Overview: Coordination of Poultry Genome Mapping under the National Animal Genome Research Program (NAGRP) is a joint effort of the Michigan State University (MSU) Department of Microbiology and the USDA, ARS, Avian Disease and Oncology Laboratory (ADOL). It is supported financially by ADOL, CSREES, and MSU. CSREES support is allocated via a National Research Service Program, NRSP-8. The NAGRP is made up of the membership of the Animal Genome Technical Committee (AGTC). That membership is divided up into Species Subcommittees, including one for Poultry.

FACILITIES AND PERSONNEL: Jerry Dodgson, Department of Microbiology, MSU, serves as Coordinator with Lyman Crittenden consulting as Coordinator Emeritus. Hans Cheng of ADOL is Co-Coordinator. Both ADOL and MSU provide facilities that support coordination efforts. Maintenance of the Poultry Genome Homepage and computer facilities is provided on a contract basis by InterDream, Inc.

OBJECTIVES: The Coordinator works with the Poultry Species Committee to achieve the following objectives: (1) Serve as custodian of poultry maps. (2) Serve as coordinator of species databases. (3) Serve coordinator of shared material and information. (4) Serve as coordinator for developing research priorities.

PROGRESS TOWARD OBJECTIVE 1. POULTRY GENOME MAPS

The Reference Map(s). A panel of 52 backcross and parental DNAs has been shipped to numerous laboratories in the UK, the Netherlands, Israel, Australia, Canada, and the US where typing is done. At present, the East Lansing, (EL) panel has been typed for 811 markers of which 784 are resolved into 43 linkage groups (preliminary evidence suggests that at least 3 small linkage groups will eventually be linked to macrochromosomes; 40 linkage groups are expected from cytogenetic studies, 38 autosomes, Z and W). The map coverage within linkage groups is over 3,200 cM which is about the estimated size of the chicken genome (see Table 1, attached). There are 388 microsatellite markers which greatly enhance the utility of this map for genome-wide QTL searches. Also, 152 Type I genes have been mapped which aid in the development of a comparative map. In collaboration with Nat Bumstead (Compton, U.K.), a consensus map of the EL and Compton genetic maps has been developed and distributed by the Coordinators. An updated version of the consensus map presently is being prepared by Cheng, Bumstead, and Martien Groenen. This year, for the first time, linkage groups have been assigned to all cytogenetically distinguishable chromosomes (macrochromosomes 1-8, sex chromosomes Z and W, and chromosome 16 containing the NOR). The latest available MapManager database continues to be available to users on the WWW Homepage.

PROGRESS TOWARD OBJECTIVE 2. DATABASE DEVELOPMENT

ChickGBASE: We previously supported Alan Hillyard, formerly of Jackson Labs, on a consultant basis for the development of ChickGBASE (in parallel, the Swine Coordinator has supported Hillyard for the development of PIGBASE). Dr. Hillyard was part of the initial development of Arkdb, the new, more inclusive version of animal databases released this past summer. However, Arkdb was primarily constructed by Andy Law, Dave Burt, Alan Archibald, and others at the Roslin Institute. ChickGBASE is available in the Arkdb format at http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html.

WWW Homepage: We maintain a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, and a variety of other genome mapping resources. The Homepage provides the latest EL maps and mapping data, an updated list of published microsatellites, descriptions of our microsatellite kits, the latest cytogenetic map, and access to a host of other information. Mechanisms for discussion groups and other electronic communication are also provided, along with copies of newsletters and access to the Crittenden reference database. A new frames version of the Homepage was developed and installed this year. Further development of the Web page has been contracted out to InterDream, Inc. It can be accessed at http://poultry.mph.msu.edu.

PROGRESS TOWARD OBJECTIVE 3: SHARED MATERIAL AND INFORMATION

Reference Panel DNA: As noted above, DNA from the East Lansing international reference population has been sent to laboratories throughout the world. Microsatellite Primer Kits: Four kits of microsatellite primer pairs are now available for free distribution. The first of these is the Population Tester Kit. This contains 9 primer pairs which define microsatellites with high polymorphic information content (numerous alleles widely distributed in several populations). For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. Three large Comprehensive Mapping Microsatellite Kits now containing a total of 519 primer pairs for markers covering most of the chicken genome are also available. The Homepage also has tables of the kit loci along with a larger table which includes information on all published microsatellite loci to date (and several unpublished ones from Hans Cheng and Martien Groenen). Still further microsatellite sequence information will be required to generate enough markers to adequately map in a variety of populations. Approximately 40 laboratories have been provided one or more of these kits. (We are now out of Kit #1, but are replacing it.)

Physical Mapping Resources: These potentially include large insert clone libraries (YACs, BACs), somatic hybrid cell panels, and radiation hybrid panels. Nat Bumstead and collaborators have developed a chicken YAC library that will hopefully be available soon for screening through Dr. Hans Lehrach in Berlin. We hope to use Coordination funds to provide and distribute sets of filters of YAC clones that can be sent (free of charge) to investigators who wish to screen such panels, but are awaiting a reply from Dr. Bumstead. At least three BAC libraries have been made or are under construction. One, made by C. Auffray, (hopefully) will be distributed by the Berlin center. Another made by Drs. R. Zimmer and Ann Gibbins is presently being tested, and arrangements have been made to distribute it through the Coordinator. A third is now being made in the Groenen lab. It appears that additional YAC or BAC libraries will be required (for reasons related to completeness, availability, and/or insert size), and the Coordinator is trying to arrange for their development. In addition, exploratory talks for the development of a radiation hybrid library are in progress, but these are not yet available for chicken or other poultry.

Newsletter: The Poultry Genome Newsletter has been established and the first 10 editions distributed. The Newsletter is published quarterly and is distributed through our WWW Homepage, electronically on the angenmap email discussion group and via hard copy to scientists worldwide. Copies are also distributed to the Poultry Breeders of America. Nomenclature: Nomenclature issues continue to be resolved, as led by Lyman Crittenden, Jim Bitgood and other interested parties. Meetings: Coordinators and NRSP-8 Technical Committee and Species Subcommittee Chaires helped develop the joint Plant and Animal Genome V held for the first time last January, jointly with the annual NAGRP meeting. Approximately 600 scientists attended and 800-1000 are expected for PAG-VI. Coordination funds helped support several Technical Committee members and students/postdocs who wish to attend. Some support was also be provided to the Quantitative Genetics Gordon Conference in Feb., 1997. The Poultry Coordinator also chaired the writing committee that prepared the NRSP-8 renewal application, critical review, and reference list. This is presently being submitted for CSREES review.

PROGRESS TOWARD OBJECTIVE 4: RESEARCH PRIORITIES

The research priorities set by the Poultry Species Subcommittee include: (1) Develop a consensus map of at least 200 microsatellite markers embedded in a dense map of other markers. (2) Develop resource populations designed to use that map to identify QTL for major economic traits. (3) Integrate the genetic, physical, and classical maps. (4) Develop resources for joint use such as primer sets and large insert DNA libraries. (5) Develop rapid mapping techniques and protocols that will allow economic and efficient use of genetic markers for a variety of purposes. (6) As resources permit, extend the map to other species of poultry in the following priority: turkeys, ducks, and Coturnix quail as a model.

Progress: Item 1 is complete, although the map still needs to become more dense and a more realistic estimate is that 1000 or more microsatellites will be needed in order to have a reasonable number that are polymorphic in most populations of interest. Groenen and colleagues have also completed a genetic linkage map using the Wageningen resource population with average marker spacing of 7 cM. Microsatellites developed in the Groenen, Cheng and Burke labs were mapped. Item 2 is well underway at several locations in the U.S. and elsewhere. Cheng and colleagues (Vallejo et al., in press) have mapped 7-8 QTL for non-MHC-based genetic resistance to Marek's Disease. Bumstead and co-workers used a combined linkage/candidate gene approach, based on comparative gene maps, to identify the NRAMP1 and TNC genes as major contributors to the Salmonellosis resistance quantitative trait in chickens. (Hu et al., Genome Research 7:693-704, 1997). Groenen and collegues have mapped numerous traits in the Wageningen/Euribred resource population mentioned above. Considerable progress has been made on Item 3, although physical and classical maps still lag behind the genetic map. Work on comparative gene mapping of chicken loci using Type I markers continues at MSU, ADOL, and elsewhere. Type I markers on the EL map increased nearly 50% this year. With regard to Item 4, available markers in free primer sets more than doubled this year, and more will be provided as data are received. Large insert libraries are complete or under construction. The major problem with Item 5 involves resources. Rapid mapping using existing microsatellite primers is best done using automated equipment, which are presently too expensive for most labs. Progress on item 6 has been limited, probably due to lack of a critical mass of investigators working with these species. Dr. Smith at Tuskegee has developed and mapped a panel of turkey microsatellites on the BYU reference population.

Recent Relevant Publications of Coordinators:

1. Crittenden, L.B., J.J. Bitgood, D.W. Burt, F.A. Ponce de Leon, and M. Tixier-Boichard. 1996. Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases. Genet. Sel. Evol. 28:289-297.

2. Smith, E.J., Cheng, H., and Vallejo, R. 1996. Mapping functional chicken genes: an alternative approach. Poultry Science 75:642-647.

3. Smith, E.J., Cheng, H.H., and Suchyta, S.P. 1997. Comparative mapping of the chicken genome using the East Lansing reference population. Poultry Science 76:743-747.

4. Dodgson, J.B., H.H. Cheng, and R. Okimoto. 1997. DNA marker technology: a revolution in animal genetics. Poultry Science 76:1108-1114.

5. Okimoto, R., H.H. Cheng and J.B. Dodgson. 1997. Characterization of CR1 repeat random PCR markers for mapping the chicken genome, Animal Genetics 28:139-145.

6. Cheng, H.H. 1997. Mapping the chicken genome. Poultry Science 76:1101-1107.

PLANS FOR THE FUTURE.

OBJECTIVE 1. POULTRY GENOME MAPS

Continued progress on the reference genome map will be encouraged by distribution of reference panel DNAs, microsatellite primers and shared data. We will continue to work with international collaborators to enhance the usefulness of the reference map and to consolidate data and map distances between the two accepted reference populations. A primary goal for the future must be integration of poultry genome maps and comparative genomics with other species maps. Mapping efforts are moving increasingly towards resource populations. We will encourage sharing of resource mapping data through our efforts in data collection and distribution.

OBJECTIVE 2. DATABASE DEVELOPMENT

Continued expansion of ChickGBASE will occur in the new Arkdb format. The Poultry Genome WWW Homepage will continue to be expanded and improved.

OBJECTIVE 3: SHARED MATERIAL AND INFORMATION

Shared information has been discussed in Objective 2 above. As noted under Objective 1, we will continue to distribute chicken reference mapping population DNAs and hope to develop resource chicken DNA panels for distribution. Further kits will be developed containing microsatellite primer pairs for the key, highly polymorphic reference markers, and these will also be distributed to interested scientists. Primers for anchor loci will be distributed as part of the above process to allow rapid localization of new genetic loci. Efforts will be made to encourage a better integration of physical, genetic and classical maps. Two to three large insert cloned DNA libraries should soon be available.

OBJECTIVE 4: RESEARCH PRIORITIES

Research priorities will continue to be developed by consensus of the Poultry Technical Subcommittee. That Subcommittee and the whole NAGRP Technical Committee will meet again at PAG-VI in January, 1998. Objectives for the competitive renewal of NRSP-8 are: 1. Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes. 2. Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes. 3. Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.

(Prepared 11/12/97)