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, CSRS, and MSU. CSRS support is allocated via a National Research Service Program, NRSP-8. The NAGRP is supported by the membership of the Animal Genome Technical Committee (AGTC). That membership is divided up into Species Subcommittees.

FACILITIES AND PERSONNEL: U.S. aspects of the coordination effort are housed at ADOL and MSU. Lyman Crittenden, Research Professor, MSU served as Coordinator through 9/30/94. Jerry Dodgson, Department of Microbiology, MSU, officially assumed the Coordinator role as of 10/01/94 with Lyman Crittenden remaining a collaborator. Hans Cheng of ADOL has been and will remain a Co-Coordinator. Both ADOL and MSU provide facilities that support coordination efforts. ARS, through ADOL, provides a part-time technician, Lenny Provencher, laboratory and office space, freezers, support of copying, mailing, shipping and some other office services. Scott Eisensmith was the Database Curator for the project, but he took another job earlier this year. He remains as a consultant to the project, hired by a monthly contract. Additional student help is also being sought. With most of the informatics activities now in a maintenance (rather than development) mode, a full time database manager is not necessary for poultry coordination.

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 numerous laboratories in the UK, the Netherlands, Israel, Australia, Canada, and the US where typing is done as well as at the two laboratories in East Lansing. At present, the East Lansing, (EL) panel has been typed for 638 markers of which 609 are resolved into 39 linkage groups (7,8). The map coverage within linkage groups is over 2,800 cM which is about the estimated size of the chicken genome. There are 340 microsatellite markers which greatly enhances the utility of this genetic map for genome-wide QTL searches (1,7,8). Also, 105 Type I genes have been mapped which will aid in the development of a comparative map (5-8). In collaboration Nat Bumstead (Compton), a consensus map of the EL and Compton genetic maps has been developed. As a result, linkage groups and loci order have been verified. Additionally, several previously separate linkage groups have been joined and chromosome assignments made; chromosomes 1-5, 7, 8, 16 and Z have been identified. Recently the latest available MapManager database has been placed on the WWW Homepage, so that users can immediately download and use the latest file. The consensus map will be widely distributed at next year's PAG-V meeting and will soon be uploaded onto the Homepage.

PROGRESS TOWARD OBJECTIVE 2. DATABASE DEVELOPMENT

ChickGBASE: We have supported Alan Hillyard, formerly of Jackson Labs, on a consultant basis for the development of ChickGBASE (3, in parallel, the Swine Coordinator has supported Hillyard for the development of PIGBASE). Dr. Hillyard has also worked with Andy Law, Dave Burt, Alan Archibald, and others at the Roslin Institute to develop a totally new, more inclusive version of animal databases that should be available very soon.

WWW Homepage: We have developed a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, the National Agricultural Library and a variety of other genome mapping resources. The Homepage provides the latest EL maps and mapping data, a 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.

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: Three 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. Two large Comprehensive Mapping Microsatellite Kits containing 120 and 124 primer pairs, respectively, that define 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). It is expected that many more microsatellite loci will become public during the coming year (M. Groenen, personal communication), which will allow us to synthesize further primer kits containing additional informative loci. Further microsatellite sequence information will be required to generate enough markers to adequately map in a variety of populations. Over 32 laboratories have been provided one or more of these kits.

Physical Mapping Resources: These potentially include large insert clone libraries (YACs, BACs), somatic hybrid cell panels, and radiation hybrid panels. Most of these resources are not yet available. Nat Bumstead and collaborators have developed a chicken YAC library now available 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. At least one BAC library has been made by Dr. Ann Gibbins and should soon be widely available. Another BAC and a PAC library are presently under construction.

Newsletter: The Poultry Genome Newsletter has been established and the first 6 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 and other interested parties (2-4). Meetings: Several excellent meetings (ISAG, AllertonII, and others) were held this year. Coordinators have worked closely to develop the joint Plant and Animal Genome V and NAGRP meeting to be held next January and support will be provided to several Technical Committee members and students/postdocs who wish to attend. This will surely provide the NAGRP meetings with higher attendance and greater international impact. Support will also be provided to the Quantitative Genetics Gordon Conference in Feb., 1997. Coordinators also attended special meetings at Argonne Nat'l Laboratories and Madison, WI on behalf of the NAGRP. A primary topic at the latter meeting was planning for the future, with the consensus being that an attempt be made to renew NRSP-8 support for the NAGRP.

PROGRESS TOWARD OBJECTIVE 4: RESEARCH PRIORITIES

The research priorities discussed at the September, 1994 NAGRP meeting 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 needs to become more dense and a more realistic estimate is that 500-1000 microsatellites will be needed in order to have a reasonable number that are polymorphic in most populations of interest. Item 2 is well underway at several locations in the U.S. and elsewhere. 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 is under way at ADOL and elsewhere. With regard to Item 4, primer sets are already available and more continue to be distributed. 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 is taking a leadership role in working on the turkey map.

Relevant Publications of Coordinators:

1. Cheng, H.H., I. Levin, R.L. Vallejo, H. Khatib, J.B. Dodgson, L.B. Crittenden, and J. Hillel. 1995. Development of a genetic map of the chicken with markers of high utility. Poultry Science 74:1855-1874.

2. Crittenden, L., J. Bitgood, and D. Burt. 1995. Chick. In "Genetic Nomenclature Guide", Trends in Genetics, pp. 33-34.

3. Burt, D.W., N. Bumstead, J.J. Bitgood, F.A. Ponce de Leon, and L.B. Crittenden. 1995. Chicken genome mapping: a new era in avian genetics. Trends in Genetics 11: 190-194.

4. 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.

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

6. 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, in press.

7. Dodgson, J.B., H.H. Cheng, and R. Okimoto. 1997. DNA marker technology: a revolution in animal genetics, Poultry Science, in press.

8. Cheng, H.H. 1996. Mapping the chicken genome. Poultry Science, in press.

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 use this data and develop methods to consolidate this data, where possible, to improve the consensus map. We will encourage sharing of resource mapping data through our efforts in data collection and distribution (see objective 2.) We will examine the possibility of distributing DNA panels from selected resource populations.

OBJECTIVE 2. DATABASE DEVELOPMENT

Continued improvements of ChickGBASE will be made. Further efforts will be made to integrate different types of genome data in a relational mode (the new ChickGBASE). 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 and turkey reference 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. One goal is that microsatellite or other polymorphic markers should be identified for each chicken chromosome. 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. We will coordinate distribution of library stocks for rapid screening purposes.

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 nest meet at PAG-V in January, 1997 in San Diego. NAGRP Coordinators participated in the organization of the meeting and the coordination activities at the meeting. Coordination activities with industry representatives at such gatherings as the Poultry Breeders' Roundtable will continue. Objectives for a proposed continuation of NRSP-8 are under consideration.

(Prepared 11/21/96)