, Groenen, and Negrini reported on the identification of a QTL for resistance to Salmonellosis on chicken chromosome 5. The use of microarrays based on Expressed Sequence Tag (EST) data received considerable discussion. Major advances in the development and use of Radiation Hybrid mapping panels for mammalian species were described. The relevance of animal genomics to questions of human genetics, genome evolution and ecology was presented. (Report contributed by Hans Cheng and Christoph Knorr.)
Upcoming meetings of interest:
Plant and Animal Genome VII; San Diego, CA, January 17-21, 1999; associated with National Animal Genome Research Program meeting and NC-168 Regional Research meeting. Abstract deadline, Oct. 16; registration deadline, Nov. 13. Information is at http://www.intl-pag.org.
From Jay Lush to Genomics: Visions for Animal Breeding and Genetics, May 16-18, 1999, Iowa State University Ames, IA. Information is at: http://www.public.iastate.edu/~ans/graduate/visions.html.
International Society of Animal Genetics (ISAG 2000), Hyatt Regency Hotel, Minneapolis, MN, July 24-27, 2000. More info to come or contact Brian Kirkpatrick, bwkirkpat@facstaff.wisc.edu.
*CHICKEN GENE PRIMERS AND OTHER RESOURCES*
Gene primers: A collection of PCR primer pairs complementary 200 chicken genes of known sequence has been synthesized. In each case, a likely primer pair for PCR was derived using primer optimization software based on Genbank sequences (most of which are from cDNA clones). A Table will soon be available on our web page (http://poultry.mph.msu.edu) 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. The primers have not been tested and may not work in all cases. Due to the possibility of introns within the sequenced region, amplification from genomic DNA, rather than from cDNA, may not work or may require special, long PCR conditions. None of these primers are fluorescently labeled. Due to the high cost of synthesis, the number of samples we have of each primer pair is limited. Furthermore, it is expected that most labs will have a specific interest in one or a few candidate genes. Therefore, 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 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). Based on the level of interest observed and coordination funds available, additional gene primer kits may be made in the future. (Thanks to S. Suchyta for help in primer design).
Microsatellite primers: As described previously, 575 fluorescent chicken microsatellite primer pairs are available in four separate kits. Information on all Kits is posted under "Microsatellite Marker Information and Available Primer Kits" in the "Maps and Tables" section of our Homepage (http://poultry.mph.msu.edu). Email as above, if interested. Publication of data on new chicken microsatellites has flattened out recently, but we will continue to make more kits, as appropriate sequence data are provided to us or are published.
Chicken BAC libraries: As also noted previously, construction of a second chicken BAC library by the Texas A&M BAC Center is well underway, and it should be available later this year. This second BAC library uses the UCD 001 Jungle Fowl line as DNA source, the same line used in the East Lansing reference map. Martien Groenen has also constructed a BAC library in collaboration with the Texas A&M Center. For more info on this library, see the Groenen homepage at http://www.zod.wau.nl/vf/chickensite/chicken.html. If you wish to screen the Wageningen BAC library, contact R. Crooijmans at richard.crooijmans@alg.vf.wau.nl.
Chicken YAC library: Information on a chicken YAC library constructed by A.A. Toye, L. Schalkwyk, H. Lehrach, and N. Bumstead can be found at http://www.rzpd.de (German Human Genome Project Resource Center). Filters for screening this library can be purchased from the Center. The Center also has a chick embryo cDNA and a chicken cosmid library available.
AFLP primers: Informal discussions with Keygene, N.V. have begun on the possibility of Coordinators providing AFLP kits that go beyond the limited ones now available from Perkin Elmer or Life Technologies, and which would allow interested researchers to test this technology on possible applications without breaking their budgets. AFLP is a patented technique which Keygene has licensed to these two companies, but the AFLP market for animal research has not been large enough to attract much development so far. (PE doesn't even list their plant AFLP kits in their latest catalogue.) We'll keep you informed of progress in this regard.
**HOT PAPERS**
C. Kwok et al. describe the "Characterization of whole genome radiation hybrid mapping resources for non-mammalian vertebrates" in Nucleic Acids Research 26:3562-3566. This includes preliminary characterization of a partial chicken radiation hybrid mapping panel. However, personal communications from Dave Burt and Nat Bumstead indicate that chicken-mammalian RH panels continue to have problems (perhaps due to the low level of integration of retained chicken fragments into mammalian chromosomes, as described herein.)
A.-K. Fridolfsson et al. describe the "Evolution of the avian sex chromosomes from an ancestral pair of autosomes" in Proc. Natl. Acad. Sci. USA 95:8147-8152. They conclude that avian sex chromosomes arose independently from mammalian sex chromosomes, possibly even more recently. All but one chicken Z-linked gene examined maps to mammalian autosomes.
McQueen et al. present further evidence in favor of their earlier proposal that most (ca. 75%) chicken genes reside on microchromosomes in "Chicken microchromosomes are hyperacetylated, early replicating, and gene rich", Genome Research 8:621-630. It remains to be seen how this hypothesis can be reconciled with data from Gene Smith, Dave Burt and others, which suggest a high level of conserved gene order between avian and human genomes (with the latter obviously not mostly on microchromosomes). These authors attribute differences between their results and the existing gene maps to bias in physical mapping, it being more difficult to localize genes to microchromosomes.
*THANKS AND BEST WISHES TO ROGER GERRITTS*
Dr. Roger J. Gerritts recently announced his retirement from the USDA-Agricultural Research Service (ARS) after 40 years of service. Although Roger's primary background was in swine research, as a member of the ARS National Program Staff, he had an important role in promoting animal genetics, including poultry genome mapping, especially at the Avian Disease and Oncology Laboratory. He also served a national and international leadership role in germplasm preservation efforts. Those of us in the East Lansing poultry group will miss his encouragement and assistance, and we wish him the best for a happy and healthy retirement.
PUT YOUR ITEM OF INTEREST HERE
We are 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 December 1, 1998 to be sure it gets into the next issue.
Addresses:
Jerry Dodgson, Poultry Coordinator; email: dodgson@pilot.msu.edu
Dept. of Microbiology, Giltner Hall
Michigan State University
East Lansing, MI 48824
Hans Cheng, Co-Coord.; email: hcheng@pilot.msu.edu
ADOL, USDA-ARS
3606 E. Mt. Hope Ave.
East Lansing, MI 48823
Lyman Crittenden, Coordinator Emeritus.; email: crittend@itis.com
8550 Highway 19
Cross Plains, WI 53528-9300
Supported by Regional Research Funds, Hatch Act, to the
National Research Service Program: NRSP-8.
National Animal Genome Research Program, Richard Frahm, Director, CSREES